ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/cmview/trunk
Sticky Revision:
Sort logs by:
Revision 818 - Directory Listing
Modified Tue Jan 28 09:58:25 2014 UTC (2 years, 6 months ago) by jmduarteg
Adding contact order in info dialog, it still has to be seen whether contact order is calculated as known in literature. At the moment it is my interpretation of  it, which might not be right.
Revision 817 - Directory Listing
Modified Tue Jan 21 16:49:42 2014 UTC (2 years, 7 months ago) by jmduarteg
Removing support for PDBASE, after changes in owl
Revision 816 - Directory Listing
Modified Tue Sep 4 07:55:22 2012 UTC (3 years, 11 months ago) by jmduarteg
Removing german text (had also non-ascii chars giving a warning on compilation)
Revision 815 - Directory Listing
Modified Tue Sep 4 07:50:14 2012 UTC (3 years, 11 months ago) by jmduarteg
Committing default owl.jar location and version values
Revision 814 - Directory Listing
Modified Thu Aug 18 08:04:34 2011 UTC (5 years ago) by jmduarteg
Extracted constants variables in top of script
Revision 811 - Directory Listing
Modified Thu Aug 18 06:52:17 2011 UTC (5 years ago) by jmduarteg
Better doc
Revision 809 - Directory Listing
Modified Wed Aug 17 13:57:53 2011 UTC (5 years ago) by jmduarteg
Packaging script now made obsolete
Revision 808 - Directory Listing
Modified Wed Aug 17 13:57:26 2011 UTC (5 years ago) by jmduarteg
Adding package target
Revision 805 - Directory Listing
Modified Wed Aug 17 13:01:39 2011 UTC (5 years ago) by jmduarteg
An ant file for CMView! Removed now obsoleted Manifest files and home-made build script
Revision 803 - Directory Listing
Modified Tue Aug 16 16:15:38 2011 UTC (5 years ago) by jmduarteg
Updating versions
Revision 801 - Directory Listing
Modified Tue Aug 16 16:03:51 2011 UTC (5 years ago) by jmduarteg
Fixed bug in running DaliLite
Revision 800 - Directory Listing
Modified Tue May 24 09:07:13 2011 UTC (5 years, 3 months ago) by jmduarteg
Minor change after change of interface in owl
Revision 799 - Directory Listing
Modified Thu May 19 14:29:22 2011 UTC (5 years, 3 months ago) by jmduarteg
Adapted to latest changes in owl (for support of HETATMs). CMView still behaves as before, ignoring HETATMS altogether.
Revision 798 - Directory Listing
Modified Tue Apr 12 14:02:12 2011 UTC (5 years, 4 months ago) by hstehr
Adding direct access link to CMView paper
Revision 797 - Directory Listing
Modified Tue Apr 12 13:53:29 2011 UTC (5 years, 4 months ago) by hstehr
adding documentation for CGAP (basic webpage, manual, screenshot)
Revision 796 - Directory Listing
Modified Tue Apr 12 13:51:34 2011 UTC (5 years, 4 months ago) by hstehr
Updating version to 1.1 (identical to 1.1rc6)
Revision 795 - Directory Listing
Modified Tue Apr 12 12:59:18 2011 UTC (5 years, 4 months ago) by hstehr
adding CMView citation info to docbook sources
Revision 790 - Directory Listing
Modified Wed Mar 30 18:54:43 2011 UTC (5 years, 4 months ago) by jmduarteg
Fixed bug: was throwing divided by zero exception in loupe when contactSize was too small and rounded to 0.
Revision 789 - Directory Listing
Modified Wed Mar 30 09:58:02 2011 UTC (5 years, 4 months ago) by jmduarteg
MAJOR CHANGE: adapted to change of interface in owl (owl-1.9.3 is the last tag before change).
Revision 787 - Directory Listing
Modified Tue Mar 22 18:15:04 2011 UTC (5 years, 5 months ago) by jmduarteg
Updating versions to 1.1rc5 before tagging
Revision 786 - Directory Listing
Modified Tue Mar 15 08:41:34 2011 UTC (5 years, 5 months ago) by jmduarteg
Refactor after refactoring in owl
Revision 785 - Directory Listing
Modified Thu Mar 3 13:22:53 2011 UTC (5 years, 5 months ago) by jmduarteg
Refactoring of xxxxError to xxxxException after refactoring in owl
Revision 783 - Directory Listing
Modified Sat Feb 26 11:08:48 2011 UTC (5 years, 5 months ago) by hstehr
Very minor change to webpage template
Revision 782 - Directory Listing
Modified Sat Feb 26 10:45:57 2011 UTC (5 years, 5 months ago) by hstehr
Updated manual and webpages
Revision 781 - Directory Listing
Modified Sat Feb 26 10:44:59 2011 UTC (5 years, 5 months ago) by hstehr
updated icons
Revision 780 - Directory Listing
Modified Fri Feb 25 20:33:51 2011 UTC (5 years, 6 months ago) by hstehr
Minor fix: state of RealTimeToggleButton was not changed when using the menu option
Revision 779 - Directory Listing
Modified Fri Feb 25 14:32:04 2011 UTC (5 years, 6 months ago) by jmduarteg
Added the toggle real-time function to main menu too (Select menu).
Revision 778 - Directory Listing
Modified Fri Feb 25 14:09:09 2011 UTC (5 years, 6 months ago) by hstehr
Minor fix: selection in PyMol was not updated when toggling 'real time' on/off
Revision 777 - Directory Listing
Modified Fri Feb 25 14:00:31 2011 UTC (5 years, 6 months ago) by jmduarteg
Made the out printwriter wrap a buffered stream (should help performance)
Revision 776 - Directory Listing
Modified Fri Feb 25 13:08:48 2011 UTC (5 years, 6 months ago) by jmduarteg
Changed icon for toggle real-time button
Revision 775 - Directory Listing
Modified Fri Feb 25 12:55:46 2011 UTC (5 years, 6 months ago) by jmduarteg
Now disabled real-time showing of tmpContacts
Revision 774 - Directory Listing
Modified Fri Feb 25 12:48:27 2011 UTC (5 years, 6 months ago) by jmduarteg
Put toggle real-time button in right place
Revision 773 - Directory Listing
Modified Fri Feb 25 12:15:07 2011 UTC (5 years, 6 months ago) by hstehr
Now real time contacts in PyMol are also updated when selecting stuff in the ruler (previously only when selectin in the main contact map)
Revision 772 - Directory Listing
Modified Fri Feb 25 12:02:22 2011 UTC (5 years, 6 months ago) by jmduarteg
Button to toggle real time contact mode.
Revision 771 - Directory Listing
Modified Fri Feb 25 11:16:35 2011 UTC (5 years, 6 months ago) by hstehr
fixed a little bug with real time contacts in neighbourhood selection mode
Revision 770 - Directory Listing
Modified Fri Feb 25 11:08:57 2011 UTC (5 years, 6 months ago) by jmduarteg
Minor fix: now when dragging only showCurrentSelection called (and not showCurrentContact as well)
Revision 769 - Directory Listing
Modified Thu Feb 24 20:48:05 2011 UTC (5 years, 6 months ago) by hstehr
Now 'real time' contacts also working fully in compare mode (hopefully)
Revision 768 - Directory Listing
Modified Thu Feb 24 19:44:45 2011 UTC (5 years, 6 months ago) by hstehr
Now 'real time' contacts works partly in compare mode (i.e. current mouse position is shown but not current selection)
Revision 767 - Directory Listing
Modified Thu Feb 24 19:20:44 2011 UTC (5 years, 6 months ago) by jmduarte
Fixed .classpath pointint to owl and not aglappe-owl
Revision 766 - Directory Listing
Modified Thu Feb 24 18:18:08 2011 UTC (5 years, 6 months ago) by hstehr
Disabling 'real time' contacts in compare mode (was causing Null Pointer Exception)
Revision 765 - Directory Listing
Modified Thu Feb 24 17:56:02 2011 UTC (5 years, 6 months ago) by hstehr
First implementation of 'real time' contacts in PyMol; minor changes to LoupePanel
Revision 764 - Directory Listing
Modified Thu Feb 24 14:25:14 2011 UTC (5 years, 6 months ago) by hstehr
adding icon for 'loupe' button
Revision 763 - Directory Listing
Modified Thu Feb 24 12:48:56 2011 UTC (5 years, 6 months ago) by hstehr
Now minimal set can be saved to a file after running cone peeling (e.g. for reconstruction)
Revision 762 - Directory Listing
Modified Thu Feb 24 11:50:01 2011 UTC (5 years, 6 months ago) by hstehr
Added documentation about Loupe function to manual; added config options to master config file
Revision 761 - Directory Listing
Modified Thu Feb 24 10:54:04 2011 UTC (5 years, 6 months ago) by hstehr
Loading from command line: 1. load first chain if no chain code given, 2. better error messages 
Revision 760 - Directory Listing
Modified Thu Feb 24 10:39:10 2011 UTC (5 years, 6 months ago) by hstehr
Changed crosshair color to light gray; Enabled loupe in compare mode
Revision 759 - Directory Listing
Modified Wed Feb 23 19:50:22 2011 UTC (5 years, 6 months ago) by hstehr
Now selection is also shown in loupe
Revision 758 - Directory Listing
Modified Wed Feb 23 18:20:17 2011 UTC (5 years, 6 months ago) by hstehr
Adding a crosshair to the loupe
Revision 757 - Directory Listing
Modified Wed Feb 23 18:03:46 2011 UTC (5 years, 6 months ago) by hstehr
First implementation of loupe function
Revision 756 - Directory Listing
Modified Wed Feb 9 15:56:41 2011 UTC (5 years, 6 months ago) by jmduarteg
Changed calls after removing AAinfo in owl.
Revision 755 - Directory Listing
Modified Wed Feb 9 11:46:36 2011 UTC (5 years, 6 months ago) by jmduarteg
Removing dependency on AAinfo
Revision 754 - Directory Listing
Modified Wed Feb 9 11:36:57 2011 UTC (5 years, 6 months ago) by jmduarteg
Now using AminoAcid instead of AAinfo
Revision 753 - Directory Listing
Modified Fri Jan 21 10:12:51 2011 UTC (5 years, 7 months ago) by jmduarteg
Refactoring following refactoring in owl (now the xxxError classes are all named xxxException as it should be)
Revision 751 - Directory Listing
Modified Fri Jan 14 20:11:00 2011 UTC (5 years, 7 months ago) by hstehr
Minor updates to manual and webpages
Revision 750 - Directory Listing
Modified Fri Jan 14 18:16:36 2011 UTC (5 years, 7 months ago) by hstehr
Updating manual, webpages and javahelp files
Revision 749 - Directory Listing
Modified Fri Jan 14 16:45:49 2011 UTC (5 years, 7 months ago) by hstehr
Major updates to Manual and FAQ. Minor changes to some screen messages in View.java.
Revision 748 - Directory Listing
Modified Tue Jan 11 16:21:37 2011 UTC (5 years, 7 months ago) by stehr
Updated manual (Background overlays)
Revision 747 - Directory Listing
Modified Sat Jan 8 17:49:06 2011 UTC (5 years, 7 months ago) by hstehr
bug fixes: disable overlays in compare mode, disable secondary structure ruler in compare mode, workaround for coordinates display (not really fixed yet)
Revision 746 - Directory Listing
Modified Fri Jan 7 21:55:03 2011 UTC (5 years, 7 months ago) by hstehr
Fixing checks for CGAP data file
Revision 745 - Directory Listing
Modified Fri Jan 7 21:30:53 2011 UTC (5 years, 7 months ago) by hstehr
Bug fix: background overlay drop down list and menu item 'diff dist map' were not synchronized; cleaning up CGAP code and adding developer's information about how to use CGAP
Revision 744 - Directory Listing
Modified Fri Jan 7 17:27:42 2011 UTC (5 years, 7 months ago) by hstehr
updating version number to 1.1rc3; updating master cmview.cfg file; updating README file for distribution
Revision 743 - Directory Listing
Modified Fri Jan 7 16:48:21 2011 UTC (5 years, 7 months ago) by hstehr
New menu option: Load from Casp TS file, enable Common Nbhd as non-experimental feature
Revision 742 - Directory Listing
Modified Tue Dec 21 15:35:52 2010 UTC (5 years, 8 months ago) by hstehr
Preparing for 1.1rc2 release:
1. Hiding more features as experimental (Swap models, Copy contacts from 2nd to 1st, Load from Sequence, Load Casp server models)
2. Renaming 'Toggle Contacts' to 'Add/Remove Contacts' and 'Minimal subset' to 'Run Cone Peeling Algorithm'
3. Creating menu commands for 'Add/Remove Contacts' and 'Run Cone Peeling'
4. Updating version number to 1.1rc2
Revision 741 - Directory Listing
Modified Sun Dec 19 18:34:29 2010 UTC (5 years, 8 months ago) by hstehr
updating year in web template
Revision 740 - Directory Listing
Modified Sun Dec 19 18:31:34 2010 UTC (5 years, 8 months ago) by hstehr
updating FAQ in docs
Revision 739 - Directory Listing
Modified Sun Dec 19 17:57:22 2010 UTC (5 years, 8 months ago) by hstehr
adding auxiliary files needed to generate docs from docbook format
Revision 738 - Directory Listing
Modified Sun Dec 19 17:30:02 2010 UTC (5 years, 8 months ago) by hstehr
updated docbook sources
Revision 737 - Directory Listing
Modified Fri Dec 17 18:56:23 2010 UTC (5 years, 8 months ago) by matt4077
resolved bug #13.5
Revision 736 - Directory Listing
Modified Fri Dec 17 18:41:14 2010 UTC (5 years, 8 months ago) by cvehlow
Interface changes CGAP
Revision 735 - Directory Listing
Modified Fri Dec 17 18:27:23 2010 UTC (5 years, 8 months ago) by cvehlow
Interface changes CGAP
Revision 734 - Directory Listing
Modified Fri Dec 17 17:18:49 2010 UTC (5 years, 8 months ago) by matt4077
fixed another bug (show threshold spheres in 3D)
Revision 733 - Directory Listing
Modified Fri Dec 17 17:08:47 2010 UTC (5 years, 8 months ago) by hstehr
removed Warning for unused method View.handleShowResidueScoringMap()
Revision 732 - Directory Listing
Modified Fri Dec 17 16:51:36 2010 UTC (5 years, 8 months ago) by hstehr
changing version number in sample cmview.cfg to 1.1
Revision 731 - Directory Listing
Modified Fri Dec 17 16:38:04 2010 UTC (5 years, 8 months ago) by cvehlow
Control database access! for CGAP
Revision 730 - Directory Listing
Modified Fri Dec 17 16:36:37 2010 UTC (5 years, 8 months ago) by cvehlow
Control database access! for CGAP
Revision 729 - Directory Listing
Modified Fri Dec 17 16:30:04 2010 UTC (5 years, 8 months ago) by matt4077
fixed a few more bugs.
Revision 728 - Directory Listing
Modified Fri Dec 17 16:18:07 2010 UTC (5 years, 8 months ago) by matt4077
mostly documentation
Revision 727 - Directory Listing
Modified Fri Dec 17 14:36:53 2010 UTC (5 years, 8 months ago) by matt4077
resolves bug #2 - check DALI on startup
Revision 726 - Directory Listing
Modified Fri Dec 17 14:06:03 2010 UTC (5 years, 8 months ago) by matt4077
fixed bug #5
Revision 725 - Directory Listing
Modified Fri Dec 17 13:36:41 2010 UTC (5 years, 8 months ago) by matt4077

Revision 724 - Directory Listing
Modified Fri Dec 17 10:45:40 2010 UTC (5 years, 8 months ago) by hstehr
Updating copyright message to 2011 and changing version number to 1.1rc1
Revision 723 - Directory Listing
Modified Fri Dec 10 16:49:33 2010 UTC (5 years, 8 months ago) by matt4077
moving features to experimental section
Revision 722 - Directory Listing
Modified Fri Dec 10 15:53:43 2010 UTC (5 years, 8 months ago) by matt4077
adding jars which were apparently missing for running CMVIew
Revision 721 - Directory Listing
Modified Fri Dec 10 14:51:02 2010 UTC (5 years, 8 months ago) by matt4077

Revision 720 - Directory Listing
Modified Fri Dec 10 14:48:35 2010 UTC (5 years, 8 months ago) by matt4077

