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Revision 477 - Directory Listing
Modified Wed Apr 23 10:06:55 2008 UTC (9 years, 10 months ago) by risbud
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 (9 years, 10 months ago) by duarte
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 (9 years, 10 months ago) by risbud
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
forgot to check in changes in View for last commit
Revision 472 - Directory Listing
Modified Mon Mar 3 15:49:03 2008 UTC (9 years, 11 months ago) by stehr
Original Path: trunk
Some code cleanup in PyMolAdaptor
Revision 471 - Directory Listing
Modified Fri Feb 29 19:31:11 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
Fixed bug;
Revision 463 - Directory Listing
Modified Thu Feb 28 18:21:53 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
Capitalized CMView
Revision 460 - Directory Listing
Modified Thu Feb 28 14:44:46 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Eliminated Cg type for the release version
Revision 458 - Directory Listing
Modified Thu Feb 28 14:27:43 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Changed version to 0.9.3
Revision 456 - Directory Listing
Modified Thu Feb 28 14:09:24 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Minor fixes in comments and error output in StreamGobbler
Revision 455 - Directory Listing
Modified Thu Feb 28 12:10:54 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
minor updates to manual.xml and tutorial.xml
Revision 453 - Directory Listing
Modified Wed Feb 27 13:01:49 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Now orient command specifies the structure
Revision 452 - Directory Listing
Modified Wed Feb 27 11:52:46 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
Reverting all the changes, no test was successful
Revision 446 - Directory Listing
Modified Mon Feb 25 17:59:18 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Another test, 10s of sleep this time
Revision 445 - Directory Listing
Modified Mon Feb 25 17:47:50 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Yet another test for the bug
Revision 444 - Directory Listing
Modified Mon Feb 25 17:46:50 2008 UTC (9 years, 11 months ago) by stehr
Original Path: trunk
checking in latest Javahelp set
Revision 443 - Directory Listing
Modified Mon Feb 25 17:41:21 2008 UTC (9 years, 11 months ago) by stehr
Original Path: trunk
removed "draft" sections from manual.xml, minor update of installation.xml
Revision 442 - Directory Listing
Modified Mon Feb 25 17:40:33 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
3rd test commit. Always trying to fix same bug
Revision 441 - Directory Listing
Modified Mon Feb 25 17:31:35 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Another test commit to try to fix the Windows bug
Revision 440 - Directory Listing
Modified Mon Feb 25 17:25:20 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
major update of manual.xml
Revision 438 - Directory Listing
Modified Mon Feb 25 16:26:13 2008 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
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 (9 years, 11 months ago) by stehr
Original Path: trunk
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 (9 years, 11 months ago) by duarte
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
updated most docbook files, main README and javahelp files
Revision 432 - Directory Listing
Modified Fri Feb 22 15:39:05 2008 UTC (10 years ago) by duarte