Revision 719 - Directory Listing
Modified Mon Nov 29 15:54:51 2010 UTC (5 years, 8 months ago) by cvehlow
Check for correct Zip-File directory (should be set in config file)
Revision 717 - Directory Listing
Modified Mon Nov 29 10:36:41 2010 UTC (5 years, 8 months ago) by cvehlow
Check for database access (for ContactGeomAnalysis Plugin)
Revision 716 - Directory Listing
Modified Wed Nov 17 13:45:46 2010 UTC (5 years, 9 months ago) by jmduarteg
Adapted to new exception PdbLoadError thrown now by PdbfilePdb
Revision 715 - Directory Listing
Modified Mon Oct 11 14:32:02 2010 UTC (5 years, 10 months ago) by vehlow
Labels within panel changed
Revision 714 - Directory Listing
Modified Tue Oct 5 08:59:56 2010 UTC (5 years, 10 months ago) by vehlow
Bug Interface Label removed.
Revision 713 - Directory Listing
Modified Thu Sep 23 12:59:27 2010 UTC (5 years, 11 months ago) by vehlow
ZipArchive handling
Revision 712 - Directory Listing
Modified Tue Sep 14 13:44:18 2010 UTC (5 years, 11 months ago) by vehlow
Default-path for SphoxelBG.zip integrated
Revision 711 - Directory Listing
Modified Tue Sep 14 11:13:01 2010 UTC (5 years, 11 months ago) by vehlow
Default-path for SphoxelBG.zip integrated
Revision 710 - Directory Listing
Modified Tue Sep 14 10:15:56 2010 UTC (5 years, 11 months ago) by vehlow
SPHOXEL_BG_FILE_PATH variable for zip archive location
Revision 709 - Directory Listing
Modified Wed Sep 1 13:30:40 2010 UTC (5 years, 11 months ago) by vehlow
contact selection -> right click fixed
Revision 708 - Directory Listing
Modified Tue Aug 31 13:42:53 2010 UTC (5 years, 11 months ago) by vehlow
Path to ZIP file
Revision 707 - Directory Listing
Modified Fri Aug 27 11:31:18 2010 UTC (6 years ago) by vehlow
Bug removed, in case contact not available for both loaded models.
Revision 706 - Directory Listing
Modified Thu Aug 26 14:42:11 2010 UTC (6 years ago) by vehlow
fn generation for png
Revision 705 - Directory Listing
Modified Thu Aug 26 14:17:39 2010 UTC (6 years ago) by vehlow
Important change: iNum and iNum2 for two models --> not necessarily the same --> changed parameter determination
Revision 704 - Directory Listing
Modified Thu Aug 26 12:25:50 2010 UTC (6 years ago) by vehlow
Change Residue Labels!
Revision 703 - Directory Listing
Modified Wed Aug 25 12:09:34 2010 UTC (6 years ago) by vehlow
Automatic filename generation for png-file!
Revision 702 - Directory Listing
Modified Wed Aug 25 11:26:52 2010 UTC (6 years ago) by vehlow
Default Panel Height adapted to make sure everything is visible.
Revision 701 - Directory Listing
Modified Wed Aug 25 10:09:35 2010 UTC (6 years ago) by vehlow
Changes to select certain Secondary Structure Type for Traces extraction!
Revision 700 - Directory Listing
Modified Tue Aug 24 07:21:21 2010 UTC (6 years ago) by vehlow
Ready for tests
Revision 699 - Directory Listing
Modified Sun Aug 22 11:16:11 2010 UTC (6 years ago) by stehr
updating version number to 1.5.0 to reflect major new features compared to v1.0. Ultimately this will become v2.
Revision 698 - Directory Listing
Modified Wed Aug 4 11:57:10 2010 UTC (6 years ago) by stehr
adding vecmath.jar to jars directory, needed for older jdk versions where java3d is not part of the core library
Revision 697 - Directory Listing
Modified Wed Aug 4 11:56:04 2010 UTC (6 years ago) by stehr
committing new merged version of the master config file
Revision 696 - Directory Listing
Modified Wed Aug 4 11:48:36 2010 UTC (6 years ago) by vehlow
StartOptions --> default path
Revision 695 - Directory Listing
Modified Wed Aug 4 11:34:40 2010 UTC (6 years ago) by stehr
again reverting to revision 408 which is a minimal config file for new users
Revision 694 - Directory Listing
Modified Fri Jul 30 13:12:45 2010 UTC (6 years ago) by vehlow
Change Menu-options (titles)
Revision 693 - Directory Listing
Modified Thu Jul 29 10:53:32 2010 UTC (6 years ago) by vehlow
Check for database-availability and adjust comboBoxes for view-selection.
Revision 692 - Directory Listing
Modified Thu Jul 29 10:19:16 2010 UTC (6 years ago) by vehlow
deltaRank in var tfFct-MAP
Revision 691 - Directory Listing
Modified Thu Jul 29 10:07:29 2010 UTC (6 years ago) by vehlow
deltaRank in var tfFct-MAP
Revision 690 - Directory Listing
Modified Tue Jul 27 09:57:37 2010 UTC (6 years, 1 month ago) by vehlow
Inclusion of DeltaRank as inputValue for variable transfer function.
Revision 689 - Directory Listing
Modified Wed Jul 21 10:26:26 2010 UTC (6 years, 1 month ago) by vehlow
Inclusion of variable Map-representation based on variable transfer function (handling via dialog).
Revision 688 - Directory Listing
Modified Fri Jul 9 11:04:54 2010 UTC (6 years, 1 month ago) by vehlow
new Zip archive, as some files (combinations)n were missing in the old one
Revision 685 - Directory Listing
Modified Fri Jul 9 08:39:00 2010 UTC (6 years, 1 month ago) by vehlow
error message removed_load pdb in view
Revision 683 - Directory Listing
Modified Thu Jul 8 14:08:19 2010 UTC (6 years, 1 month ago) by susdalze
Including the scoring function-Saurabh
Revision 682 - Directory Listing
Modified Tue Jul 6 12:20:52 2010 UTC (6 years, 1 month ago) by vehlow
Changes in HistogramView --> distribution of nodes within annulus around centre of selection.
Revision 681 - Directory Listing
Modified Tue Jul 6 10:45:56 2010 UTC (6 years, 1 month ago) by vehlow
Histograms for selections (node distribution)
Revision 680 - Directory Listing
Modified Tue Jun 29 13:41:21 2010 UTC (6 years, 1 month ago) by vehlow
Test
Revision 679 - Directory Listing
Modified Fri Jun 25 13:39:32 2010 UTC (6 years, 2 months ago) by vehlow
TemplateTrace drawn --> check for consistency in translation rotation framework.
Revision 678 - Directory Listing
Modified Thu Jun 24 10:29:14 2010 UTC (6 years, 2 months ago) by vehlow
Dublicate Icon removed.
Revision 677 - Directory Listing
Modified Thu Jun 24 10:28:24 2010 UTC (6 years, 2 months ago) by vehlow
New Icons added.
Display of single template trace in ContactPane.
Therefore geometry extracted when loading pdb-file.
Revision 676 - Directory Listing
Modified Wed Jun 23 09:47:21 2010 UTC (6 years, 2 months ago) by winkelma
New Residuescoringfunctionimplementation
Revision 675 - Directory Listing
Modified Fri Jun 18 10:35:23 2010 UTC (6 years, 2 months ago) by vehlow
Model now includes instance of RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
Revision 674 - Directory Listing
Modified Wed Jun 16 15:08:51 2010 UTC (6 years, 2 months ago) by vehlow
Changes in edge-cluster direction!
Revision 673 - Directory Listing
Modified Wed Jun 16 08:29:29 2010 UTC (6 years, 2 months ago) by vehlow
Geodesic  Lines --> implementation changed!
Revision 672 - Directory Listing
Modified Mon Jun 14 13:21:08 2010 UTC (6 years, 2 months ago) by vehlow
Save and Load settings of SphoxelMap_Traces_View.
Revision 671 - Directory Listing
Modified Wed Jun 9 14:59:11 2010 UTC (6 years, 2 months ago) by vehlow
Cluster-edge direction evaluated and visualised via arrows.
Revision 670 - Directory Listing
Modified Wed Jun 9 08:46:02 2010 UTC (6 years, 2 months ago) by vehlow
Clustering implemented and performed.
Revision 669 - Directory Listing
Modified Tue Jun 8 17:31:13 2010 UTC (6 years, 2 months ago) by vehlow
Clustering implemented and performed.
Map projection, to fold a sphere.
Revision 668 - Directory Listing
Modified Wed Jun 2 14:13:07 2010 UTC (6 years, 2 months ago) by vehlow
Adjustments in azimuthal projection --> correct selection
Adjustements in colorScaleView --> trace colouring
Revision 667 - Directory Listing
Modified Tue Jun 1 15:59:22 2010 UTC (6 years, 2 months ago) by vehlow
A set of optimal SubStrings is computed and offert within ComboBox.
Revision 666 - Directory Listing
Modified Tue Jun 1 15:56:48 2010 UTC (6 years, 2 months ago) by vehlow
new Icon for SphoxelTraces 
Revision 665 - Directory Listing
Modified Tue Jun 1 11:22:59 2010 UTC (6 years, 2 months ago) by stehr
removing @override annotations to make code java 1.5 compliant
Revision 664 - Directory Listing
Modified Tue Jun 1 11:18:37 2010 UTC (6 years, 2 months ago) by vehlow
overrides removed
Revision 663 - Directory Listing
Modified Tue Jun 1 11:04:38 2010 UTC (6 years, 2 months ago) by vehlow
geodesic lines
Revision 662 - Directory Listing
Modified Mon May 31 15:40:24 2010 UTC (6 years, 2 months ago) by vehlow
Changes in menu (status bar)
Revision 661 - Directory Listing
Modified Mon May 31 13:04:35 2010 UTC (6 years, 2 months ago) by vehlow
Bugs of azimuthal projection removed.
Icons changed.
Revision 660 - Directory Listing
Modified Mon May 31 13:03:28 2010 UTC (6 years, 2 months ago) by vehlow
MenuIcon for SphoxelMenu changed.
Revision 659 - Directory Listing
Modified Mon May 31 12:59:58 2010 UTC (6 years, 2 months ago) by vehlow
Icons for SphoxelNBHS Frame
Revision 658 - Directory Listing
Modified Fri May 28 14:01:55 2010 UTC (6 years, 2 months ago) by vehlow
Running version of azimuthal projection.
Revision 657 - Directory Listing
Modified Fri May 28 07:37:20 2010 UTC (6 years, 3 months ago) by vehlow
AzimuthalProjection
Revision 656 - Directory Listing
Modified Tue May 25 14:14:44 2010 UTC (6 years, 3 months ago) by vehlow
Phi changed to lampda and theta changed to phi --> definition from literature:
longitude = lampda
latitude = phi
Revision 655 - Directory Listing
Modified Tue May 25 13:56:41 2010 UTC (6 years, 3 months ago) by vehlow
First implementation of azimuthal projection.
Revision 654 - Directory Listing
Modified Tue May 25 09:04:03 2010 UTC (6 years, 3 months ago) by vehlow
Changes in NBHSselpanel
Revision 653 - Directory Listing
Modified Thu May 20 11:12:49 2010 UTC (6 years, 3 months ago) by vehlow
NBHString residue selection (toggle single residues of string on or off) added to menu.
Revision 652 - Directory Listing
Modified Tue May 18 09:22:02 2010 UTC (6 years, 3 months ago) by winkelma
little refactoring. We had to ContactMap classes which created a conflict in our not-yet-very-smart build script.
Revision 651 - Directory Listing
Modified Mon May 17 13:33:00 2010 UTC (6 years, 3 months ago) by vehlow
Changes for panning the map projection (correct turn down).
Adjustments in histogram (scale etc. added).
Revision 650 - Directory Listing
Modified Mon May 17 07:51:42 2010 UTC (6 years, 3 months ago) by vehlow
HistogramView (for selections) implemented.
Revision 649 - Directory Listing
Modified Wed May 12 16:53:04 2010 UTC (6 years, 3 months ago) by stehr
Now asking before assigning consensus secondary structure for "Load from Casp Server Models"
Revision 648 - Directory Listing
Modified Wed May 12 16:37:43 2010 UTC (6 years, 3 months ago) by stehr
now consensus secondary structure is automatically assigned for "Load from Casp Server Models"
Revision 647 - Directory Listing
Modified Wed May 12 13:07:51 2010 UTC (6 years, 3 months ago) by stehr
now reading the target number when loading casp server predictions
Revision 646 - Directory Listing
Modified Wed May 12 12:04:06 2010 UTC (6 years, 3 months ago) by stehr
first working version of feature "Load from Casp Server Models", still missing: assign consensus secondary structure, load model number
Revision 645 - Directory Listing
Modified Mon May 10 10:37:09 2010 UTC (6 years, 3 months ago) by stehr
adding a main method for testing and debugging
Revision 644 - Directory Listing
Modified Sun May 9 21:59:36 2010 UTC (6 years, 3 months ago) by stehr
new feature "Load from Casp Server Models" (not working yet)
Revision 643 - Directory Listing
Modified Sun May 9 21:56:19 2010 UTC (6 years, 3 months ago) by stehr
new feature "Load from Casp Server Models" (not working yet)
Revision 642 - Directory Listing
Modified Fri May 7 13:38:12 2010 UTC (6 years, 3 months ago) by stehr
New layout for JPred progress dialog (to try do File->Load from sequence)
Revision 641 - Directory Listing
Modified Fri May 7 12:00:37 2010 UTC (6 years, 3 months ago) by stehr
moving JPred related classes to new subpackage cmview.jpredAdapter; deleting obsolete class ZVTMView
Revision 640 - Directory Listing
Modified Fri May 7 11:54:41 2010 UTC (6 years, 3 months ago) by stehr
First working version of JPred secondary structure prediction with a progress dialog.
Revision 639 - Directory Listing
Modified Thu May 6 12:42:16 2010 UTC (6 years, 3 months ago) by vehlow
actual status
Revision 637 - Directory Listing
Modified Tue May 4 13:12:32 2010 UTC (6 years, 3 months ago) by vehlow
Changes considering map projections.
Revision 636 - Directory Listing
Modified Tue May 4 11:41:36 2010 UTC (6 years, 3 months ago) by vehlow
Changes in selection and interaction handling: values adapted correctly to map projection type.
Revision 633 - Directory Listing
Modified Mon May 3 15:51:14 2010 UTC (6 years, 3 months ago) by winkelma
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 632 - Directory Listing
Modified Mon May 3 10:37:36 2010 UTC (6 years, 3 months ago) by vehlow
PseudoCylindricalProjection first implementation.
BackgroundSphoxelimages included into resources.
Revision 631 - Directory Listing
Modified Wed Apr 28 23:54:43 2010 UTC (6 years, 3 months ago) by stehr
New method view.updateTitle now shows in window title whether a loaded contact map has been modified (edges added or deleted); Model now contains a flag "modified" which is being set when edges are added/removed; minor refactoring: moving two methods from cmPane to View (which should be called Controller)
Revision 630 - Directory Listing
Modified Wed Apr 28 21:43:11 2010 UTC (6 years, 3 months ago) by stehr
Reverting default cmview.cfg to rev 406 which is a minimal config file for external users
Revision 629 - Directory Listing
Modified Wed Apr 28 14:43:50 2010 UTC (6 years, 3 months ago) by vehlow
Changes in interface optic and interactions.
Revision 628 - Directory Listing
Modified Tue Apr 27 16:09:34 2010 UTC (6 years, 4 months ago) by stehr
Now assigning the default contact type and distance cutoff to the graph in SequenceModel (this is what you get when you File->Load from sequence)
Revision 627 - Directory Listing
Modified Tue Apr 27 15:32:54 2010 UTC (6 years, 4 months ago) by stehr
New feature: Use predicted secondary structure when loading from sequence (File->Load from->Sequence); Internal: SecondaryStructure now stored in Model object (previously using the one in Pdb)
Revision 626 - Directory Listing
Modified Tue Apr 27 12:57:59 2010 UTC (6 years, 4 months ago) by vehlow
eventHandling handed over to ContactView if contact clicked
Revision 625 - Directory Listing
Modified Tue Apr 27 11:04:12 2010 UTC (6 years, 4 months ago) by vehlow
Static final var included.
Revision 624 - Directory Listing
Modified Mon Apr 26 16:14:42 2010 UTC (6 years, 4 months ago) by duarte
Minor refactoring following refactoring in SecondaryStructure class.
Revision 623 - Directory Listing
Modified Mon Apr 26 15:50:03 2010 UTC (6 years, 4 months ago) by stehr
committing missing class SequenceModel
Revision 622 - Directory Listing
Modified Mon Apr 26 12:55:26 2010 UTC (6 years, 4 months ago) by stehr
New function in compare mode: Copy selected contacts from second to first.
Revision 621 - Directory Listing
Modified Thu Apr 22 07:55:36 2010 UTC (6 years, 4 months ago) by vehlow
Correct panning via mouse and arrow buttons.
Revision 620 - Directory Listing
Modified Wed Apr 21 13:32:03 2010 UTC (6 years, 4 months ago) by stehr
New feature 'Load from sequence'. Will create an empty contact map (except for chain connectivity) for ab-initio modelling.
Revision 619 - Directory Listing
Modified Wed Apr 21 10:56:53 2010 UTC (6 years, 4 months ago) by vehlow
Interaction in interface --> panning within view possible.
Revision 618 - Directory Listing
Modified Wed Apr 21 07:03:16 2010 UTC (6 years, 4 months ago) by vehlow
Selected angle ranges are handed over to owl.gmbp instance within model.
Revision 617 - Directory Listing
Modified Tue Apr 20 14:00:05 2010 UTC (6 years, 4 months ago) by duarte
Removing bin dir commited by error.
Revision 616 - Directory Listing
Modified Tue Apr 20 10:31:52 2010 UTC (6 years, 4 months ago) by winkelma

Revision 615 - Directory Listing
Modified Tue Apr 20 10:20:44 2010 UTC (6 years, 4 months ago) by vehlow
Selected angle ranges are handed over to owl.gmbp instance within model.
Revision 614 - Directory Listing
Modified Mon Apr 19 09:48:39 2010 UTC (6 years, 4 months ago) by stehr
Adding package-info.java file
Revision 613 - Directory Listing
Modified Mon Apr 19 09:40:03 2010 UTC (6 years, 4 months ago) by vehlow
Moving sphoxel related classes to cmview.gmbp package
Revision 612 - Directory Listing
Modified Fri Apr 16 13:27:20 2010 UTC (6 years, 4 months ago) by vehlow
Faster SQL queries
Revision 611 - Directory Listing
Modified Fri Apr 16 13:06:24 2010 UTC (6 years, 4 months ago) by stehr
preparing LoadDialog for loading from sequence
Revision 610 - Directory Listing
Modified Thu Apr 15 15:28:46 2010 UTC (6 years, 4 months ago) by vehlow
Changes in interface (ruler and sliders etc)
Revision 609 - Directory Listing
Modified Thu Apr 15 09:29:31 2010 UTC (6 years, 4 months ago) by duarte
Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!
Revision 608 - Directory Listing
Modified Wed Apr 14 16:01:03 2010 UTC (6 years, 4 months ago) by vehlow
Changes in ContactView class and contained views:
ruler added
changes in slider optic
window showing angle range
Revision 607 - Directory Listing
Modified Wed Apr 14 09:17:29 2010 UTC (6 years, 4 months ago) by stehr
updated version number to 1.2.1 (not yet tagged)
Revision 606 - Directory Listing
Modified Wed Apr 14 09:08:20 2010 UTC (6 years, 4 months ago) by stehr
committing eclipse project and classpath files

Revision 605 - Directory Listing
Modified Tue Apr 13 17:17:17 2010 UTC (6 years, 4 months ago) by vehlow
GuiState for ContactView
Revision 604 - Directory Listing
Modified Tue Apr 13 17:16:51 2010 UTC (6 years, 4 months ago) by vehlow
StatusBar for sphoxel representation adjustment.
Revision 603 - Directory Listing
Modified Tue Apr 13 17:16:02 2010 UTC (6 years, 4 months ago) by vehlow
Sliders for radius range and resolution added.
First mouse motion evaluation.
Revision 602 - Directory Listing
Modified Tue Apr 13 13:52:22 2010 UTC (6 years, 4 months ago) by stehr
In compare mode: adding option for showing difference map to background overlay drop down list. Currently not quite synchronized with similar function in compare menu, but works.
Revision 601 - Directory Listing
Modified Tue Apr 13 12:48:09 2010 UTC (6 years, 4 months ago) by stehr
Replacing GUI occurrances of text "Tinker" with "Distance geometry" or "Distgeom"
Revision 600 - Directory Listing
Modified Tue Apr 13 12:35:57 2010 UTC (6 years, 4 months ago) by stehr
follow-up to previous: suppress weighted contact controls in StatusBar if USE_EXPERIMENTAL_FEATURES=false or SHOW_WEIGHTED_CONTACTS=FALSE
Revision 599 - Directory Listing
Modified Tue Apr 13 12:30:18 2010 UTC (6 years, 4 months ago) by stehr
marked DeltaRank functions, Cone peeling and Sphoxel display as experimental (only shown if USE_EXPERIMENTAL_FEATURES=true in cmview.cfg)
Revision 598 - Directory Listing
Modified Mon Apr 12 15:28:42 2010 UTC (6 years, 4 months ago) by stehr
now also drawing weighted contacts in compare mode (if weighted contact map loaded and USE_EXPERIMENTAL_FEATURES=true and Start.SHOW_WEIGHTED_CONTACTS=true)
Revision 597 - Directory Listing
Modified Mon Apr 12 14:25:19 2010 UTC (6 years, 4 months ago) by stehr
New option "load all models" in load menu. Will load a weighted contact map of the ensembl of all models. Currently, for simplicity, only one model is loaded in PyMol (as before).
Revision 596 - Directory Listing
Modified Mon Apr 12 11:08:52 2010 UTC (6 years, 4 months ago) by winkelma
Swap Models
Revision 595 - Directory Listing
Modified Sat Apr 10 22:15:23 2010 UTC (6 years, 4 months ago) by stehr
committing jar files required for building CMView
Revision 594 - Directory Listing
Modified Fri Apr 9 15:28:06 2010 UTC (6 years, 4 months ago) by stehr
adding discretization controls for weighted graphs: when loading a weighted graph from a contact map file (e.g. CMView/test/sample_files/ensemble_aligned.cm), the status bar will show a new group of controls for discretizing the weighted graph using a slider to choose the cutoff or the length/10 or length/5 highest weight contacts
Revision 593 - Directory Listing
Modified Fri Apr 9 15:26:18 2010 UTC (6 years, 4 months ago) by vehlow
warnings removed
Revision 592 - Directory Listing
Modified Fri Apr 9 15:21:25 2010 UTC (6 years, 4 months ago) by vehlow
actual commit
Revision 591 - Directory Listing
Modified Fri Apr 9 14:51:25 2010 UTC (6 years, 4 months ago) by stehr
adding sample files with various flaws and flavours for testing
Revision 590 - Directory Listing
Modified Fri Apr 9 13:14:31 2010 UTC (6 years, 4 months ago) by vehlow
First Version of Sphoxel-Representation (via Right-Click PopupMenu).
Revision 589 - Directory Listing
Modified Fri Apr 9 12:30:54 2010 UTC (6 years, 4 months ago) by stehr
deleting obsolete directory bin
Revision 588 - Directory Listing
Modified Fri Apr 9 12:30:16 2010 UTC (6 years, 4 months ago) by gmueller
icon file added
Revision 587 - Directory Listing
Modified Fri Apr 9 11:25:03 2010 UTC (6 years, 4 months ago) by gmueller
unnecessary exception clauses removed

Revision 586 - Directory Listing
Modified Fri Apr 9 11:18:54 2010 UTC (6 years, 4 months ago) by gmueller
an new method added in Model, which runs the cone peeling algorithm as implemented in the embed.ConePeeler class
note, that the graph field of this class contains the minimal subset after calling this method

calling cone peeler from button bar, so View class was modified accordingly
Revision 585 - Directory Listing
Modified Fri Apr 9 09:02:14 2010 UTC (6 years, 4 months ago) by stehr
adding gui for multiModelGroup (so far w/o function)
Revision 584 - Directory Listing
Modified Thu Apr 8 15:19:12 2010 UTC (6 years, 4 months ago) by stehr
Reorganized code for delta rank related controls: new JPanel deltaRankGroup in StatusBar can be initialized with initDeltaRankGroup() and activated with showDeltaRankGroup(true)
Revision 583 - Directory Listing
Modified Thu Apr 8 14:41:38 2010 UTC (6 years, 4 months ago) by stehr
cleaned up code in StatusBar: coordinate drawing now in CoordinatesPanel, events for local gui elements handled by status bar itself
Revision 582 - Directory Listing
Modified Thu Apr 8 14:27:20 2010 UTC (6 years, 4 months ago) by winkelma
fixed bug #35: resize rulers when DR bar is added/removed.
Revision 581 - Directory Listing
Modified Thu Apr 8 13:17:18 2010 UTC (6 years, 4 months ago) by winkelma
fixed bug #34: immediate repaint to remove delta rank bar.
Revision 580 - Directory Listing
Modified Thu Apr 1 14:03:25 2010 UTC (6 years, 4 months ago) by winkelma
draw smaller contact dots if a background is also selected
Revision 579 - Directory Listing
Modified Thu Apr 1 12:45:38 2010 UTC (6 years, 4 months ago) by stehr
updated javadoc for StatusBar and minor layout change of overlayGroup
Revision 578 - Directory Listing
Modified Thu Apr 1 10:53:41 2010 UTC (6 years, 4 months ago) by stehr
created JPanel for holding the drop down lists in status bar
Revision 577 - Directory Listing
Modified Wed Mar 31 16:08:42 2010 UTC (6 years, 4 months ago) by stehr
updated imports after major refactoring of aglappe/owl
Revision 575 - Directory Listing
Modified Tue Mar 30 15:39:33 2010 UTC (6 years, 4 months ago) by stehr
merged ContactMapPane.drawCoordinates() and drawRulerCoordinates(), now coordinates are drawn correctly in ruler mode (both single and compare)
Revision 574 - Directory Listing
Modified Tue Mar 30 12:46:06 2010 UTC (6 years, 4 months ago) by stehr
restructured StatusPane.drawCoordinates: now correctly shows coordinates in compare mode and code should be more readable
Revision 573 - Directory Listing
Modified Mon Mar 29 15:25:30 2010 UTC (6 years, 4 months ago) by stehr
some layout changes: background of residue ruler is now transparent, coordinates in status bar are now blue with white background
Revision 572 - Directory Listing
Modified Mon Mar 29 13:51:43 2010 UTC (6 years, 4 months ago) by stehr
replaced literal 'delta' character (which was not working in linux) by unicode character
Revision 571 - Directory Listing
Modified Mon Mar 29 10:14:26 2010 UTC (6 years, 4 months ago) by duarte
Removed unneeded import
Revision 570 - Directory Listing
Modified Mon Mar 29 10:13:50 2010 UTC (6 years, 4 months ago) by duarte
Changed call to DsspRunner (now static)
Revision 569 - Directory Listing
Modified Mon Mar 29 09:14:08 2010 UTC (6 years, 4 months ago) by winkelma
fixed null pointer bug
Revision 568 - Directory Listing
Modified Thu Mar 18 12:03:40 2010 UTC (6 years, 5 months ago) by duarte
Adapted runDssp call to new structure in owl library.
Revision 567 - Directory Listing
Modified Wed Mar 17 17:04:38 2010 UTC (6 years, 5 months ago) by winkelma
test
Revision 566 - Directory Listing
Modified Wed Mar 17 15:43:42 2010 UTC (6 years, 5 months ago) by duarte
Updating FileTypeGuesser references (hadn't been done after refactoring in owl)
Revision 565 - Directory Listing
Modified Mon Mar 15 17:05:15 2010 UTC (6 years, 5 months ago) by winkelma
test
Revision 564 - Directory Listing
Modified Fri Feb 12 15:30:40 2010 UTC (6 years, 6 months ago) by duarte
Refactoring following rearrangment of classes in aglappe.
Revision 563 - Directory Listing
Modified Mon Feb 8 15:39:00 2010 UTC (6 years, 6 months ago) by duarte
Refactoring following refactoring in aglappe
Revision 562 - Directory Listing
Modified Fri Jan 29 12:56:50 2010 UTC (6 years, 6 months ago) by duarte
Refactoring following refactoring in aglappe

Revision 560 - Directory Listing
Modified Wed Jan 27 17:04:41 2010 UTC (6 years, 6 months ago) by duarte
Now database connection parameters are read from .my.cnf file (not tested on windows or mac!). Removed the second db connection for delta rank.
Revision 559 - Directory Listing
Modified Fri Jan 22 16:44:01 2010 UTC (6 years, 7 months ago) by winkelma
hide delta rank bar until needed, inverted colors in heatmap
Revision 558 - Directory Listing
Modified Fri Jan 22 16:32:39 2010 UTC (6 years, 7 months ago) by winkelma
corrected of-by-1 bug, warning, missing frames in CM and added white frames to dr view
Revision 557 - Directory Listing
Modified Fri Jan 22 16:12:13 2010 UTC (6 years, 7 months ago) by winkelma
contact map rainbows
Revision 556 - Directory Listing
Modified Mon Jan 18 09:21:50 2010 UTC (6 years, 7 months ago) by duarte
Got rid of Override annotation that was showing as compiling error
Revision 555 - Directory Listing
Modified Fri Jan 15 17:49:43 2010 UTC (6 years, 7 months ago) by winkelma
many ui changes, including a new status bar, a second contact map and delta rank backgrounds
Revision 554 - Directory Listing
Modified Thu Jan 7 19:00:12 2010 UTC (6 years, 7 months ago) by winkelma
Delta Rank Visualization
Revision 553 - Directory Listing
Modified Wed Nov 11 09:36:56 2009 UTC (6 years, 9 months ago) by winkelma
Tinker results selection table
Revision 552 - Directory Listing
Modified Fri Oct 30 10:32:55 2009 UTC (6 years, 9 months ago) by winkelma
added some comments and got started on a tinker result set selection list
Revision 551 - Directory Listing
Modified Tue Oct 27 17:31:26 2009 UTC (6 years, 9 months ago) by winkelma
Use correct forcefield and parallel option for tinker reconstruction
Revision 550 - Directory Listing
Modified Tue Oct 27 15:54:16 2009 UTC (6 years, 9 months ago) by duarte
Fixed bug: was declaring twice some fields in Model and some subclasses. 
Revision 549 - Directory Listing
Modified Mon Oct 26 14:46:34 2009 UTC (6 years, 10 months ago) by winkelma
Merged tinker into trunk
Revision 535 - Directory Listing
Modified Wed Oct 14 17:11:38 2009 UTC (6 years, 10 months ago) by winkelma
tolerate unobserved residues in DALI alignments
Revision 534 - Directory Listing
Modified Tue Oct 13 10:29:38 2009 UTC (6 years, 10 months ago) by stehr
added DALI Alignment option
Revision 533 - Directory Listing
Modified Wed Aug 12 08:12:15 2009 UTC (7 years ago) by duarte
Removed msd related stuff (following removal in aglappe)
Revision 532 - Directory Listing
Modified Tue Aug 11 13:08:00 2009 UTC (7 years ago) by stehr
updated version to 1.2.0 (not yet tagged)
Revision 530 - Directory Listing
Modified Tue Aug 11 12:57:54 2009 UTC (7 years ago) by stehr
updated version number to 1.1.1 for tagging
Revision 529 - Directory Listing
Modified Tue Aug 11 12:55:31 2009 UTC (7 years ago) by duarte
Changed versions in Manifests before tagging
Revision 528 - Directory Listing
Modified Thu Feb 19 10:25:47 2009 UTC (7 years, 6 months ago) by duarte
Reverted colors for the weights coloring (now from blue=0 to red=1)
Revision 527 - Directory Listing
Modified Wed Feb 18 17:35:31 2009 UTC (7 years, 6 months ago) by duarte
New feature: weights can now be shown in color gradient setting property SHOW_WEIGHTS_IN_COLOR=true
Revision 526 - Directory Listing
Modified Thu Jan 29 14:18:22 2009 UTC (7 years, 6 months ago) by duarte
Fixed bug: PyMolAdaptor.getAtom was NullPointing in compare mode when drawing an absent contact that mapped to an unobserved residue.
Revision 525 - Directory Listing
Modified Wed Sep 24 18:21:37 2008 UTC (7 years, 11 months ago) by duarte
Changed call to writeToFasta following change in Alignment class
Revision 524 - Directory Listing
Modified Tue Sep 23 09:16:04 2008 UTC (7 years, 11 months ago) by stehr
bugfix: interactive mode was not working after introducing -I option
Revision 523 - Directory Listing
Modified Tue Sep 16 09:57:52 2008 UTC (7 years, 11 months ago) by stehr
added command line option -I for saving preloaded CM directly to image file
Revision 522 - Directory Listing
Modified Tue Sep 16 09:55:36 2008 UTC (7 years, 11 months ago) by stehr
set javaversion to 1.5 for compatibility
Revision 521 - Directory Listing
Modified Fri Sep 12 17:15:48 2008 UTC (7 years, 11 months ago) by duarte
Adapted to change of exceptions in Alignment.
Revision 520 - Directory Listing
Modified Thu Aug 28 13:22:08 2008 UTC (7 years, 11 months ago) by duarte
Added script to create test cases (xml files for abbot)
Revision 518 - Directory Listing
Modified Wed Aug 27 13:58:51 2008 UTC (8 years ago) by stehr
Added a serialVersionUID to avoid a compiler warning
Revision 514 - Directory Listing
Modified Tue Aug 26 12:30:31 2008 UTC (8 years ago) by duarte
Removing test
Revision 513 - Directory Listing
Modified Tue Aug 26 11:18:50 2008 UTC (8 years ago) by duarte
Test commit: back to old eclipse-3.4 using keyring option (duarte)
Revision 512 - Directory Listing
Modified Tue Aug 26 11:09:23 2008 UTC (8 years ago) by stehr
testing commit from clean eclipse as stehr
Revision 511 - Directory Listing
Modified Tue Aug 26 11:07:05 2008 UTC (8 years ago) by duarte
Test commit, clean eclipse 3.4 install (duarte)
Revision 510 - Directory Listing
Modified Tue Aug 26 11:03:26 2008 UTC (8 years ago) by stehr
testing commit from clean eclipse as stehr
Revision 509 - Directory Listing
Modified Tue Aug 26 11:00:12 2008 UTC (8 years ago) by duarte
testing commit from clean eclipse as stehr
Revision 508 - Directory Listing
Modified Tue Aug 26 10:58:03 2008 UTC (8 years ago) by duarte
testing commit from clean eclipse as stehr
Revision 507 - Directory Listing
Modified Tue Aug 26 10:55:15 2008 UTC (8 years ago) by duarte
Test commit, clean eclipse 3.4 install (duarte)
Revision 506 - Directory Listing
Modified Tue Aug 26 10:49:21 2008 UTC (8 years ago) by stehr
testing commit from clean eclipse as stehr
Revision 505 - Directory Listing
Modified Tue Aug 26 10:32:51 2008 UTC (8 years ago) by duarte
Test commit, clean eclipse 3.4 install (duarte)
Revision 504 - Directory Listing
Modified Tue Aug 26 09:41:49 2008 UTC (8 years ago) by stehr
Test commit from new workspace (duarte)
Revision 503 - Directory Listing
Modified Tue Aug 26 08:56:55 2008 UTC (8 years ago) by stehr
test commit, eclipse started with NO javahl library pointing to /project/StruPPi/lib (duarte)
Revision 502 - Directory Listing
Modified Tue Aug 26 08:47:55 2008 UTC (8 years ago) by duarte
test commit from svn command line (duarte)
Revision 501 - Directory Listing
Modified Mon Aug 25 17:13:17 2008 UTC (8 years ago) by stehr
dummy commit, testing (duarte)
Revision 500 - Directory Listing
Modified Mon Aug 25 16:44:29 2008 UTC (8 years ago) by stehr
dummy commit, testing (duarte)
Revision 499 - Directory Listing
Modified Mon Aug 25 15:45:46 2008 UTC (8 years ago) by stehr
dummy commit, testing (duarte)
Revision 498 - Directory Listing
Modified Mon Aug 25 15:44:56 2008 UTC (8 years ago) by stehr
testing commit (commited by stehr)
Revision 497 - Directory Listing
Modified Mon Aug 4 15:04:25 2008 UTC (8 years ago) by duarte
Switching to JUNG2 beta1. Updated Manifests and make script.
Revision 494 - Directory Listing
Modified Mon Jun 23 10:59:12 2008 UTC (8 years, 2 months ago) by duarte
Removed copying of PymolServerOutputStream, not needed anymore.
Revision 493 - Directory Listing
Modified Mon Jun 23 10:45:40 2008 UTC (8 years, 2 months ago) by duarte
Got rid of references to old jar also in README
Revision 492 - Directory Listing
Modified Mon Jun 23 10:40:35 2008 UTC (8 years, 2 months ago) by duarte
Updated version to 1.1.0 (and got rid of old jars references)
Revision 491 - Directory Listing
Modified Mon Jun 23 10:35:58 2008 UTC (8 years, 2 months ago) by duarte
Now -f can be any kind of file (contact map or pdb file). New non-documented option -Y (don't start pymol).
Revision 490 - Directory Listing
Modified Mon Jun 23 10:30:44 2008 UTC (8 years, 2 months ago) by duarte
Copied from: branches/CMView-dev revision 489

Revision 479 - Directory Listing
Modified Thu May 15 16:22:27 2008 UTC (8 years, 3 months ago) by duarte
Original Path: branches/CMView-dev
Changed call to SecondaryStructure constructor (now a String with sequence must be passed)
Revision 477 - Directory Listing
Modified Wed Apr 23 10:06:55 2008 UTC (8 years, 4 months ago) by risbud
Original Path: branches/CMView-dev
Added the following features:
1. Show Threshold Spheres
2. Show Neighbour Relationships within the first shell
3. Show second shell

New methods added, are:
1. IntPairSet getfirstShellNbrs(Model, int) (ContactMapPane.java)
2. IntPairSet getfirstShellNbrRels(Model, int) (ContactMapPane.java)
3. void getmousePos() (ContactMapPane.java)
4. void drawSpheres(Model, Model, String, Pair<Integer>) (PyMolAdaptor.java)
5. void drawSpheres(Model, Model, String, IntPairSet) (PyMolAdaptor.java)
6. void showSpheres(Model, Pair<Integer>) (PyMolAdaptor.java)
7. void showSpheres(Model, IntPairSet) (PyMolAdaptor.java)
8. void showSecShell(Model, IntPairSet) (PyMolAdaptor.java)
9. void showShellRels(Model, IntPairSet) (PyMolAdaptor.java)
10. void handleShowSpheres3D() (View.java)
11. void handleShowShellRels() (View.java)
12. void handleShowSecShell() (View.java)

Apart from the new methods, some new variables have been introduces in View.java, to create icons, etc. The names are self-explanatory to correlate them with the above changes.