Original Path: trunk
Now setting WAIT_CURSOR when loading alignment from file.
Revision 431 - Directory Listing
Modified Thu Feb 21 17:13:49 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Minor update of manual and index
Revision 428 - Directory Listing
Modified Wed Feb 20 16:42:22 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Minor update of index, installation and manual
Revision 422 - Directory Listing
Modified Tue Feb 19 18:57:11 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Updated version to 1.0-rc1
Revision 419 - Directory Listing
Modified Tue Feb 19 16:06:46 2008 UTC (10 years ago) by stehr
Original Path: trunk
Checking in latest javahelp files
Revision 418 - Directory Listing
Modified Tue Feb 19 16:03:38 2008 UTC (10 years ago) by stehr
Original Path: trunk
commented out missing section in Manual before tagging test version
Revision 417 - Directory Listing
Modified Tue Feb 19 15:51:52 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Minor changes to Installation and Manual
Revision 415 - Directory Listing
Modified Tue Feb 19 13:20:28 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Added a message when current config file is written
Revision 412 - Directory Listing
Modified Tue Feb 19 11:22:56 2008 UTC (10 years ago) by stehr
Original Path: trunk
New master config file
Revision 411 - Directory Listing
Modified Tue Feb 19 11:21:16 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
reordered and grouped config variables
Revision 406 - Directory Listing
Modified Thu Feb 14 16:21:29 2008 UTC (10 years ago) by stehr
Original Path: trunk
some cleanup in Start (made some session variables private)
Revision 405 - Directory Listing
Modified Thu Feb 14 16:01:33 2008 UTC (10 years ago) by stehr
Original Path: trunk
same as before, forgot to check in files other than Start
Revision 404 - Directory Listing
Modified Thu Feb 14 16:00:56 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
SHOW_ALIGNMENT_COORDS now goes through GUIState
Revision 402 - Directory Listing
Modified Thu Feb 14 15:16:30 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Added command line parameters section
Revision 398 - Directory Listing
Modified Mon Feb 11 20:01:52 2008 UTC (10 years ago) by stehr
Original Path: trunk
Minor changes to installation.xml
Revision 397 - Directory Listing
Modified Mon Feb 11 19:46:26 2008 UTC (10 years ago) by duarte
Original Path: trunk
Some more fixes
Revision 396 - Directory Listing
Modified Mon Feb 11 19:40:50 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Updated download.xml, faq.xml, index.xml and java help files.
Revision 392 - Directory Listing
Modified Mon Feb 11 16:07:55 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Adding small versions of the images (for web)
Revision 389 - Directory Listing
Modified Mon Feb 11 15:18:11 2008 UTC (10 years ago) by duarte
Original Path: trunk
Added all images, lots of fixes
Revision 388 - Directory Listing
Modified Mon Feb 11 15:17:58 2008 UTC (10 years ago) by duarte
Original Path: trunk
Initial commit of screenshots.xml
Revision 387 - Directory Listing
Modified Mon Feb 11 14:21:05 2008 UTC (10 years ago) by stehr
Original Path: trunk
Fixed bug that newly opened windows would not be focused.
Revision 386 - Directory Listing
Modified Sat Feb 9 10:45:28 2008 UTC (10 years ago) by duarte
Original Path: trunk
Added new java help jar to make script and manifests