New icon file is created (spheres.png) for "Show Threshold Spheres"

The backend Python script "cmview.py" has been edited to include method to draw sphere CGOs.
Revision 476 - Directory Listing
Modified Fri Apr 11 12:52:02 2008 UTC (8 years, 4 months ago) by duarte
Original Path: branches/CMView-dev
New feature: now contacts are shown on the actual atoms corresponding to the given contact type instead of always on CAs.
Not fully tested.
Increased massively the time-out for PyMolAdaptor
Revision 475 - Directory Listing
Modified Thu Apr 10 08:15:09 2008 UTC (8 years, 4 months ago) by risbud
Original Path: branches/CMView-dev
Copied from: trunk revision 474
Creating dev branch for developing out of the 1.0 release (in trunk)
Revision 474 - Directory Listing
Modified Wed Mar 5 11:26:52 2008 UTC (8 years, 5 months ago) by duarte
Now calling Model.getResType from drawCoordinates. Reimplemented getRestype with code from drawCoordinates, this should be more consistent + now should be safe to use getResType elsewhere
Revision 473 - Directory Listing
Modified Mon Mar 3 15:49:56 2008 UTC (8 years, 5 months ago) by stehr
forgot to check in changes in View for last commit
Revision 472 - Directory Listing
Modified Mon Mar 3 15:49:03 2008 UTC (8 years, 5 months ago) by stehr
Some code cleanup in PyMolAdaptor
Revision 471 - Directory Listing
Modified Fri Feb 29 19:31:11 2008 UTC (8 years, 5 months ago) by duarte
Now (finally!) all pymol specific code is in PyMolAdaptor. No more PyMol code lying around in View.
Fixed bug: show triangles was not randomising well the colors, now simply going round the color array choosing one at a time.
Revision 470 - Directory Listing
Modified Fri Feb 29 16:15:46 2008 UTC (8 years, 5 months ago) by stehr
Moved selection counter from View to PymolAdaptor (where it really really should be)
Revision 469 - Directory Listing
Modified Fri Feb 29 15:42:51 2008 UTC (8 years, 5 months ago) by stehr
Moved runPymol() from Start to PymolAdaptor (and renamed it to startup()); connectin status is now handled by PymolAdaptor
Revision 468 - Directory Listing
Modified Fri Feb 29 15:02:31 2008 UTC (8 years, 5 months ago) by stehr
removed unneccesary pymol commands; align commands now align the second to the first structure (was the other way round)
Revision 467 - Directory Listing
Modified Fri Feb 29 13:30:46 2008 UTC (8 years, 5 months ago) by duarte
Fixed bug: we can't delete callbackFile/command buffer file on exit
Revision 466 - Directory Listing
Modified Fri Feb 29 11:32:47 2008 UTC (8 years, 5 months ago) by duarte
MAJOR CHANGE: new pymol communication mechanism. Mixed of the 2 before: we use command buffer file and "load" commands sent through pymol's stdin. This way we get the best of both worlds: no xml-rpc (no dependencies, better stability), fast command execution thanks to the "load" command.
Revision 465 - Directory Listing
Modified Fri Feb 29 11:19:16 2008 UTC (8 years, 5 months ago) by duarte
Dummy commit: last comment was missing. Should have read: fixed bug, was not running the cmview.py script on initialisation
Revision 464 - Directory Listing
Modified Fri Feb 29 11:17:45 2008 UTC (8 years, 5 months ago) by duarte
Fixed bug;
Revision 463 - Directory Listing
Modified Thu Feb 28 18:21:53 2008 UTC (8 years, 5 months ago) by duarte
Minor fixes: using println instead of write for sendCommand. Fixed comments and got rid of old code.
Revision 462 - Directory Listing
Modified Thu Feb 28 15:39:42 2008 UTC (8 years, 5 months ago) by duarte
MAJOR CHANGE: pymol connection not anymore through xml-rpc but directly through stdin (pymol's -p option). Works well so far, except slower than sending commands through the command buffer. Needs a bit of tweaking to make it faster but otherwise should be much more stable than the xml-rpc server (and needs less external dependencies).
Many configuration variables are now gone (all the ones to do with the PyMol connection and command buffering). 
Revision 461 - Directory Listing
Modified Thu Feb 28 15:04:58 2008 UTC (8 years, 5 months ago) by duarte
Capitalized CMView
Revision 460 - Directory Listing
Modified Thu Feb 28 14:44:46 2008 UTC (8 years, 5 months ago) by duarte
Eliminated Cg type for the release version
Revision 458 - Directory Listing
Modified Thu Feb 28 14:27:43 2008 UTC (8 years, 5 months ago) by duarte
Changed version to 0.9.3
Revision 456 - Directory Listing
Modified Thu Feb 28 14:09:24 2008 UTC (8 years, 5 months ago) by duarte
Minor fixes in comments and error output in StreamGobbler
Revision 455 - Directory Listing
Modified Thu Feb 28 12:10:54 2008 UTC (8 years, 5 months ago) by duarte
FIXED BUG: Finally! the fix for PyMol hanging: new StreamGobbler class sends pymol stdout/stderr to new threads so that there's no blocking of the pymol subprocess.
Revision 454 - Directory Listing
Modified Wed Feb 27 15:39:23 2008 UTC (8 years, 5 months ago) by stehr
minor updates to manual.xml and tutorial.xml
Revision 453 - Directory Listing
Modified Wed Feb 27 13:01:49 2008 UTC (8 years, 5 months ago) by duarte
Now orient command specifies the structure
Revision 452 - Directory Listing
Modified Wed Feb 27 11:52:46 2008 UTC (8 years, 5 months ago) by duarte
Got rid totally of left-over code for old mechanism of sending commands to pymol (without command buffer file)
Added better java docs
Revision 451 - Directory Listing
Modified Wed Feb 27 10:40:27 2008 UTC (8 years, 5 months ago) by duarte
MAJOR CHANGE: now doing pymol communication through a command buffer file, by sending load commands. Using original Lars' code with many bug fixes and an improved flush() method: in flush() we introduce a waiting routine that checks whether the command buffer is ready to be read and then if pymol is already finished executing it.
The whole thing works perfectly (even faster than before), we tested many selections without problem: BUT only when PyMol is started independently (PYMOL_LOAD_ON_START=false). If PyMol is started by CMView then PyMol freezes after ~2 big selections (tested 7adhA,Cb8, sent first all contacts fine, then sending all contacts again it freezes)
Revision 450 - Directory Listing
Modified Tue Feb 26 11:23:37 2008 UTC (8 years, 6 months ago) by duarte
Another attempt to fix the "loosing pymol" windows-only bug: now we do the loadStructure() in a new thread, so hopefully the strange interactions won't happen. Cross fingers....
Revision 449 - Directory Listing
Modified Tue Feb 26 10:59:50 2008 UTC (8 years, 6 months ago) by duarte
New configuration variable in Start: PYMOL_RECONNECT_TRIES. Now PyMolAdaptor uses that one instead of hard-coded. Set default to 1.
Now catching NumberFormatException in applyUserProperties. If a value was incorrectly specified in config file then we print message and exit.
Revision 448 - Directory Listing
Modified Tue Feb 26 08:46:42 2008 UTC (8 years, 6 months ago) by duarte
Rearrange order of things in spawnNewViewWindow and got rid of toFront() call that didn't belong there but in constructor. This might help to solve the bug "loosing pymol connection" in Windows
Revision 447 - Directory Listing
Modified Mon Feb 25 18:02:27 2008 UTC (8 years, 6 months ago) by duarte
Reverting all the changes, no test was successful
Revision 446 - Directory Listing
Modified Mon Feb 25 17:59:18 2008 UTC (8 years, 6 months ago) by duarte
Another test, 10s of sleep this time
Revision 445 - Directory Listing
Modified Mon Feb 25 17:47:50 2008 UTC (8 years, 6 months ago) by duarte
Yet another test for the bug
Revision 444 - Directory Listing
Modified Mon Feb 25 17:46:50 2008 UTC (8 years, 6 months ago) by stehr
checking in latest Javahelp set
Revision 443 - Directory Listing
Modified Mon Feb 25 17:41:21 2008 UTC (8 years, 6 months ago) by stehr
removed "draft" sections from manual.xml, minor update of installation.xml
Revision 442 - Directory Listing
Modified Mon Feb 25 17:40:33 2008 UTC (8 years, 6 months ago) by duarte
3rd test commit. Always trying to fix same bug
Revision 441 - Directory Listing
Modified Mon Feb 25 17:31:35 2008 UTC (8 years, 6 months ago) by duarte
Another test commit to try to fix the Windows bug
Revision 440 - Directory Listing
Modified Mon Feb 25 17:25:20 2008 UTC (8 years, 6 months ago) by duarte
Test commit: commenting out EventQueue.invokeLater to test whether this affects the "loosing connection to pymol when loading small structures" bug in Windows.
Revision 439 - Directory Listing
Modified Mon Feb 25 17:07:41 2008 UTC (8 years, 6 months ago) by stehr
major update of manual.xml
Revision 438 - Directory Listing
Modified Mon Feb 25 16:26:13 2008 UTC (8 years, 6 months ago) by duarte
Changing version of xmlrpc jars from 3.0 to 3.1 in Manifest and make scripts. After preliminary testing in Linux it looks like the libraries work as before. Want to try it now in Windows and Mac, so need to commit.
Revision 437 - Directory Listing
Modified Mon Feb 25 16:23:21 2008 UTC (8 years, 6 months ago) by stehr
Changed menu label 'Load second structure from' to 'Load Second Contact Map From'
Revision 436 - Directory Listing
Modified Mon Feb 25 15:09:11 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: view common neighborhood size menu item in View menu was not taken as experimental.
Revision 435 - Directory Listing
Modified Fri Feb 22 17:28:35 2008 UTC (8 years, 6 months ago) by duarte
Better error messages for sequence missmatch when loading alignment from file. Now we align the missmatching sequences (the one loaded from CMView and the one coming from the file) and show the alignment in stdout so that at least the user can see what's the missmatch.
Revision 434 - Directory Listing
Modified Fri Feb 22 16:48:06 2008 UTC (8 years, 6 months ago) by duarte
Now trashing to a dummy file unwanted output from jaligner (coming from a Logger)
Revision 433 - Directory Listing
Modified Fri Feb 22 16:24:51 2008 UTC (8 years, 6 months ago) by stehr
updated most docbook files, main README and javahelp files
Revision 432 - Directory Listing
Modified Fri Feb 22 15:39:05 2008 UTC (8 years, 6 months ago) by duarte
Now setting WAIT_CURSOR when loading alignment from file.
Revision 431 - Directory Listing
Modified Thu Feb 21 17:13:49 2008 UTC (8 years, 6 months ago) by stehr
Fixed bug: When loading second structure and no common contacts exist, a PyMol 'align' will be executed instead of the usual 'pair_fit' (previously an exception would be thrown)
Revision 430 - Directory Listing
Modified Thu Feb 21 12:36:10 2008 UTC (8 years, 6 months ago) by stehr
New feature: Show Contact map overlap in info screen + acc and cov in experimental mode; Included Neighbourhood selection mode in non-experimental features
Revision 429 - Directory Listing
Modified Wed Feb 20 16:48:58 2008 UTC (8 years, 6 months ago) by stehr
Minor update of manual and index
Revision 428 - Directory Listing
Modified Wed Feb 20 16:42:22 2008 UTC (8 years, 6 months ago) by stehr
Moved constant SHOW_WEIGHTED_CONTACTS from ContactMapPane to Start, can now also be set in the config file
Revision 427 - Directory Listing
Modified Wed Feb 20 16:05:07 2008 UTC (8 years, 6 months ago) by stehr
Moved constant NO_SEQ_SEP_VAL from Start to ProtStructGraph; Removed constant NO_SEQ_SEP_STR from Start; removed constant NULL_CHAIN_CODE in Start, using the one from Pdb; removed members minSeqSep and maxSeqSep from Model, now using the values from graph, except in constructors of subclasses, where a 'local' member minSeqSep and maxSeqSep is still needed as a workaround in order to not change the interface of the constructors and load() methods at the moment.
Revision 426 - Directory Listing
Modified Wed Feb 20 13:56:23 2008 UTC (8 years, 6 months ago) by duarte
New feature: now showing weights as gray-shaded contacts. Can be turned on/off through SHOW_WIGHTED_CONTACTS constant
Revision 425 - Directory Listing
Modified Wed Feb 20 11:17:53 2008 UTC (8 years, 6 months ago) by stehr
Minor update of index, installation and manual
Revision 422 - Directory Listing
Modified Tue Feb 19 18:57:11 2008 UTC (8 years, 6 months ago) by duarte
Fixed bugs: found_pymol and found_database being set to false by default caused side effects: we weren't initialising dashes in Pymol and database menu items were appearing when USE_EXPERIMENTAL_FEATURES was false
Revision 420 - Directory Listing
Modified Tue Feb 19 16:15:52 2008 UTC (8 years, 6 months ago) by duarte
Updated version to 1.0-rc1
Revision 419 - Directory Listing
Modified Tue Feb 19 16:06:46 2008 UTC (8 years, 6 months ago) by stehr
Checking in latest javahelp files
Revision 418 - Directory Listing
Modified Tue Feb 19 16:03:38 2008 UTC (8 years, 6 months ago) by stehr
commented out missing section in Manual before tagging test version
Revision 417 - Directory Listing
Modified Tue Feb 19 15:51:52 2008 UTC (8 years, 6 months ago) by duarte
New script package_for_distribution
New executable scripts for Linux and Windows cmview.sh and cmview.bat
Fixes in make script:
- now takes a cleaned up contactTypes.dat
- now adds license headers to all java files
Cleaned up and restructured README
Revision 416 - Directory Listing
Modified Tue Feb 19 15:50:49 2008 UTC (8 years, 6 months ago) by stehr
Minor changes to Installation and Manual
Revision 415 - Directory Listing
Modified Tue Feb 19 13:20:28 2008 UTC (8 years, 6 months ago) by stehr
New message in about window; initial screen size set to 650 to match default laptop screen resolution 1280x800
Revision 414 - Directory Listing
Modified Tue Feb 19 12:01:52 2008 UTC (8 years, 6 months ago) by duarte
Adding a cleaned up contactTypes.dat for use in CMView final distribution
Revision 413 - Directory Listing
Modified Tue Feb 19 11:24:17 2008 UTC (8 years, 6 months ago) by stehr
Added a message when current config file is written
Revision 412 - Directory Listing
Modified Tue Feb 19 11:22:56 2008 UTC (8 years, 6 months ago) by stehr
New master config file
Revision 411 - Directory Listing
Modified Tue Feb 19 11:21:16 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: canExecute() is java 6, we want java 5 compatibility so using canRead()
Revision 410 - Directory Listing
Modified Tue Feb 19 10:56:27 2008 UTC (8 years, 6 months ago) by stehr
Bugfixes: 1. dssp_found is properly set now; 2. drawRulerCoordinates was throwing null pointer exception if model had to 3d coordinates
Revision 409 - Directory Listing
Modified Mon Feb 18 18:12:38 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: was throwing null pointer exceptions when loading CASP RR files since show pdb residue serials is default. We have no pdb res serials when loading from CASP RR. Now drawCoordinates checks that mod has3Dcoordinates
Disabled the menu item show pdb residue serials (now default is always show them)
Revision 408 - Directory Listing
Modified Mon Feb 18 17:15:07 2008 UTC (8 years, 6 months ago) by duarte
Now cmview.cfg is a final user-ready config file
Added a more complete cmview.cfg to test/config_files
Added README, LICENSE and gpl.txt files
Revision 407 - Directory Listing
Modified Thu Feb 14 16:27:41 2008 UTC (8 years, 6 months ago) by stehr
reordered and grouped config variables
Revision 406 - Directory Listing
Modified Thu Feb 14 16:21:29 2008 UTC (8 years, 6 months ago) by stehr
some cleanup in Start (made some session variables private)
Revision 405 - Directory Listing
Modified Thu Feb 14 16:01:33 2008 UTC (8 years, 6 months ago) by stehr
same as before, forgot to check in files other than Start
Revision 404 - Directory Listing
Modified Thu Feb 14 16:00:56 2008 UTC (8 years, 6 months ago) by stehr
Renaming constants in Start:
SHOW_PDB_RES_NUMBERS -> SHOW_PDB_RES_NUMS
PRELOAD_PYMOL -> PYMOL_LOAD_ON_START
SHUTDOWN_PYMOL_ON_EXIT -> PYMOL_SHUTDOWN_ON_EXIT
FORCE_DSSP -> USE_DSSP
INCLUDE_GROUP_INTERNALS -> USE_EXPERIMENTAL_FEATURES
Revision 403 - Directory Listing
Modified Thu Feb 14 15:32:12 2008 UTC (8 years, 6 months ago) by stehr
SHOW_ALIGNMENT_COORDS now goes through GUIState
Revision 402 - Directory Listing
Modified Thu Feb 14 15:16:30 2008 UTC (8 years, 6 months ago) by stehr
some clean up of constants in Start (new: SHOW_PDB_RES_NUMBERS, deleted: ICON_BAR_FLOATABLE, renamed: SHOW_RULERS_ON_STARTUP -> SHOW_RULERS)
Revision 401 - Directory Listing
Modified Tue Feb 12 16:01:51 2008 UTC (8 years, 6 months ago) by stehr
reverted apple.laf.useScreenMenuBar setting for MacOS as it caused a null pointer exception
Revision 400 - Directory Listing
Modified Tue Feb 12 15:23:39 2008 UTC (8 years, 6 months ago) by stehr
updated version info to 0.9.3; updated copyright info in About screen to 2008; set property to show menus on top of screen in MacOS
Revision 399 - Directory Listing
Modified Tue Feb 12 11:42:40 2008 UTC (8 years, 6 months ago) by duarte
Added command line parameters section
Revision 398 - Directory Listing
Modified Mon Feb 11 20:01:52 2008 UTC (8 years, 6 months ago) by stehr
Minor changes to installation.xml
Revision 397 - Directory Listing
Modified Mon Feb 11 19:46:26 2008 UTC (8 years, 6 months ago) by duarte
Some more fixes
Revision 396 - Directory Listing
Modified Mon Feb 11 19:40:50 2008 UTC (8 years, 6 months ago) by stehr
Disabled Print, Write example config file, Show Rulers, Show Icon bar; Added function to write current configuration to file (for debugging); Fixed reading from config file (added missing parameters)
Revision 395 - Directory Listing
Modified Mon Feb 11 17:35:57 2008 UTC (8 years, 6 months ago) by stehr
added cmview.css to version control; added cmview.css to publish_to_web.sh; minimal changes to index.html and template.html
Revision 394 - Directory Listing
Modified Mon Feb 11 17:20:03 2008 UTC (8 years, 6 months ago) by stehr
updated faq.xml (got rid of 'Why is there no content here?')
Revision 393 - Directory Listing
Modified Mon Feb 11 17:07:24 2008 UTC (8 years, 6 months ago) by stehr
Updated download.xml, faq.xml, index.xml and java help files.
Revision 392 - Directory Listing
Modified Mon Feb 11 16:07:55 2008 UTC (8 years, 6 months ago) by duarte
Added some explanations for screenshots
Added sections in installation
Added links to pdb files in tutorial
Revision 391 - Directory Listing
Modified Mon Feb 11 15:28:09 2008 UTC (8 years, 6 months ago) by stehr
split generate_docs.sh into two scripts (generate_docs.sh and publish_to_web.sh); added docbook sources for download-, faq- and index page; updated scripts to generate all webpages.
Revision 390 - Directory Listing
Modified Mon Feb 11 15:21:58 2008 UTC (8 years, 6 months ago) by duarte
Adding small versions of the images (for web)
Revision 389 - Directory Listing
Modified Mon Feb 11 15:18:11 2008 UTC (8 years, 6 months ago) by duarte
Added all images, lots of fixes
Revision 388 - Directory Listing
Modified Mon Feb 11 15:17:58 2008 UTC (8 years, 6 months ago) by duarte
Initial commit of screenshots.xml
Revision 387 - Directory Listing
Modified Mon Feb 11 14:21:05 2008 UTC (8 years, 6 months ago) by stehr
Fixed bug that newly opened windows would not be focused.
Revision 386 - Directory Listing
Modified Sat Feb 9 10:45:28 2008 UTC (8 years, 6 months ago) by duarte
Added new java help jar to make script and manifests

Revision 385 - Directory Listing
Modified Fri Feb 8 18:57:57 2008 UTC (8 years, 6 months ago) by duarte
Much more markup, icons added
Revision 384 - Directory Listing
Modified Fri Feb 8 17:47:52 2008 UTC (8 years, 6 months ago) by duarte
Better markup and some corrections
Revision 383 - Directory Listing
Modified Fri Feb 8 17:04:34 2008 UTC (8 years, 6 months ago) by stehr
added F1 key binding to open help window, added proper ids to most of the sections in manual.xml
Revision 382 - Directory Listing
Modified Fri Feb 8 14:19:21 2008 UTC (8 years, 6 months ago) by duarte
Added more content
Revision 381 - Directory Listing
Modified Fri Feb 8 11:22:21 2008 UTC (8 years, 6 months ago) by stehr
Fixed bugs in generate_docs.sh
Revision 380 - Directory Listing
Modified Fri Feb 8 10:16:36 2008 UTC (8 years, 6 months ago) by stehr
Added title to installation.xml
Revision 379 - Directory Listing
Modified Thu Feb 7 17:53:00 2008 UTC (8 years, 6 months ago) by stehr
updated function_reference.xml and renamed it to manual.xml; created script to create all documentation (web, pdf, javahelp) from xml
Revision 378 - Directory Listing
Modified Thu Feb 7 17:52:11 2008 UTC (8 years, 6 months ago) by duarte
Initial commit of installation.xml. Very raw draft
Revision 377 - Directory Listing
Modified Thu Feb 7 17:02:00 2008 UTC (8 years, 6 months ago) by duarte
Reordered dirs, changed section tags in tutorial.xml and added script for creation of cmview web pages from template.html (also added) and a source content file (the html file converted from docbook xmls)
Revision 376 - Directory Listing
Modified Thu Feb 7 11:19:23 2008 UTC (8 years, 6 months ago) by stehr

Revision 375 - Directory Listing
Modified Thu Feb 7 11:00:27 2008 UTC (8 years, 6 months ago) by duarte
Changed size of blanks to 8 to match java's default
Revision 374 - Directory Listing
Modified Wed Feb 6 18:35:36 2008 UTC (8 years, 6 months ago) by duarte
Fixed bugs:
- cheap solution to bug chain/model combos not displaying fully opened when more than 1 member (java takes the size of the box as the number of items present before the willBecomeVisible event, see bug http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4743225). Our solution here is simply initialising/resetting the combo boxes with a few blanks so at least the user can see that there is more than 1 item. Of course with this solution if the combo happens to have only 1 item it looks a bit ugly because the box is unnecessarily big.
- clearComboModel wasn't updating correctly prevComboModelItems
Revision 373 - Directory Listing
Modified Wed Feb 6 16:58:55 2008 UTC (8 years, 6 months ago) by stehr
Added proper Javahelp, bound to the help button in the help menu; fixed some resulting issue that shutdown didn't work by reintroducing the counting of View instances in Start
Revision 372 - Directory Listing
Modified Mon Feb 4 14:41:40 2008 UTC (8 years, 6 months ago) by duarte
Made CONFIG_FILE_NAME final
Revision 371 - Directory Listing
Modified Mon Feb 4 14:25:19 2008 UTC (8 years, 6 months ago) by stehr
moved Manifest files to /src folder, updated make script
Revision 370 - Directory Listing
Modified Mon Feb 4 14:18:03 2008 UTC (8 years, 6 months ago) by stehr
Moved resources/ into /src folder; moved icons/ to /src/resources/icons; updated paths to icons in View
Revision 369 - Directory Listing
Modified Mon Feb 4 13:23:24 2008 UTC (8 years, 6 months ago) by stehr
Moved all java sources from project root to folder /src
Revision 368 - Directory Listing
Modified Fri Feb 1 16:31:34 2008 UTC (8 years, 6 months ago) by duarte
Now runTests will do all tests starting with load
Revision 367 - Directory Listing
Modified Fri Feb 1 16:29:46 2008 UTC (8 years, 6 months ago) by duarte
Added java test runer. 
Changed relative path in test scripts so that files can be run correctly from eclipse with the java tester runTests
Revision 366 - Directory Listing
Modified Thu Jan 31 14:42:11 2008 UTC (8 years, 6 months ago) by duarte
Reverting to revision 356 (last commit was wrong)
Revision 365 - Directory Listing
Modified Thu Jan 31 14:37:02 2008 UTC (8 years, 6 months ago) by stehr
Now multiple selections can be done with ctrl key on win and linux and using apple key on mac (before was not working on mac)
Revision 362 - Directory Listing
Modified Thu Jan 31 11:21:34 2008 UTC (8 years, 6 months ago) by stehr
- Fixed missing error popup when loading from OnlinePDB fails
- Fixed bug: Now loading chain codes in Mac should work
Revision 359 - Directory Listing
Modified Thu Jan 31 09:32:06 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: forgot to skip gaps when getting residue types
Revision 357 - Directory Listing
Modified Thu Jan 31 08:59:56 2008 UTC (8 years, 6 months ago) by stehr
nice indention of function_reference.xml
Revision 356 - Directory Listing
Modified Wed Jan 30 11:05:26 2008 UTC (8 years, 6 months ago) by stehr
updated version to 0.9.2
Revision 355 - Directory Listing
Modified Wed Jan 30 10:57:40 2008 UTC (8 years, 6 months ago) by stehr
- Removed VIEWINSTANCES variable in start and view
- PyMolAdaptor: removed url parameter in shutdown method
- Start: Some cleanup of constants
Revision 354 - Directory Listing
Modified Wed Jan 30 10:30:21 2008 UTC (8 years, 6 months ago) by duarte
First commit of xml docbooks
Revision 353 - Directory Listing
Modified Tue Jan 29 12:09:18 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: now residue types shown for all residues we know (taken from sequence) in coordinates
Fixed bug in secondary structure handling: secondary structure in Graph and Pdb where ending up to be different some times causing that display of coordinates could differ with rulers display. 
In Model secondary structure is always taken from Pdb object now, we don't even check for it in the Graph object
Got rid of some fields and initializators in Model.
Revision 352 - Directory Listing
Modified Fri Jan 25 08:40:41 2008 UTC (8 years, 7 months ago) by stehr
Changed message "Second model loaded" to "second contact map loaded".
Revision 351 - Directory Listing
Modified Wed Jan 23 17:34:47 2008 UTC (8 years, 7 months ago) by duarte
Made tool bar separators look better
Revision 350 - Directory Listing
Modified Wed Jan 23 16:09:03 2008 UTC (8 years, 7 months ago) by duarte
Now GraphDbModel tries to load structure from pdbase instead of msdsd
Revision 349 - Directory Listing
Modified Wed Jan 23 11:26:59 2008 UTC (8 years, 7 months ago) by duarte
Coordinates display prettier, show pdb residue numbers work on compare mode: not printing i,j
Show pdb res numbers menu item now enabled in compare mode
Got rid of quit and print icons on tool bar

Revision 348 - Directory Listing
Modified Fri Jan 18 17:32:24 2008 UTC (8 years, 7 months ago) by duarte
Another test
Revision 347 - Directory Listing
Modified Fri Jan 18 16:53:19 2008 UTC (8 years, 7 months ago) by stehr
Made sequence field mandatory in (native and casp) contact map files. Before, missing sequence would cause an ArrayIndexOutOfBounds exception in al2seq/seq2al
Revision 346 - Directory Listing
Modified Fri Jan 18 16:09:30 2008 UTC (8 years, 7 months ago) by stehr
Fixed bug: Right click was causing a null-pointer exception if USE_PYMOL=false, Major refactoring: Moved many gui status variables including getter and setter methods from View to new class GUIState.
Revision 345 - Directory Listing
Modified Thu Jan 17 17:55:21 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: loading of a new second structure was not resetting correctly the existing common, uniqueToFirst, uniqueToSecond contact sets. Fixed it both in setSecondModel and reloadContacts.
Revision 344 - Directory Listing
Modified Thu Jan 17 16:47:17 2008 UTC (8 years, 7 months ago) by stehr
added run_tests.sh in /test/abbot_scripts/ and fixed load_from_casp_rr_file.xml (added assertion to check for frame title)
Revision 343 - Directory Listing
Modified Thu Jan 17 15:58:04 2008 UTC (8 years, 7 months ago) by stehr
new abbot scripts for loading contact maps from different sources, new directories sample_files/ and config_files/ under /test/
Revision 342 - Directory Listing
Modified Thu Jan 17 15:55:00 2008 UTC (8 years, 7 months ago) by stehr
LoadDialog: changed error message "UNKNOWN!!!" to "ERROR" (appearing when chain code or model not found)
*Model: Fixed bug that temporary pdb files were always called null.pdb (now name of model is created before writing the temp file)
Revision 341 - Directory Listing
Modified Thu Jan 17 14:42:04 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: confirm overwrite check was not working when saving config file.
Now added confirm overwrite checks for all other saving file actions (new method confirmOverwrite)
Revision 340 - Directory Listing
Modified Thu Jan 17 14:15:37 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: was not checking for pymol availability in compare mode
Some clean up and refactoring
Revision 339 - Directory Listing
Modified Wed Jan 16 18:00:30 2008 UTC (8 years, 7 months ago) by duarte
Got rid of classpath in abbot scripts. Now they should be run with classpath taken from environment.
Revision 338 - Directory Listing
Modified Wed Jan 16 17:59:10 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug! actually it was not an abbot bug but our own, now calling Start.class correctly (instead of System.getRunTime()....). With this abbot runs fine without any dirty fixes
Revision 337 - Directory Listing
Modified Wed Jan 16 16:34:47 2008 UTC (8 years, 7 months ago) by stehr
added new abbot script to load a second structure
Revision 336 - Directory Listing
Modified Wed Jan 16 15:36:46 2008 UTC (8 years, 7 months ago) by duarte
Initial commit of first abbot GUI testing scripts created with Abbot's graphical end Costello
Revision 335 - Directory Listing
Modified Wed Jan 16 15:36:03 2008 UTC (8 years, 7 months ago) by duarte
Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.
Revision 334 - Directory Listing
Modified Tue Jan 15 17:10:00 2008 UTC (8 years, 7 months ago) by stehr
Cleaned up menu item names, extracted constants for all labels used at least twice
Revision 333 - Directory Listing
Modified Tue Jan 15 15:58:09 2008 UTC (8 years, 7 months ago) by duarte
Moved Selection Modes to Select menu. 
Now allowing loading of new second structure.
Revision 332 - Directory Listing
Modified Tue Jan 15 14:49:13 2008 UTC (8 years, 7 months ago) by duarte
Now diagonal selection behaves more naturally in undirected case (directed should work as before)
Revision 331 - Directory Listing
Modified Tue Jan 15 14:22:59 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug in LoadDialog, wasn't updating correctly the models combo box after changing the pdb code.
Revision 330 - Directory Listing
Modified Tue Jan 15 13:21:02 2008 UTC (8 years, 7 months ago) by duarte
Changed everything according to changes in Alignment class (now alignment indices start at 1). 
Revision 329 - Directory Listing
Modified Mon Jan 14 14:40:30 2008 UTC (8 years, 7 months ago) by duarte
Redesign handling of alignment and models. Now neither models nor their graphs are changed when we align. In ContactMapPane we use always the alignment to map between alignment and sequences whenever we need to. Even in single model case we also introduce a (trivial) alignment, so there's no conceptual difference in that sense between single/pairwise modes.
Revision 328 - Directory Listing
Modified Mon Jan 14 10:07:42 2008 UTC (8 years, 7 months ago) by stehr
ContactMapPane: now writing lists of neighbors in comma separated format for easier copy/pasting to "select by residue number"
View: renamed all occurances of "Node neighbourhood" to "neighbourhood", now asking user before overwriting example config file, added some javadocs

Revision 327 - Directory Listing
Modified Fri Jan 11 11:49:01 2008 UTC (8 years, 7 months ago) by duarte
Removed changeVisibilityCompareButtons, now doing that in the same way as with other buttons: using setAccessibility and so on.