Revision 385 - Directory Listing
Modified Fri Feb 8 18:57:57 2008 UTC (10 years ago) by duarte
Original Path: trunk
Much more markup, icons added
Revision 384 - Directory Listing
Modified Fri Feb 8 17:47:52 2008 UTC (10 years ago) by duarte
Original Path: trunk
Better markup and some corrections
Revision 383 - Directory Listing
Modified Fri Feb 8 17:04:34 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Added more content
Revision 381 - Directory Listing
Modified Fri Feb 8 11:22:21 2008 UTC (10 years ago) by stehr
Original Path: trunk
Fixed bugs in generate_docs.sh
Revision 380 - Directory Listing
Modified Fri Feb 8 10:16:36 2008 UTC (10 years ago) by stehr
Original Path: trunk
Added title to installation.xml
Revision 379 - Directory Listing
Modified Thu Feb 7 17:53:00 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Initial commit of installation.xml. Very raw draft
Revision 377 - Directory Listing
Modified Thu Feb 7 17:02:00 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk

Revision 375 - Directory Listing
Modified Thu Feb 7 11:00:27 2008 UTC (10 years ago) by duarte
Original Path: trunk
Changed size of blanks to 8 to match java's default
Revision 374 - Directory Listing
Modified Wed Feb 6 18:35:36 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Made CONFIG_FILE_NAME final
Revision 371 - Directory Listing
Modified Mon Feb 4 14:25:19 2008 UTC (10 years ago) by stehr
Original Path: trunk
moved Manifest files to /src folder, updated make script
Revision 370 - Directory Listing
Modified Mon Feb 4 14:18:03 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Moved all java sources from project root to folder /src
Revision 368 - Directory Listing
Modified Fri Feb 1 16:31:34 2008 UTC (10 years ago) by duarte
Original Path: trunk
Now runTests will do all tests starting with load
Revision 367 - Directory Listing
Modified Fri Feb 1 16:29:46 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by duarte
Original Path: trunk
Reverting to revision 356 (last commit was wrong)
Revision 365 - Directory Listing
Modified Thu Jan 31 14:37:02 2008 UTC (10 years ago) by stehr
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
- 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 (10 years ago) by duarte
Original Path: trunk
Fixed bug: forgot to skip gaps when getting residue types
Revision 357 - Directory Listing
Modified Thu Jan 31 08:59:56 2008 UTC (10 years ago) by stehr
Original Path: trunk
nice indention of function_reference.xml
Revision 356 - Directory Listing
Modified Wed Jan 30 11:05:26 2008 UTC (10 years ago) by stehr
Original Path: trunk
updated version to 0.9.2
Revision 355 - Directory Listing
Modified Wed Jan 30 10:57:40 2008 UTC (10 years ago) by stehr
Original Path: trunk
- 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 (10 years ago) by duarte
Original Path: trunk
First commit of xml docbooks
Revision 353 - Directory Listing
Modified Tue Jan 29 12:09:18 2008 UTC (10 years ago) by duarte
Original Path: trunk
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 (10 years ago) by stehr
Original Path: trunk
Changed message "Second model loaded" to "second contact map loaded".
Revision 351 - Directory Listing
Modified Wed Jan 23 17:34:47 2008 UTC (10 years ago) by duarte
Original Path: trunk
Made tool bar separators look better
Revision 350 - Directory Listing
Modified Wed Jan 23 16:09:03 2008 UTC (10 years ago) by duarte
Original Path: trunk
Now GraphDbModel tries to load structure from pdbase instead of msdsd
Revision 349 - Directory Listing
Modified Wed Jan 23 11:26:59 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
Another test
Revision 347 - Directory Listing
Modified Fri Jan 18 16:53:19 2008 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
added new abbot script to load a second structure
Revision 336 - Directory Listing
Modified Wed Jan 16 15:36:46 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
Was missing jaligner.jar in Struppi manifest
Revision 318 - Directory Listing
Modified Thu Jan 10 16:58:44 2008 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
Major change: corrected a typo in a comment
Revision 315 - Directory Listing
Modified Thu Jan 10 14:50:03 2008 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
fixed bug in getSelectedContacts(...,false): subtraction of 1 was missing
Revision 309 - Directory Listing
Modified Tue Jan 8 10:09:12 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
added INCLUDE_GROUP_INTERALS=true and removed some clutter
Revision 307 - Directory Listing
Modified Mon Jan 7 16:42:25 2008 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
New contact map info dialog with sequence tooltip
Revision 299 - Directory Listing
Modified Thu Jan 3 17:48:23 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
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 (10 years, 1 month ago) by stehr
Original Path: trunk
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 (10 years, 1 month ago) by duarte
Original Path: trunk
Fixed issues with config file (not fully tested yet!)
Revision 295 - Directory Listing
Modified Wed Jan 2 14:34:14 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Added command line option for version
Revision 293 - Directory Listing
Modified Wed Jan 2 13:59:24 2008 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
Changed version number to 0.9
Revision 292 - Directory Listing
Modified Wed Jan 2 13:32:11 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Copying branch CMView-jung into trunk

Revision 291 - Directory Listing
Modified Wed Jan 2 13:27:12 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Removing everything from trunk before replacing with branch CMView-jung