Revision 324 - Directory Listing
Modified Thu Jan 10 17:24:33 2008 UTC (8 years, 7 months ago) by duarte
What's wrong with Manifest again!!! trying putting trailing spaces in the jar lines. Let's see if now it works
Revision 321 - Directory Listing
Modified Thu Jan 10 17:14:35 2008 UTC (8 years, 7 months ago) by duarte
Was missing jaligner.jar in Struppi manifest
Revision 318 - Directory Listing
Modified Thu Jan 10 16:58:44 2008 UTC (8 years, 7 months ago) by stehr
Yet again fixed some issues with config file loading, removed references to local directories in source code (should be in config file only)
Revision 316 - Directory Listing
Modified Thu Jan 10 16:22:52 2008 UTC (8 years, 7 months ago) by stehr
Major change: corrected a typo in a comment
Revision 315 - Directory Listing
Modified Thu Jan 10 14:50:03 2008 UTC (8 years, 7 months ago) by stehr
changed version to 0.9.1, set internal default for database server and password to dummy values (has to be set in config file)
Revision 314 - Directory Listing
Modified Thu Jan 10 14:37:38 2008 UTC (8 years, 7 months ago) by duarte
Fixed bugs:
- selection mode being reset to square selection when second model loaded
- current selection reset in compare mode when hiding a set of contacts with the toggle buttons
- secondary structure now correct (hopefully!!) in show coordinates in compare mode
Made a new constant for toggling between showing alignment coordinates/only sequence coordinates
Some more refactoring and clean up in ContactMapPane
Revision 313 - Directory Listing
Modified Wed Jan 9 18:47:32 2008 UTC (8 years, 7 months ago) by duarte
Rationalised and cleaned up completely selections:
- New method getCurrentContactSet encapsulating the 8+1 possible states of the GUI
- Fixed bugs of selection in compare mode: click and release in diagonal mode wasn't selecting current diagonal, click and release in square wasn't selecting current contact
- Refactored addSecondModel to setSecondModel to be more consistent with setModel. Removed setAlignment, now part of setSecondModel. 
- Initialisation of contacts now done where it belongs: setSecondModel (instead of drawComparedMap)
- Added code to also reload second structure data in reload method
Revision 312 - Directory Listing
Modified Wed Jan 9 15:48:18 2008 UTC (8 years, 7 months ago) by duarte
Major clean up, refactor and elimination of redundancy in View and ContactMapPane. Now should be much clearer what things do, specially selection code is much easier to follow
Fixed all issues with getSelectecContacts, now refactored to getSetsOfSelectedContactsFor3D since it is used strictly only to show contacs in pymol. All other functions needing selected contacts now call getSelContacts()
Revision 311 - Directory Listing
Modified Wed Jan 9 10:09:50 2008 UTC (8 years, 7 months ago) by stehr
modified info dialog (now showing unique and common contacts and name but not pdb and chain code)
Revision 310 - Directory Listing
Modified Wed Jan 9 10:08:39 2008 UTC (8 years, 7 months ago) by stehr
fixed bug in getSelectedContacts(...,false): subtraction of 1 was missing
Revision 309 - Directory Listing
Modified Tue Jan 8 10:09:12 2008 UTC (8 years, 7 months ago) by duarte
Now alignment always keeps the order of the structures as they were loaded in. Saving alignment and then loading should work correctly. 
Added supressed warnings in SADPDialog 
Revision 308 - Directory Listing
Modified Mon Jan 7 16:43:48 2008 UTC (8 years, 7 months ago) by stehr
added INCLUDE_GROUP_INTERALS=true and removed some clutter
Revision 307 - Directory Listing
Modified Mon Jan 7 16:42:25 2008 UTC (8 years, 7 months ago) by stehr
changed default value of INCLUDE_GROUP_INTERNALS to false, but added it to config file
Revision 306 - Directory Listing
Modified Mon Jan 7 16:36:53 2008 UTC (8 years, 7 months ago) by stehr
added experimental support for selecting node neighbourhoods in sequence window
(only works if INCLUDE_GROUP_INTERNALS is turned on in config file)
Revision 305 - Directory Listing
Modified Mon Jan 7 15:12:21 2008 UTC (8 years, 7 months ago) by stehr
cmPane: show actual alpha and beta as secondary structure characters in corner
PymolAdaptor: got rid of 'START loading model', 'DONE loading model' output
Revision 304 - Directory Listing
Modified Mon Jan 7 14:25:36 2008 UTC (8 years, 7 months ago) by stehr
new sequence view window (class SequenceViewDialog)
updated info window
alignment options in comparison mode reordered and greedy mapping removed
in loadDialog switched order of chain and model input fields
Revision 303 - Directory Listing
Modified Mon Jan 7 13:44:34 2008 UTC (8 years, 7 months ago) by duarte
In aligning when taking alignment from file is now based on the order the sequences appear on the file rather than their tags (which won't be known by the user)
Revision 302 - Directory Listing
Modified Fri Jan 4 18:19:00 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: now pymol selections work correctly in all cases (duplicate pdbCodes, CASP targets, missing pdb code...) by consistently using the getLoadedGraphID as unique identifier of the structure in PyMOL. 
Cleaned up PyMolAdapter of unused code
Revision 301 - Directory Listing
Modified Fri Jan 4 14:59:39 2008 UTC (8 years, 7 months ago) by duarte
Fixed issues with alignment tags and identifiers of the 2 structures in compare mode: now should work even if no pdb code or CASP target is present. Also works when 2 compared structures have the same pdbCode+chainCode or the same targetNumber
New member in Model: loadedGraphID (unique for a user-loaded graph, also copied over to the aligned one). Also kept in Start.loadedGraphs
Got rid of aliTags in ContactMapPane (was redundant since we have mod.getLoadedGraphID()
Revision 300 - Directory Listing
Modified Fri Jan 4 11:23:44 2008 UTC (8 years, 7 months ago) by stehr
New contact map info dialog with sequence tooltip
Revision 299 - Directory Listing
Modified Thu Jan 3 17:48:23 2008 UTC (8 years, 7 months ago) by duarte
Pdb structure is now loaded from db or online CIF file when loading CM file and pdb code/chain code present
Revision 298 - Directory Listing
Modified Thu Jan 3 17:33:37 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: load from CM file was not working since addition of chains/models como boxes in LoadDialog
New feature: now can load/save from CASP RR files
Revision 297 - Directory Listing
Modified Thu Jan 3 15:22:37 2008 UTC (8 years, 7 months ago) by stehr
Changes to info dialog:
- show the model number
- show "none" if pdb code or chain code missing
- show "directed" only if group internals are switched on
Changes in start:
- read constant INCLUDE_GROUP_INTERNALS from config file
Changes to load dialog:
- title "Load from contact map file" was too long, changed to "Load from CM file"
Revision 296 - Directory Listing
Modified Wed Jan 2 14:50:02 2008 UTC (8 years, 7 months ago) by duarte
Fixed issues with config file (not fully tested yet!)
Revision 295 - Directory Listing
Modified Wed Jan 2 14:34:14 2008 UTC (8 years, 7 months ago) by duarte
Added command line option for version
Revision 293 - Directory Listing
Modified Wed Jan 2 13:59:24 2008 UTC (8 years, 7 months ago) by stehr
Changed version number to 0.9
Revision 292 - Directory Listing
Modified Wed Jan 2 13:32:11 2008 UTC (8 years, 7 months ago) by duarte
Copying branch CMView-jung into trunk

Revision 291 - Directory Listing
Modified Wed Jan 2 13:27:12 2008 UTC (8 years, 7 months ago) by duarte
Removing everything from trunk before replacing with branch CMView-jung

Revision 289 - Directory Listing
Modified Wed Jan 2 11:11:01 2008 UTC (8 years, 7 months ago) by duarte
Updated version to 0.8.7
Revision 257 - Directory Listing
Modified Wed Dec 12 11:35:21 2007 UTC (8 years, 8 months ago) by lpetzo
exception indicating LoadDialog errors
Revision 256 - Directory Listing
Modified Wed Dec 12 11:33:35 2007 UTC (8 years, 8 months ago) by lpetzo
commit -m "- changed loading scheme in *Pdb: Constructor of *Model no longer constructs the Graph and Pdb object
- introduced new function: 
	load(...) -> loads the structure from the source, 
	getChains() -> gets all possible chains codes in the source, 
	getModels() -> gets all possible model serials in the source
Revision 255 - Directory Listing
Modified Wed Dec 12 11:30:55 2007 UTC (8 years, 8 months ago) by lpetzo
- changed loading scheme in *Pdb: Constructor of *Model no longer constructs the Graph and Pdb object
- introduced new function: 
	load(...) -> loads the structure from the source, 
	getChains() -> gets all possible chains codes in the source, 
	getModels() -> gets all possible model serials in the source
Revision 246 - Directory Listing
Modified Wed Nov 28 16:38:03 2007 UTC (8 years, 8 months ago) by duarte
Updated manifest's classpath with jaligner.jar 
Revision 245 - Directory Listing
Modified Wed Nov 28 16:33:05 2007 UTC (8 years, 8 months ago) by duarte
Updated versions to 0.8.6 for tagging
Revision 238 - Directory Listing
Modified Tue Nov 27 15:31:58 2007 UTC (8 years, 9 months ago) by lpetzo
removed tbShowSel3D from the set of buttons to be disabled in function compareModeButtonAccessibility()
Revision 237 - Directory Listing
Modified Tue Nov 27 15:29:35 2007 UTC (8 years, 9 months ago) by lpetzo
added jaligner.jar to the class-path
Revision 236 - Directory Listing
Modified Thu Nov 22 11:51:49 2007 UTC (8 years, 9 months ago) by lpetzo
added SADP-adapter related stuff to the javac command line
Revision 235 - Directory Listing
Modified Thu Nov 22 11:46:56 2007 UTC (8 years, 9 months ago) by lpetzo
class ContactMapPane:
- new functions:
  * getCommonContacts(int,int)
  * getModelContacts(int)
- changed indentation mode

class PyMolAdapter:
- a couple of type corrections due to new IntervalSet types etc., whenever the Interval type is favored over the Edge type we made the change
- changed indentation mode

class View:
- added code to implement the new SADPResult functionality
Revision 234 - Directory Listing
Modified Thu Nov 22 11:44:59 2007 UTC (8 years, 9 months ago) by lpetzo
NEW TYPES
----------
- SADPResult

MODIFICATIONS
-------------
class SADPDialog:
- a couple of changes were done due to the new type SADPResult which takes over the functionality of storing the result of a SADP run from class SADPRunner

class SADPDialogDoneNofifier:
- is now working on the new type SADPResult

class SADPRunner:
- as ToolRunner now is implementing the Callable<V> interface instead of the Runnable interface we have to comply with this by implementing the call() instead of the run() function
- SADPResults is from now on storing the results of SADP instead of SADPRunner
- changed many function from being public to private
- changed indentation mode
Revision 233 - Directory Listing
Modified Thu Nov 22 11:43:48 2007 UTC (8 years, 9 months ago) by lpetzo
NEW TYPES
---------
- AlignmentToolResult
- ToolResult

MODIFICATIONS
-------------
class ToolRunner
- now implementing the Callable<V> interface instead of the Runnable interface
- changed indentation mode
Revision 232 - Directory Listing
Modified Tue Nov 20 13:39:27 2007 UTC (8 years, 9 months ago) by duarte
Added new jar dependency jaligner.jar
Revision 231 - Directory Listing
Modified Mon Nov 19 10:10:06 2007 UTC (8 years, 9 months ago) by duarte
Now printing some output when loading structure from msd in GraphDBModel
Revision 230 - Directory Listing
Modified Mon Nov 19 09:40:06 2007 UTC (8 years, 9 months ago) by lpetzo
class View:
- decoupled GUI initialisation and visualization in the constructor
- better error handling in spawnNewViewWindow(Model)
- better handling of the positioning of the new View window created in spawnNewWindow(Model): if the previous windows ("this-pointer") was empty -- not containing any contact map -- the new window is placed directly on top of the previous one, otherwise we place it somewhere else
Revision 229 - Directory Listing
Modified Thu Nov 15 16:16:53 2007 UTC (8 years, 9 months ago) by duarte
Added "case sensitive" comment in load dialog
Revision 228 - Directory Listing
Modified Tue Nov 13 14:38:48 2007 UTC (8 years, 9 months ago) by lpetzo
class ContactMapPane:
- selectAllContacts(): selecting of all visible contacts should work with all combinations of activated contact types (only mod1, only mod2, common)
Revision 227 - Directory Listing
Modified Mon Nov 12 16:24:06 2007 UTC (8 years, 9 months ago) by lpetzo
class View:
- deleted some output stuff for debugging
Revision 226 - Directory Listing
Modified Mon Nov 12 15:57:04 2007 UTC (8 years, 9 months ago) by stehr
new feature: pairwise sequence alignment for comparison
Revision 225 - Directory Listing
Modified Mon Nov 12 15:53:43 2007 UTC (8 years, 9 months ago) by duarte
Fixed bug: fileChooser and colorChooser were not being set with the native look and feel
Revision 224 - Directory Listing
Modified Mon Nov 12 13:44:19 2007 UTC (8 years, 9 months ago) by duarte
Added new packages sadp and actionTools to the jar
Revision 223 - Directory Listing
Modified Thu Nov 8 11:47:20 2007 UTC (8 years, 9 months ago) by lpetzo
MODIFICATIONS
-------------

class SADPDialogDoneNotifier:
- added a line secureNotify() -> doClick() (without that line nothing will happen in the GUI)
Revision 222 - Directory Listing
Modified Wed Nov 7 18:21:36 2007 UTC (8 years, 9 months ago) by lpetzo
NEW TYPES
----------
- DifferentContactMapSizeError

MODIFICATIONS
-------------

class ContactMapPane:
- addSecondModel now throws an exception if the contact maps have different size

class ScreenBuffer:
- deleted redundant if clause

class View:
- added new "Save to" feature -> save to alignment
- added new stuff to to functions compareMode[...]Accessibility
- changed prototype of handlePairwiseAlignment(Model,Model) to handlePairwiseAlignment()
- complete code reconstruction in function handlePairwiseAlignment():
  * added code to proper handle the selection of alignment input source (external, internal, greedy)
  * moved GUI accessibility changes to a new function -> setGUIStatusCompareMode
- reduced the functionality of SADPDialog in doPairwiseAlignment(Model,Model) to the Cancel button, SADPRunner is called via "startbutton".doClick() in the code
- added comments to some functions
- complete code reconstruction in function handleInfo() to allow for the printing of multiple info-tags in one info-popup window
- new functions:
  * setGUIStatusCompareMode()
  * doLoadPairwiseAlignment(Model,Model)
  * doGreedyPairwiseAlignment(Model,Model)
  * doLoadOntoContactMapPane(Model,Model,Alignment,String,String)
  * doLoadOntoVisualizer(Model)
  
Revision 221 - Directory Listing
Modified Wed Nov 7 18:20:48 2007 UTC (8 years, 9 months ago) by lpetzo
MODIFICATIONS
-------------

class Model:
- added new abstract function copy() which shall be implemented as a shallow copy function
- added implementation to each subclass of this class
Revision 220 - Directory Listing
Modified Wed Nov 7 18:19:54 2007 UTC (8 years, 9 months ago) by lpetzo
MODIFICATIONS
-------------

class SADPDialog:
- modified the Doer for the SADPRunner -> changed function being invoked to set the status of the SADPDialog from notify(Integer) to secureNotify(Integer)

class SADPDialogDoneNotifier:
- added comments
- some minor stuff
- new function:
  * secureNotify(Interger)

class SADPRunner:
- removed the nasty runtime error-prone type conversion code in getXoutputModel(Model,Graph)
- some functions throw exception thrown by class Alignment
Revision 219 - Directory Listing
Modified Wed Nov 7 18:18:52 2007 UTC (8 years, 9 months ago) by lpetzo
MODIFICATIONS
-------------

class ToolDialog:
- added new construction states
- added some comments
- new functions:
  * getConstructionStatus()
Revision 218 - Directory Listing
Modified Tue Nov 6 18:33:49 2007 UTC (8 years, 9 months ago) by filippis
ResidueRuler:
-OTHER_COLOR added to take into account other regions that are now numbered in DSSP

ContactMapPane:
-selectInterSsContacts and selectIntraSsContacts take now into account the sheet serial and explicitly ignore other regions

Revision 217 - Directory Listing
Modified Fri Nov 2 18:10:16 2007 UTC (8 years, 9 months ago) by lpetzo
function getDiffDistMatrix(Alignment,Model) now employs the new PDB.getDiffDistMap(...) function which takes a sequence alignment as an input
Revision 216 - Directory Listing
Modified Fri Nov 2 18:05:57 2007 UTC (8 years, 9 months ago) by lpetzo
changed accessibility of class field CONSTRUCT_EVERYTHING from private to public
Revision 215 - Directory Listing
Modified Fri Nov 2 18:04:38 2007 UTC (8 years, 9 months ago) by lpetzo
modified prototype of the constructor
Revision 214 - Directory Listing
Modified Fri Nov 2 18:03:28 2007 UTC (8 years, 9 months ago) by lpetzo
- new data fields for the handling of menu-items (smFile,smCompare,menu2idx,popupMenu2Parent,disregardedTypes)
- added code encapsulation of UI element for the use of experimental stuff (nbh stuff)
- new functions:
  * addToJMenuBar(JMenu)
  * setAccessibility(Component, boolean, boolean, Component, Collection<Class<?>>)
  * setAccessibility(Map<Component, Boolean>, boolean, Component, Collection<Class<?>>)
  * initMenuBarAccessibility(boolean)
  * compareModeButtonAccessibility()
  * compareModeMenuBarAccessibility()
  * compareModePopupMenuAccessibility()
  * getMenuItemToggleMap()
  -> all these function are somehow connected to a new GUI functionality: one can define accessibility rules for each menu- and toolbar item to enable/disable the features with respect to the current GUI state
  -> in the compare mode when the second structure has been loaded many GUI features are disabled now
- construction of SADPDialog: for group internal use (to be toggled by Start.INCLUDE_GROUP_INTERNALS) the preferences button is still available (though still not working :( )
- when the second model has been loaded to PyMOL the whole thing will be oriented towards both loaded structures
Revision 213 - Directory Listing
Modified Fri Nov 2 17:40:49 2007 UTC (8 years, 9 months ago) by lpetzo
added new static flag to class Start which shall be used to encapsulate code fragments (or rather UI stuff that make these methods available in the GUI) of rather experimental kind -> INCLUDE_GROUP_INTERNALS
Revision 212 - Directory Listing
Modified Fri Nov 2 17:30:42 2007 UTC (8 years, 9 months ago) by lpetzo
whenever a difference distance map is to be computed the new getDiffDistMap(...) which takes a sequence alignment as an input is employed.
Revision 211 - Directory Listing
Modified Wed Oct 31 10:19:00 2007 UTC (8 years, 9 months ago) by lpetzo

Revision 210 - Directory Listing
Modified Thu Oct 25 15:02:04 2007 UTC (8 years, 10 months ago) by lpetzo
Tool utilities are designed to serve as super classes for any kind of non-trivial data processing, e.g., the calling of external programs whose runtime behavior can be manipulated through different kinds of preference settings. These user interactions are supposed to be realized via subclassing class ToolDialog, preference settings can be implemented via class PreferencesDialog.
Revision 209 - Directory Listing
Modified Mon Oct 22 08:48:32 2007 UTC (8 years, 10 months ago) by stehr
updating Manifest-StuPPi to name CMView and version 0.8.5
Revision 207 - Directory Listing
Modified Wed Oct 17 15:18:31 2007 UTC (8 years, 10 months ago) by stehr
fixed bug in selectByResNum(), now using new node class instead of integer, are there more errors of this kind?
Revision 206 - Directory Listing
Modified Thu Oct 11 12:52:48 2007 UTC (8 years, 10 months ago) by duarte
Added '...' to menus that open dialogs
Revision 205 - Directory Listing
Modified Thu Oct 11 12:50:06 2007 UTC (8 years, 10 months ago) by stehr
Fixed ContactMapPane and ResidueRuler to work with new NodeSet class
Revision 204 - Directory Listing
Modified Thu Oct 4 13:28:44 2007 UTC (8 years, 10 months ago) by dinse
changed View and PyMolAdaptor for grouping in PyMol
changed colors on the ruler again
Revision 203 - Directory Listing
Modified Mon Oct 1 08:29:01 2007 UTC (8 years, 10 months ago) by stehr
added missing icon color_swatch.png
Revision 202 - Directory Listing
Modified Thu Sep 20 16:01:36 2007 UTC (8 years, 11 months ago) by stehr
added contact selection by color
Revision 201 - Directory Listing
Modified Thu Sep 20 14:54:43 2007 UTC (8 years, 11 months ago) by duarte
Changed aminoacid information calls from AA to AAinfo
Revision 200 - Directory Listing
Modified Thu Sep 20 11:01:14 2007 UTC (8 years, 11 months ago) by dinse
disable all old objects and selections and enable the current ones (PymolAdaptor.setView)
center and zoom into the structure
fixed side chain problem in PyMol (both in edgeSelection)  
Revision 199 - Directory Listing
Modified Wed Sep 19 16:51:57 2007 UTC (8 years, 11 months ago) by stehr
added menu item 'select by residue number'
Revision 198 - Directory Listing
Modified Wed Sep 19 14:24:30 2007 UTC (8 years, 11 months ago) by stehr
added menu item to hide/show icon bar, made icon bar non-floatable because the twi things are not working well together and floatable icon bar had some graphical bugs
Revision 197 - Directory Listing
Modified Wed Sep 19 12:04:13 2007 UTC (8 years, 11 months ago) by stehr
now, selection mode buttons are also being updated when the mode is changed from somewhere else (main- or popup menu)
Revision 196 - Directory Listing
Modified Wed Sep 19 10:56:09 2007 UTC (8 years, 11 months ago) by stehr
rearranged selection mode menu items and made toggle buttons for them
Revision 195 - Directory Listing
Modified Tue Sep 18 15:27:42 2007 UTC (8 years, 11 months ago) by stehr
added menu items for selecting various contacts between secondary structure objects, changed title of main window when comparing
Revision 194 - Directory Listing
Modified Tue Sep 18 15:21:13 2007 UTC (8 years, 11 months ago) by stehr
when aligning two structures, the order was reversed and a 'zoom' added (otherwise, contacts in the original structure are out of place)
Revision 193 - Directory Listing
Modified Tue Sep 18 14:13:25 2007 UTC (8 years, 11 months ago) by stehr
always use Ca (or other single atom model specified in config file) for distance map calculation
Revision 192 - Directory Listing
Modified Tue Sep 18 13:59:04 2007 UTC (8 years, 11 months ago) by stehr
renamed menu 'Tools' to 'Compare', hide comparison icons before second contact map is loaded, new method 'makeMenuItem' for simpler creation of new menu items
Revision 191 - Directory Listing
Modified Tue Sep 18 10:13:53 2007 UTC (8 years, 11 months ago) by stehr
added constants SHOW_ICON_BAR and ICON_BAR_FLOATABLE
Revision 190 - Directory Listing
Modified Tue Sep 18 08:46:31 2007 UTC (8 years, 11 months ago) by stehr
updated version number to 0.8.5
Revision 189 - Directory Listing
Modified Tue Sep 18 08:45:58 2007 UTC (8 years, 11 months ago) by stehr
added difference distance map in comparison mode, updated Manifest to v0.8.5
Revision 188 - Directory Listing
Modified Mon Sep 17 16:11:17 2007 UTC (8 years, 11 months ago) by stehr
using new constructor from ciffilePdb for loading directly from online pdb
Revision 187 - Directory Listing
Modified Mon Sep 17 14:25:50 2007 UTC (8 years, 11 months ago) by dinse
view: inserted new icons in toolbar for contact map comparison
cmPane: adapted contact map comparison changes
PyMolAdaptor: changed edgeSelection method

Revision 186 - Directory Listing
Modified Thu Sep 13 16:08:14 2007 UTC (8 years, 11 months ago) by duarte
New model PdbFtpModel to load from online PDB. Added to Load and Tools menu
Revision 185 - Directory Listing
Modified Mon Sep 10 11:05:34 2007 UTC (8 years, 11 months ago) by dinse
changed colours of rulers
Revision 184 - Directory Listing
Modified Mon Sep 10 10:33:23 2007 UTC (8 years, 11 months ago) by dinse

Revision 183 - Directory Listing
Modified Thu Sep 6 13:54:21 2007 UTC (8 years, 11 months ago) by stehr
fixed some problems with make-script
Revision 182 - Directory Listing
Modified Thu Sep 6 08:05:33 2007 UTC (8 years, 11 months ago) by dinse

Revision 181 - Directory Listing
Modified Thu Sep 6 08:05:07 2007 UTC (8 years, 11 months ago) by dinse
changed objectSelName - output to PyMol
Revision 180 - Directory Listing
Modified Tue Sep 4 13:20:16 2007 UTC (8 years, 11 months ago) by dinse

Revision 179 - Directory Listing
Modified Tue Sep 4 13:20:09 2007 UTC (8 years, 11 months ago) by dinse

Revision 178 - Directory Listing
Modified Tue Sep 4 13:19:55 2007 UTC (8 years, 11 months ago) by dinse
changed selections for comparing maps 
Revision 177 - Directory Listing
Modified Tue Sep 4 13:17:51 2007 UTC (8 years, 11 months ago) by dinse
changed viewer in comparing maps 
Revision 176 - Directory Listing
Modified Tue Sep 4 12:44:30 2007 UTC (8 years, 11 months ago) by dinse
added specific functions and altered existing ones to show and work with the compared maps (2 different structures at the same time) 
Revision 175 - Directory Listing
Modified Mon Sep 3 13:37:26 2007 UTC (8 years, 11 months ago) by dinse
tested some changes in the sendCommand -fct, deleted afterwards
Revision 174 - Directory Listing
Modified Fri Aug 31 08:51:54 2007 UTC (8 years, 11 months ago) by dinse
added alignStructure function
Revision 173 - Directory Listing
Modified Wed Aug 29 14:03:44 2007 UTC (8 years, 11 months ago) by dinse
changed for comparing contact maps
Revision 172 - Directory Listing
Modified Wed Aug 29 14:03:33 2007 UTC (8 years, 11 months ago) by dinse
changed for comparing contact maps
Revision 171 - Directory Listing
Modified Wed Aug 29 14:03:02 2007 UTC (8 years, 11 months ago) by dinse
added specific functions and altered existing ones to show the compared maps (2 different structures at the same time) 
Revision 169 - Directory Listing
Modified Mon Aug 27 14:30:31 2007 UTC (9 years ago) by stehr
added console message when saving to graph db
Revision 168 - Directory Listing
Modified Tue Aug 14 10:03:58 2007 UTC (9 years ago) by stehr
using new SecondaryStructure object
Revision 167 - Directory Listing
Modified Mon Aug 13 10:40:01 2007 UTC (9 years ago) by stehr
added function call for saving to graph db, added 3 new options to config file, updated version number in Manifest
Revision 166 - Directory Listing
Modified Fri Aug 10 16:41:43 2007 UTC (9 years ago) by stehr
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Revision 165 - Directory Listing
Modified Thu Aug 9 13:48:45 2007 UTC (9 years ago) by stehr
added menu item "Save to graph db" (but implementation in Graph still missing)
Revision 163 - Directory Listing
Modified Mon Aug 6 15:43:38 2007 UTC (9 years ago) by stehr
printing version number of startup, added new color scheme for distance map, allow changing database in load dialogs for pdbase and msdsd
Revision 162 - Directory Listing
Modified Mon Aug 6 14:39:30 2007 UTC (9 years ago) by stehr
added Jama.jar to Manifests, fixed yet another bug in make script
Revision 161 - Directory Listing
Modified Mon Aug 6 14:27:26 2007 UTC (9 years ago) by stehr
updated make script, fixed a bug and added Jama.jar to the classpath
Revision 160 - Directory Listing
Modified Fri Jul 13 12:35:02 2007 UTC (9 years, 1 month ago) by stehr
now coordinates also being updated while dragging in ruler, tried to also show "crosshair" while mouse is in ruler but more diffucult than anticipated, disabled
Revision 159 - Directory Listing
Modified Fri Jul 13 10:19:27 2007 UTC (9 years, 1 month ago) by stehr
added code to experiment with toolbar, statusbar and background loading of maps (all disabled by default)
Revision 158 - Directory Listing
Modified Tue Jul 10 14:15:58 2007 UTC (9 years, 1 month ago) by duarte
Refactoring:
ContactList -> EdgeSet
Contact -> Edge
Now EdgeSet is a TreeSet which improves performance quite nicely
Revision 157 - Directory Listing
Modified Tue Jul 10 10:19:12 2007 UTC (9 years, 1 month ago) by stehr
updated Manifest files and make scripts to include vecmath.jar
Revision 156 - Directory Listing
Modified Mon Jul 9 17:29:37 2007 UTC (9 years, 1 month ago) by stehr
added dragging in ruler, started implementing tool bar (currently disabled)
Revision 155 - Directory Listing
Modified Mon Jul 9 15:37:26 2007 UTC (9 years, 1 month ago) by stehr
added secondary structure selection, changes to background loading but still disabled and not really working
Revision 154 - Directory Listing
Modified Mon Jul 9 15:06:28 2007 UTC (9 years, 1 month ago) by duarte
Now in call to calculate_dist_matrix in initDistMatrix we get directly the matrix with pairs of residue serials as indices. Only need to scale it.
Revision 153 - Directory Listing
Modified Fri Jul 6 17:12:18 2007 UTC (9 years, 1 month ago) by stehr
code rearrangements in View, common nbh sizes and density map now calculated once and saved for later, started to implement loading them in background (currenlty disabled)
Revision 152 - Directory Listing
Modified Fri Jul 6 13:06:44 2007 UTC (9 years, 1 month ago) by stehr
forgot to add ScreenBuffer class to version control, should be there now
Revision 151 - Directory Listing
Modified Fri Jul 6 13:06:06 2007 UTC (9 years, 1 month ago) by stehr
major code rearrangements in ContactMapPane, implemented buffering strategy for contact map and background maps, change mouse cursor to hourglass while calculating bg maps
Revision 150 - Directory Listing
Modified Thu Jul 5 13:44:55 2007 UTC (9 years, 1 month ago) by duarte
Changed distance matrix to be a HashMap instead of a TreeMap. Gaining slightly in speed
Revision 149 - Directory Listing
Modified Wed Jul 4 15:55:22 2007 UTC (9 years, 1 month ago) by duarte
Now painting secondary structure as filled rectangles
New member in Model secstruct2resinterval, initialising it in initializeContactMap
Making sure we call has3Dcoordinates() every time we call secondary structure methods from model
Revision 148 - Directory Listing
Modified Wed Jul 4 13:55:03 2007 UTC (9 years, 1 month ago) by stehr
added zoom command when showing triangles in pymol, extracted constants for (action) menu item labels, renamed icon variables
Revision 146 - Directory Listing
Modified Tue Jul 3 15:40:30 2007 UTC (9 years, 1 month ago) by duarte
Displaying secondary structure with color ticks in rulers and also displaying the secondary structure elements together with coordinates (both while mouse moved on contact map or on rulers)
Revision 145 - Directory Listing
Modified Mon Jul 2 09:45:49 2007 UTC (9 years, 1 month ago) by stehr
updated and simplified class comments (removed class,package,author,... clutter)
Revision 144 - Directory Listing
Modified Fri Jun 29 18:00:19 2007 UTC (9 years, 1 month ago) by stehr
made PyMolAdaptor independent of View, now a global PyMolAdaptor is created
in Start and used by all Views.
Revision 143 - Directory Listing
Modified Fri Jun 29 16:01:53 2007 UTC (9 years, 1 month ago) by stehr
moved file chooser and color chooser to Start to remember last selected dir
Revision 142 - Directory Listing
Modified Fri Jun 29 15:29:41 2007 UTC (9 years, 1 month ago) by stehr
added optional pymol shutdown on exit,
some cleanup of code and comments
Revision 141 - Directory Listing
Modified Fri Jun 29 13:30:12 2007 UTC (9 years, 1 month ago) by stehr
created alternative Manifest.txt with relative classpath for external jars,
make script now takes additional parameter to specify manifest file
Revision 140 - Directory Listing
Modified Fri Jun 29 13:11:46 2007 UTC (9 years, 1 month ago) by stehr
still the same mac issue: try to getCanonicalPath() before running pymol executable
Revision 139 - Directory Listing
Modified Fri Jun 29 13:04:52 2007 UTC (9 years, 1 month ago) by stehr
workaround for Mac: start pymol even though the executable seems not to exist
Revision 138 - Directory Listing
Modified Fri Jun 29 11:04:14 2007 UTC (9 years, 1 month ago) by stehr
renamed constant DEFAULT_EDGETYPE to DEFAULT_CONTACT_TYPE and show default contact type in load dialogs
Revision 137 - Directory Listing
Modified Fri Jun 29 10:39:27 2007 UTC (9 years, 1 month ago) by stehr
some updates to pymol startup process:
check for running pymol server before starting a new one,
use callback file trick to make sure pymol is responding
Revision 136 - Directory Listing
Modified Fri Jun 29 09:28:35 2007 UTC (9 years, 1 month ago) by stehr
renamed file graph.py to cmview.py, renamed menu item "save config file"
Revision 135 - Directory Listing
Modified Thu Jun 28 16:30:48 2007 UTC (9 years, 2 months ago) by stehr
clicking while ctrl is pressed now does not reset selection,
disabled dragging with right mouse button
Revision 134 - Directory Listing
Modified Thu Jun 28 15:47:28 2007 UTC (9 years, 2 months ago) by stehr
forgot to add LoadDialogInputError to version control, should be there now
Revision 133 - Directory Listing
Modified Thu Jun 28 15:44:23 2007 UTC (9 years, 2 months ago) by stehr
Models catch new exceptions from Pdb and Graph classes, LoadDialog now checks user input
Revision 132 - Directory Listing
Modified Wed Jun 27 16:01:37 2007 UTC (9 years, 2 months ago) by duarte
Now also catching SQLException for queries (as well as for connections) that were not thrown before
Revision 131 - Directory Listing
Modified Wed Jun 27 15:15:04 2007 UTC (9 years, 2 months ago) by duarte
Added error handling for wrong pdb or cm file formats 
Revision 130 - Directory Listing
Modified Wed Jun 27 14:42:07 2007 UTC (9 years, 2 months ago) by stehr
changed command string to select nodes in pymol
Revision 129 - Directory Listing
Modified Wed Jun 27 13:35:12 2007 UTC (9 years, 2 months ago) by stehr
changed all database models to work with new Pdb and Graph subclasses
using the database connection created in Start for all database operations
new help menu item "write default config file"
Revision 128 - Directory Listing
Modified Wed Jun 27 12:39:16 2007 UTC (9 years, 2 months ago) by stehr
using config file
Revision 127 - Directory Listing
Modified Tue Jun 26 17:11:38 2007 UTC (9 years, 2 months ago) by duarte
Using getter methods for graph calls instead of directly calling member variables
Revision 125 - Directory Listing
Modified Tue Jun 26 17:04:47 2007 UTC (9 years, 2 months ago) by stehr
warning dialogs in view now have consistent look
Revision 124 - Directory Listing
Modified Tue Jun 26 16:33:43 2007 UTC (9 years, 2 months ago) by stehr
updated classpath in make script for using PyMolServerOutputStream with apache xmlrpc 3.0
Revision 123 - Directory Listing
Modified Tue Jun 26 16:26:46 2007 UTC (9 years, 2 months ago) by stehr
classpath in manifest now contains 3 new dependencies for using PyMolServerOutputStream with apache xmlrpc 3.0
Revision 122 - Directory Listing
Modified Tue Jun 26 14:27:26 2007 UTC (9 years, 2 months ago) by duarte
Improved error handling for database and pymol connection
Implemented tryConnectingToPymol in Start
Using new version of xmlrpc 3.0 (PyMolServerOutputStream rev 203)
Moved is...ConnectionAvailable to Start as static
Revision 121 - Directory Listing
Modified Tue Jun 26 12:06:31 2007 UTC (9 years, 2 months ago) by stehr
check for database and pymol connection on startup,
some minor rearrangements in Start
Revision 120 - Directory Listing
Modified Mon Jun 25 14:28:46 2007 UTC (9 years, 2 months ago) by stehr
adding missing icon
Revision 119 - Directory Listing
Modified Mon Jun 25 14:27:38 2007 UTC (9 years, 2 months ago) by stehr
new context menu function: show current residue pair as edge in pymol
Revision 118 - Directory Listing
Modified Mon Jun 25 13:27:04 2007 UTC (9 years, 2 months ago) by stehr
using new pymol version with localhost as server
Revision 117 - Directory Listing
Modified Mon Jun 25 13:01:24 2007 UTC (9 years, 2 months ago) by stehr
added constant USE_PYMOL to enable/disable pymol related menu items
Revision 116 - Directory Listing
Modified Mon Jun 25 10:12:14 2007 UTC (9 years, 2 months ago) by stehr
fixed minor bug in make script
Revision 115 - Directory Listing
Modified Mon Jun 25 10:09:00 2007 UTC (9 years, 2 months ago) by stehr
graph.py now being loaded from subdir 'recources'
Revision 114 - Directory Listing
Modified Fri Jun 22 09:58:05 2007 UTC (9 years, 2 months ago) by stehr
some error handling for pymol output stream
Revision 113 - Directory Listing
Modified Fri Jun 22 09:22:52 2007 UTC (9 years, 2 months ago) by stehr
proper error handling for loading models
Revision 112 - Directory Listing
Modified Thu Jun 21 14:54:28 2007 UTC (9 years, 2 months ago) by stehr
delete temp pdb files on exit,
cleaned up constants in Start
Revision 111 - Directory Listing
Modified Wed Jun 20 15:45:40 2007 UTC (9 years, 2 months ago) by duarte
Now dealing with cases when pdb is null in the Model object. 
Using new method has3DCoordinates for that
Revision 110 - Directory Listing
Modified Wed Jun 20 11:55:07 2007 UTC (9 years, 2 months ago) by duarte
Minor clean up
Revision 109 - Directory Listing
Modified Wed Jun 20 11:54:33 2007 UTC (9 years, 2 months ago) by stehr
Catch all exceptions in ContactMapFileModel when trying to load structure from pdbase
(pretty bad style but will allow to open CM files without database before
proper DB error handling is implemented)
Revision 108 - Directory Listing
Modified Wed Jun 20 11:35:00 2007 UTC (9 years, 2 months ago) by stehr
added missing icons for 'View' and 'Color' menu
Revision 107 - Directory Listing
Modified Tue Jun 19 17:10:47 2007 UTC (9 years, 2 months ago) by stehr
pretty icons for 'View' and 'Color' menu
Revision 106 - Directory Listing
Modified Tue Jun 19 13:34:03 2007 UTC (9 years, 2 months ago) by stehr
bug fix: toggle rulers won't resize window
implemented component resize listener
Revision 104 - Directory Listing
Modified Tue Jun 19 12:26:30 2007 UTC (9 years, 2 months ago) by stehr
now showing residue numbers when mouse is in ruler
updated version number for 0.7.1
Revision 103 - Directory Listing
Modified Tue Jun 19 09:42:46 2007 UTC (9 years, 2 months ago) by duarte
Fixed bug. Was not working for tags and was not checking for existance of dirs correctly
Revision 101 - Directory Listing
Modified Tue Jun 19 09:22:37 2007 UTC (9 years, 2 months ago) by stehr
few minor changes for 0.7 release
Revision 100 - Directory Listing
Modified Mon Jun 18 17:42:52 2007 UTC (9 years, 2 months ago) by duarte
New feature: showing of color graded distance matrix (only single atom models)
Revision 99 - Directory Listing
Modified Mon Jun 18 16:55:34 2007 UTC (9 years, 2 months ago) by stehr
added colorMapMatlab and colorMapGrayscale (currently commented out)
Revision 98 - Directory Listing
Modified Mon Jun 18 16:37:47 2007 UTC (9 years, 2 months ago) by stehr
changed color constants in contactMapPane to variables set in constructor
Revision 97 - Directory Listing
Modified Mon Jun 18 15:59:07 2007 UTC (9 years, 2 months ago) by duarte
Renamed make-cmview to make-cm2pymol 
Revision 96 - Directory Listing
Modified Mon Jun 18 15:50:31 2007 UTC (9 years, 2 months ago) by duarte
Initial commit of a make script to compile this project and aglappe into one single big jar file
Revision 95 - Directory Listing
Modified Mon Jun 18 15:46:24 2007 UTC (9 years, 2 months ago) by duarte
Got rid of aglappe.jar classpath link in Manifest
Revision 94 - Directory Listing
Modified Mon Jun 18 15:30:09 2007 UTC (9 years, 2 months ago) by stehr
new function: show contact density
Revision 93 - Directory Listing
Modified Mon Jun 18 09:44:27 2007 UTC (9 years, 2 months ago) by stehr
added proper error messages for 'select all' and 'delete contacts' when no CM is loaded
updated help page
changed behaviour of diagonal select
some refactoring
Revision 92 - Directory Listing
Modified Fri Jun 15 17:13:44 2007 UTC (9 years, 2 months ago) by stehr
added some experimental code to show multiple contact maps in one window
(currently commented out)
Revision 91 - Directory Listing
Modified Fri Jun 15 16:01:58 2007 UTC (9 years, 2 months ago) by stehr
added draw contacts as crosses and draw contacts as arcs
turned out to be not useful, so they are commented out
Revision 90 - Directory Listing
Modified Fri Jun 15 15:28:13 2007 UTC (9 years, 2 months ago) by duarte
NEW FEATURE: delete selected edges
Revision 89 - Directory Listing
Modified Fri Jun 15 14:51:48 2007 UTC (9 years, 2 months ago) by stehr
made the way the icon files are accessed compliant with jar packaging
Revision 88 - Directory Listing
Modified Fri Jun 15 14:42:29 2007 UTC (9 years, 2 months ago) by duarte
New diagonal selection mode
Crosshairs now in separate method drawCursor, new type of cursor for diagonal selection mode
Fixed small bug in PyMolAdaptor: when sending an empty selection was throwing exception
Revision 87 - Directory Listing
Modified Fri Jun 15 13:42:35 2007 UTC (9 years, 2 months ago) by stehr
added SelectAll menu item, color chooser now without ugly preview panel,
selection now being reset after coloring
Revision 86 - Directory Listing
Modified Fri Jun 15 09:55:07 2007 UTC (9 years, 2 months ago) by stehr
added option to restrict max seq sep when loading (many files changed)
Revision 84 - Directory Listing
Modified Thu Jun 14 14:42:52 2007 UTC (9 years, 2 months ago) by duarte
Back to no letters ruler. Last missing tick now shown
Rulers optional (new in View menu)
Updates for 0.6 release
Revision 83 - Directory Listing
Modified Thu Jun 14 13:27:25 2007 UTC (9 years, 2 months ago) by duarte
Painting residue types in rulers, not very useful
Revision 82 - Directory Listing
Modified Thu Jun 14 10:48:37 2007 UTC (9 years, 2 months ago) by duarte
Now repainting ResidueRuler after node neighbourhood selection
New color menu, renamed the actions
Revision 81 - Directory Listing
Modified Thu Jun 14 10:03:08 2007 UTC (9 years, 2 months ago) by duarte
Added selection of node neighbours, both from ruler and contact map
Revision 80 - Directory Listing
Modified Thu Jun 14 08:48:14 2007 UTC (9 years, 2 months ago) by duarte
Refactored squareSelStart and squareSelEnd. Changed squareSelection method to no arguments
Revision 79 - Directory Listing
Modified Thu Jun 14 08:01:30 2007 UTC (9 years, 2 months ago) by stehr
added grid and tickmarks (currently commented out)
Revision 78 - Directory Listing
Modified Wed Jun 13 16:57:42 2007 UTC (9 years, 2 months ago) by duarte
First very basic implementation of rulers: 
new class ResidueRuler and adding 2 more panes to the View frame
Revision 77 - Directory Listing
Modified Wed Jun 13 15:07:44 2007 UTC (9 years, 2 months ago) by duarte
Fixed small bug: tmpContacts, squareSelStart, squareSelEnd were not been initialised 
Now printing to stdout the common neighbours and motif
Revision 76 - Directory Listing
Modified Wed Jun 13 14:25:08 2007 UTC (9 years, 2 months ago) by duarte
Using AA.contactTypes() to get the contact types
Revision 75 - Directory Listing
Modified Wed Jun 13 10:43:14 2007 UTC (9 years, 2 months ago) by duarte
Much improved common neighbours display: crosses are scaled (from a minimum) and centered in cells. Triangles centered in cells
Refactored markPointWithCross to drawCrossOnContact
New methods getCellCenter, getCellUpperRight etc
Revision 74 - Directory Listing
Modified Tue Jun 12 18:29:26 2007 UTC (9 years, 2 months ago) by duarte
Fixed potential bug: getContacts was deep copying, now just referencing
Revision 73 - Directory Listing
Modified Tue Jun 12 18:13:41 2007 UTC (9 years, 2 months ago) by stehr
warning screen (no contact map loaded yet) for more functions (hopefully all now)
Revision 72 - Directory Listing
Modified Tue Jun 12 18:07:18 2007 UTC (9 years, 2 months ago) by stehr
New help screen, indicate contact by little line between residue types,
show error screen if certain functions are selected before a contact map is loaded.
Revision 71 - Directory Listing
Modified Tue Jun 12 17:14:51 2007 UTC (9 years, 2 months ago) by duarte
New feature: coloring edges
Revision 70 - Directory Listing
Modified Tue Jun 12 16:27:09 2007 UTC (9 years, 2 months ago) by duarte
NEW FEATURE: highlight of common neighbours by size