Revision 289 - Directory Listing
Modified Wed Jan 2 11:11:01 2008 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Updated version to 0.8.7
Revision 257 - Directory Listing
Modified Wed Dec 12 11:35:21 2007 UTC (10 years, 2 months ago) by lpetzo
Original Path: trunk
exception indicating LoadDialog errors
Revision 256 - Directory Listing
Modified Wed Dec 12 11:33:35 2007 UTC (10 years, 2 months ago) by lpetzo
Original Path: trunk
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 (10 years, 2 months ago) by lpetzo
Original Path: trunk
- 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 (10 years, 2 months ago) by duarte
Original Path: trunk
Updated manifest's classpath with jaligner.jar 
Revision 245 - Directory Listing
Modified Wed Nov 28 16:33:05 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Updated versions to 0.8.6 for tagging
Revision 238 - Directory Listing
Modified Tue Nov 27 15:31:58 2007 UTC (10 years, 2 months ago) by lpetzo
Original Path: trunk
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 (10 years, 2 months ago) by lpetzo
Original Path: trunk
added jaligner.jar to the class-path
Revision 236 - Directory Listing
Modified Thu Nov 22 11:51:49 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
added SADP-adapter related stuff to the javac command line
Revision 235 - Directory Listing
Modified Thu Nov 22 11:46:56 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by duarte
Original Path: trunk
Added new jar dependency jaligner.jar
Revision 231 - Directory Listing
Modified Mon Nov 19 10:10:06 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Now printing some output when loading structure from msd in GraphDBModel
Revision 230 - Directory Listing
Modified Mon Nov 19 09:40:06 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by duarte
Original Path: trunk
Added "case sensitive" comment in load dialog
Revision 228 - Directory Listing
Modified Tue Nov 13 14:38:48 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
class View:
- deleted some output stuff for debugging
Revision 226 - Directory Listing
Modified Mon Nov 12 15:57:04 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
new feature: pairwise sequence alignment for comparison
Revision 225 - Directory Listing
Modified Mon Nov 12 15:53:43 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
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 (10 years, 3 months ago) by duarte
Original Path: trunk
Added new packages sadp and actionTools to the jar
Revision 223 - Directory Listing
Modified Thu Nov 8 11:47:20 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by filippis
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
changed accessibility of class field CONSTRUCT_EVERYTHING from private to public
Revision 215 - Directory Listing
Modified Fri Nov 2 18:04:38 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
modified prototype of the constructor
Revision 214 - Directory Listing
Modified Fri Nov 2 18:03:28 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
- 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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 3 months ago) by lpetzo
Original Path: trunk

Revision 210 - Directory Listing
Modified Thu Oct 25 15:02:04 2007 UTC (10 years, 3 months ago) by lpetzo
Original Path: trunk
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 (10 years, 4 months ago) by stehr
Original Path: trunk
updating Manifest-StuPPi to name CMView and version 0.8.5
Revision 207 - Directory Listing
Modified Wed Oct 17 15:18:31 2007 UTC (10 years, 4 months ago) by stehr
Original Path: trunk
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 (10 years, 4 months ago) by duarte
Original Path: trunk
Added '...' to menus that open dialogs
Revision 205 - Directory Listing
Modified Thu Oct 11 12:50:06 2007 UTC (10 years, 4 months ago) by stehr
Original Path: trunk
Fixed ContactMapPane and ResidueRuler to work with new NodeSet class
Revision 204 - Directory Listing
Modified Thu Oct 4 13:28:44 2007 UTC (10 years, 4 months ago) by dinse
Original Path: trunk
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 (10 years, 4 months ago) by stehr
Original Path: trunk
added missing icon color_swatch.png
Revision 202 - Directory Listing
Modified Thu Sep 20 16:01:36 2007 UTC (10 years, 5 months ago) by stehr
Original Path: trunk
added contact selection by color
Revision 201 - Directory Listing
Modified Thu Sep 20 14:54:43 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Changed aminoacid information calls from AA to AAinfo
Revision 200 - Directory Listing
Modified Thu Sep 20 11:01:14 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
added menu item 'select by residue number'
Revision 198 - Directory Listing
Modified Wed Sep 19 14:24:30 2007 UTC (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
rearranged selection mode menu items and made toggle buttons for them
Revision 195 - Directory Listing
Modified Tue Sep 18 15:27:42 2007 UTC (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
added constants SHOW_ICON_BAR and ICON_BAR_FLOATABLE
Revision 190 - Directory Listing
Modified Tue Sep 18 08:46:31 2007 UTC (10 years, 5 months ago) by stehr
Original Path: trunk
updated version number to 0.8.5
Revision 189 - Directory Listing
Modified Tue Sep 18 08:45:58 2007 UTC (10 years, 5 months ago) by stehr
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
using new constructor from ciffilePdb for loading directly from online pdb
Revision 187 - Directory Listing
Modified Mon Sep 17 14:25:50 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
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 (10 years, 5 months ago) by duarte
Original Path: trunk
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 (10 years, 5 months ago) by dinse
Original Path: trunk
changed colours of rulers
Revision 184 - Directory Listing
Modified Mon Sep 10 10:33:23 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk

Revision 183 - Directory Listing
Modified Thu Sep 6 13:54:21 2007 UTC (10 years, 5 months ago) by stehr
Original Path: trunk
fixed some problems with make-script
Revision 182 - Directory Listing
Modified Thu Sep 6 08:05:33 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk

Revision 181 - Directory Listing
Modified Thu Sep 6 08:05:07 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
changed objectSelName - output to PyMol
Revision 180 - Directory Listing
Modified Tue Sep 4 13:20:16 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk

Revision 179 - Directory Listing
Modified Tue Sep 4 13:20:09 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk

Revision 178 - Directory Listing
Modified Tue Sep 4 13:19:55 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
changed selections for comparing maps 
Revision 177 - Directory Listing
Modified Tue Sep 4 13:17:51 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
changed viewer in comparing maps 
Revision 176 - Directory Listing
Modified Tue Sep 4 12:44:30 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
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 (10 years, 5 months ago) by dinse
Original Path: trunk
tested some changes in the sendCommand -fct, deleted afterwards
Revision 174 - Directory Listing
Modified Fri Aug 31 08:51:54 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
added alignStructure function
Revision 173 - Directory Listing
Modified Wed Aug 29 14:03:44 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
changed for comparing contact maps
Revision 172 - Directory Listing
Modified Wed Aug 29 14:03:33 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
changed for comparing contact maps
Revision 171 - Directory Listing
Modified Wed Aug 29 14:03:02 2007 UTC (10 years, 5 months ago) by dinse
Original Path: trunk
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 (10 years, 5 months ago) by stehr
Original Path: trunk
added console message when saving to graph db
Revision 168 - Directory Listing
Modified Tue Aug 14 10:03:58 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
using new SecondaryStructure object
Revision 167 - Directory Listing
Modified Mon Aug 13 10:40:01 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
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 (10 years, 6 months ago) by stehr
Original Path: trunk
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 (10 years, 6 months ago) by stehr
Original Path: trunk
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 (10 years, 6 months ago) by stehr
Original Path: trunk
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 (10 years, 6 months ago) by stehr
Original Path: trunk
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 (10 years, 6 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
updated Manifest files and make scripts to include vecmath.jar
Revision 156 - Directory Listing
Modified Mon Jul 9 17:29:37 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
added dragging in ruler, started implementing tool bar (currently disabled)
Revision 155 - Directory Listing
Modified Mon Jul 9 15:37:26 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
updated and simplified class comments (removed class,package,author,... clutter)
Revision 144 - Directory Listing
Modified Fri Jun 29 18:00:19 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
forgot to add LoadDialogInputError to version control, should be there now
Revision 133 - Directory Listing
Modified Thu Jun 28 15:44:23 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
Added error handling for wrong pdb or cm file formats 
Revision 130 - Directory Listing
Modified Wed Jun 27 14:42:07 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
changed command string to select nodes in pymol
Revision 129 - Directory Listing
Modified Wed Jun 27 13:35:12 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
using config file
Revision 127 - Directory Listing
Modified Tue Jun 26 17:11:38 2007 UTC (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
warning dialogs in view now have consistent look
Revision 124 - Directory Listing
Modified Tue Jun 26 16:33:43 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by duarte
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
adding missing icon
Revision 119 - Directory Listing
Modified Mon Jun 25 14:27:38 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
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 (10 years, 7 months ago) by stehr
Original Path: trunk
using new pymol version with localhost as server
Revision 117 - Directory Listing
Modified Mon Jun 25 13:01:24 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
added constant USE_PYMOL to enable/disable pymol related menu items
Revision 116 - Directory Listing
Modified Mon Jun 25 10:12:14 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
fixed minor bug in make script
Revision 115 - Directory Listing
Modified Mon Jun 25 10:09:00 2007 UTC (10 years, 7 months ago) by stehr
Original Path: trunk
graph.py now being loaded from subdir 'recources'
Revision 114 - Directory Listing
Modified Fri Jun 22 09:58:05 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
some error handling for pymol output stream
Revision 113 - Directory Listing
Modified Fri Jun 22 09:22:52 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
proper error handling for loading models
Revision 112 - Directory Listing
Modified Thu Jun 21 14:54:28 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
delete temp pdb files on exit,
cleaned up constants in Start
Revision 111 - Directory Listing
Modified Wed Jun 20 15:45:40 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Minor clean up
Revision 109 - Directory Listing
Modified Wed Jun 20 11:54:33 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
added missing icons for 'View' and 'Color' menu
Revision 107 - Directory Listing
Modified Tue Jun 19 17:10:47 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
pretty icons for 'View' and 'Color' menu
Revision 106 - Directory Listing
Modified Tue Jun 19 13:34:03 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
few minor changes for 0.7 release
Revision 100 - Directory Listing
Modified Mon Jun 18 17:42:52 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
added colorMapMatlab and colorMapGrayscale (currently commented out)
Revision 98 - Directory Listing
Modified Mon Jun 18 16:37:47 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
changed color constants in contactMapPane to variables set in constructor
Revision 97 - Directory Listing
Modified Mon Jun 18 15:59:07 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
Renamed make-cmview to make-cm2pymol 
Revision 96 - Directory Listing
Modified Mon Jun 18 15:50:31 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Got rid of aglappe.jar classpath link in Manifest
Revision 94 - Directory Listing
Modified Mon Jun 18 15:30:09 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
new function: show contact density
Revision 93 - Directory Listing
Modified Mon Jun 18 09:44:27 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
NEW FEATURE: delete selected edges
Revision 89 - Directory Listing
Modified Fri Jun 15 14:51:48 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Painting residue types in rulers, not very useful
Revision 82 - Directory Listing
Modified Thu Jun 14 10:48:37 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Added selection of node neighbours, both from ruler and contact map
Revision 80 - Directory Listing
Modified Thu Jun 14 08:48:14 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
Refactored squareSelStart and squareSelEnd. Changed squareSelection method to no arguments
Revision 79 - Directory Listing
Modified Thu Jun 14 08:01:30 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
added grid and tickmarks (currently commented out)
Revision 78 - Directory Listing
Modified Wed Jun 13 16:57:42 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Using AA.contactTypes() to get the contact types
Revision 75 - Directory Listing
Modified Wed Jun 13 10:43:14 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Fixed potential bug: getContacts was deep copying, now just referencing
Revision 73 - Directory Listing
Modified Tue Jun 12 18:13:41 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
New feature: coloring edges
Revision 70 - Directory Listing
Modified Tue Jun 12 16:27:09 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
NEW FEATURE: highlight of common neighbours by size