Revision 69 - Directory Listing
Modified Tue Jun 12 15:07:13 2007 UTC (9 years, 2 months ago) by stehr
printing works now, prints the right size, but the implementation is not very elegant
Revision 68 - Directory Listing
Modified Tue Jun 12 13:35:20 2007 UTC (9 years, 2 months ago) by duarte
NEW FEATURE: optionally showing pdb residue numbers
Now Model and not Graph is a member of ContactMapPane, calling only Model methods now (implemented the new ones needed from Graph and Pdb)
New "view" menu in View
Revision 67 - Directory Listing
Modified Tue Jun 12 12:42:35 2007 UTC (9 years, 2 months ago) by stehr
Fixed null pointer exception in Start class when running without command line parameters.
Added functionality to select and deselect single contacts.
Revision 66 - Directory Listing
Modified Tue Jun 12 10:25:58 2007 UTC (9 years, 2 months ago) by stehr
updated javadoc comments
Revision 65 - Directory Listing
Modified Mon Jun 11 15:19:42 2007 UTC (9 years, 2 months ago) by duarte
Fixed bug: taking accession code and chain code from command line now works correctly
Revision 61 - Directory Listing
Modified Mon Jun 11 14:03:30 2007 UTC (9 years, 2 months ago) by duarte
Changed to version 0.5
Revision 60 - Directory Listing
Modified Mon Jun 11 14:02:54 2007 UTC (9 years, 2 months ago) by duarte
Made version a constant in Start
Revision 59 - Directory Listing
Modified Mon Jun 11 14:00:23 2007 UTC (9 years, 2 months ago) by duarte
Residue selections now for common nbhds and edges
In View: got rid of button click to send pdb file to pymol, refactoring
Fixed bug: pymol adaptor was not passed to new view objects
Revision 58 - Directory Listing
Modified Mon Jun 11 10:11:22 2007 UTC (9 years, 2 months ago) by duarte
Coordinates are drawn now in columns, using '?' when res type is null
Setting mouseIn to false when out of window, was fixed in 52 but overwritten in 53

Revision 57 - Directory Listing
Modified Fri Jun 8 16:06:22 2007 UTC (9 years, 2 months ago) by duarte
Slight improvements in the mouse events, a bit better behaved
Revision 56 - Directory Listing
Modified Fri Jun 8 15:51:41 2007 UTC (9 years, 2 months ago) by duarte
NEW FEATURE: Now Start can take pdbCode and chainCode from command line and display default contact map for it
Revision 55 - Directory Listing
Modified Fri Jun 8 14:38:16 2007 UTC (9 years, 2 months ago) by duarte
Now printing residue types as well as i, j coordinates
Light gray corridor for common neighbours now displayed horizontal or vertical from the center of segment i->j
Revision 54 - Directory Listing
Modified Fri Jun 8 13:55:38 2007 UTC (9 years, 2 months ago) by duarte
FIXED common neighbours display and send to PyMol
Now the graph object a member variable
Getting common neighbours from Graph's getEdgeNbh
Common neighbours displayed simplified and well commented
Revision 53 - Directory Listing
Modified Thu Jun 7 16:35:57 2007 UTC (9 years, 2 months ago) by duarte
FIXED MANY BUGS: everything related to indices in contact map and screen coordinates
NEW FEATURE: supporting CTRL+click for square+fill selections
Not using matrices anymore for selection, but ContactsList
Major clean up of unused stuff, specially in ContactMapPane
Common neighbours display doesn't work. It's just not been called properly, I haven't touched the methods to draw them
Revision 52 - Directory Listing
Modified Fri May 25 15:14:29 2007 UTC (9 years, 3 months ago) by stehr
removed menu item "Load Structure in Pymol",
hide crosshair when mouse is leaving contact map window
Revision 51 - Directory Listing
Modified Fri May 25 12:57:53 2007 UTC (9 years, 3 months ago) by duarte
Put everything into packages
Revision 50 - Directory Listing
Modified Fri May 25 12:39:49 2007 UTC (9 years, 3 months ago) by duarte
Got rid of OldModel, PaintController (now ContactMapPane)
Renamed MyTestPyMol to PymolAdaptor
Start is now the starting point again. Contains strictly only static methods

Revision 48 - Directory Listing
Modified Thu May 24 12:03:22 2007 UTC (9 years, 3 months ago) by stehr
changes classpath in Manifest
Revision 47 - Directory Listing
Modified Thu May 24 10:29:49 2007 UTC (9 years, 3 months ago) by stehr
New version with many changes. The contact map window can now be opened directly using the main function in View.
Revision 46 - Directory Listing
Modified Tue May 15 14:05:56 2007 UTC (9 years, 3 months ago) by stehr
Created different contact map data model classes
Revision 45 - Directory Listing
Modified Mon May 14 11:15:08 2007 UTC (9 years, 3 months ago) by stehr
Renamed ModelTemp to Model, now it is how i wanted it to be :)
Revision 44 - Directory Listing
Modified Mon May 14 11:12:56 2007 UTC (9 years, 3 months ago) by stehr
Temporary commit, extracted Interface from class Model but couldn't call it model again
Revision 43 - Directory Listing
Modified Mon May 14 09:03:24 2007 UTC (9 years, 3 months ago) by stehr
Some code cleanup, added dummy menu bar
Revision 34 - Directory Listing
Modified Thu May 10 14:41:50 2007 UTC (9 years, 3 months ago) by stehr
Updated version number before tagging
Revision 33 - Directory Listing
Modified Mon May 7 14:05:46 2007 UTC (9 years, 3 months ago) by stehr
Structure is now loaded automatically when contact map windows opens
Revision 32 - Directory Listing
Modified Mon May 7 10:39:50 2007 UTC (9 years, 3 months ago) by stehr
Added some icons for the context menu
Revision 31 - Directory Listing
Modified Mon May 7 10:25:27 2007 UTC (9 years, 3 months ago) by stehr
Changes to all classes. Now, multiple contact maps can be opened and modified in the same pymol session.
Revision 30 - Directory Listing
Modified Thu May 3 14:50:55 2007 UTC (9 years, 3 months ago) by stehr
New functionality: context menu, see selection rectangle and coordinates while dragging
Revision 27 - Directory Listing
Modified Mon Apr 30 14:29:10 2007 UTC (9 years, 3 months ago) by stehr
Fixed problems with null chain codes
Revision 26 - Directory Listing
Modified Fri Apr 27 11:13:41 2007 UTC (9 years, 4 months ago) by stehr
Made selecting structures nicer: Now combo boxes with preselection in the startup dialog
Revision 25 - Directory Listing
Modified Thu Apr 26 13:52:01 2007 UTC (9 years, 4 months ago) by stehr
Read user name from environment and run pymol automatically.
Revision 24 - Directory Listing
Modified Thu Apr 26 08:27:53 2007 UTC (9 years, 4 months ago) by duarte
Model.java: hardcoded db server, user etc are now taken from static variables in Start
Start.java:
- now takes graph database as optional argument at startup
- hostname for pymol URL now set automatically with new static method getHostName
- corrected indentation
Revision 23 - Directory Listing
Modified Wed Apr 11 14:05:18 2007 UTC (9 years, 4 months ago) by stehr
Constants for accessing the database and the pymol server can now be set globally in the Start class
Revision 21 - Directory Listing
Modified Fri Mar 30 13:29:00 2007 UTC (9 years, 4 months ago) by dinse

Revision 20 - Directory Listing
Modified Fri Mar 30 13:02:24 2007 UTC (9 years, 4 months ago) by dinse

Revision 19 - Directory Listing
Modified Fri Mar 30 13:02:10 2007 UTC (9 years, 4 months ago) by dinse

Revision 18 - Directory Listing
Modified Thu Mar 29 15:15:01 2007 UTC (9 years, 4 months ago) by dinse

Revision 17 - Directory Listing
Modified Thu Mar 29 12:57:35 2007 UTC (9 years, 5 months ago) by dinse

Revision 16 - Directory Listing
Modified Thu Mar 29 12:57:18 2007 UTC (9 years, 5 months ago) by dinse

Revision 15 - Directory Listing
Modified Thu Mar 29 11:51:06 2007 UTC (9 years, 5 months ago) by dinse

Revision 14 - Directory Listing
Modified Thu Mar 29 11:50:56 2007 UTC (9 years, 5 months ago) by dinse

Revision 13 - Directory Listing
Modified Wed Mar 28 13:40:49 2007 UTC (9 years, 5 months ago) by dinse

Revision 12 - Directory Listing
Modified Wed Mar 28 13:40:39 2007 UTC (9 years, 5 months ago) by dinse

Revision 11 - Directory Listing
Modified Wed Mar 28 08:07:32 2007 UTC (9 years, 5 months ago) by dinse

Revision 10 - Directory Listing
Modified Tue Mar 27 12:46:15 2007 UTC (9 years, 5 months ago) by dinse

Revision 9 - Directory Listing
Modified Tue Mar 27 12:46:05 2007 UTC (9 years, 5 months ago) by dinse

Revision 8 - Directory Listing
Modified Thu Mar 22 09:16:14 2007 UTC (9 years, 5 months ago) by dinse

Revision 7 - Directory Listing
Modified Tue Mar 20 09:09:46 2007 UTC (9 years, 5 months ago) by dinse

Revision 6 - Directory Listing
Modified Tue Mar 20 09:09:39 2007 UTC (9 years, 5 months ago) by dinse

Revision 5 - Directory Listing
Modified Mon Mar 19 08:27:34 2007 UTC (9 years, 5 months ago) by dinse

Revision 4 - Directory Listing
Modified Mon Mar 19 08:27:25 2007 UTC (9 years, 5 months ago) by dinse

Revision 3 - Directory Listing
Modified Mon Mar 19 08:27:16 2007 UTC (9 years, 5 months ago) by dinse

Revision 2 - Directory Listing
Modified Mon Mar 19 08:27:06 2007 UTC (9 years, 5 months ago) by dinse

Revision 1 - Directory Listing
Added Wed Mar 14 09:18:10 2007 UTC (9 years, 5 months ago) by dinse
Initial import of the CM2PyMol project