Revision 69 - Directory Listing
Modified Tue Jun 12 15:07:13 2007 UTC (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
updated javadoc comments
Revision 65 - Directory Listing
Modified Mon Jun 11 15:19:42 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Changed to version 0.5
Revision 60 - Directory Listing
Modified Mon Jun 11 14:02:54 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
Made version a constant in Start
Revision 59 - Directory Listing
Modified Mon Jun 11 14:00:23 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Slight improvements in the mouse events, a bit better behaved
Revision 56 - Directory Listing
Modified Fri Jun 8 15:51:41 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 8 months ago) by stehr
Original Path: trunk
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 (10 years, 8 months ago) by duarte
Original Path: trunk
Put everything into packages
Revision 50 - Directory Listing
Modified Fri May 25 12:39:49 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
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 (10 years, 9 months ago) by stehr
Original Path: trunk
changes classpath in Manifest
Revision 47 - Directory Listing
Modified Thu May 24 10:29:49 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
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 (10 years, 9 months ago) by stehr
Original Path: trunk
Created different contact map data model classes
Revision 45 - Directory Listing
Modified Mon May 14 11:15:08 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
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 (10 years, 9 months ago) by stehr
Original Path: trunk
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 (10 years, 9 months ago) by stehr
Original Path: trunk
Some code cleanup, added dummy menu bar
Revision 34 - Directory Listing
Modified Thu May 10 14:41:50 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
Updated version number before tagging
Revision 33 - Directory Listing
Modified Mon May 7 14:05:46 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
Structure is now loaded automatically when contact map windows opens
Revision 32 - Directory Listing
Modified Mon May 7 10:39:50 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
Added some icons for the context menu
Revision 31 - Directory Listing
Modified Mon May 7 10:25:27 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
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 (10 years, 9 months ago) by stehr
Original Path: trunk
New functionality: context menu, see selection rectangle and coordinates while dragging
Revision 27 - Directory Listing
Modified Mon Apr 30 14:29:10 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
Fixed problems with null chain codes
Revision 26 - Directory Listing
Modified Fri Apr 27 11:13:41 2007 UTC (10 years, 9 months ago) by stehr
Original Path: trunk
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 (10 years, 9 months ago) by stehr
Original Path: trunk
Read user name from environment and run pymol automatically.
Revision 24 - Directory Listing
Modified Thu Apr 26 08:27:53 2007 UTC (10 years, 9 months ago) by duarte
Original Path: trunk
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 (10 years, 10 months ago) by stehr
Original Path: trunk
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 (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 20 - Directory Listing
Modified Fri Mar 30 13:02:24 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

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

Revision 18 - Directory Listing
Modified Thu Mar 29 15:15:01 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 17 - Directory Listing
Modified Thu Mar 29 12:57:35 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 16 - Directory Listing
Modified Thu Mar 29 12:57:18 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 15 - Directory Listing
Modified Thu Mar 29 11:51:06 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 14 - Directory Listing
Modified Thu Mar 29 11:50:56 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 13 - Directory Listing
Modified Wed Mar 28 13:40:49 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 12 - Directory Listing
Modified Wed Mar 28 13:40:39 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 11 - Directory Listing
Modified Wed Mar 28 08:07:32 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

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

Revision 9 - Directory Listing
Modified Tue Mar 27 12:46:05 2007 UTC (10 years, 10 months ago) by dinse
Original Path: trunk

Revision 8 - Directory Listing
Modified Thu Mar 22 09:16:14 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 7 - Directory Listing
Modified Tue Mar 20 09:09:46 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 6 - Directory Listing
Modified Tue Mar 20 09:09:39 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 5 - Directory Listing
Modified Mon Mar 19 08:27:34 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 4 - Directory Listing
Modified Mon Mar 19 08:27:25 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 3 - Directory Listing
Modified Mon Mar 19 08:27:16 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 2 - Directory Listing
Modified Mon Mar 19 08:27:06 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk

Revision 1 - Directory Listing
Added Wed Mar 14 09:18:10 2007 UTC (10 years, 11 months ago) by dinse
Original Path: trunk
Initial import of the CM2PyMol project