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root/cmview/branches/CMView-jung/cmview/Start.java
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Revision 249 - (view) (annotate) - [select for diffs]
Modified Tue Dec 4 15:27:58 2007 UTC (11 years, 4 months ago) by lpetzo
File length: 22875 byte(s)
Diff to previous 242
class Start:
- some changes in function preloadModel(...) due to the new loading scheme for models
- changed default settings for the contact type and the contact distance according to Michael's suggestions

class View:
- adapted new loading scheme for the models
- implemented chain code and model serial Getters for the retrieval of all present chain codes and model serials in the source
Revision 242 - (view) (annotate) - [select for diffs]
Modified Wed Nov 28 15:25:08 2007 UTC (11 years, 4 months ago) by lpetzo
File length: 22459 byte(s)
Diff to previous 239
added mapping from pdb code to the filename of the local copy of the file containing the structure
Revision 239 - (view) (annotate) - [select for diffs]
Modified Wed Nov 28 09:00:54 2007 UTC (11 years, 4 months ago) by duarte
File length: 21595 byte(s)
Diff to previous 225
Branching for development with new JUNG framework (in aglappe-jung branch)
Revision 225 - (view) (annotate) - [select for diffs]
Modified Mon Nov 12 15:53:43 2007 UTC (11 years, 5 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 21595 byte(s)
Diff to previous 213
Fixed bug: fileChooser and colorChooser were not being set with the native look and feel
Revision 213 - (view) (annotate) - [select for diffs]
Modified Fri Nov 2 17:40:49 2007 UTC (11 years, 5 months ago) by lpetzo
Original Path: trunk/cmview/Start.java
File length: 21593 byte(s)
Diff to previous 211
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 211 - (view) (annotate) - [select for diffs]
Modified Wed Oct 31 10:19:00 2007 UTC (11 years, 5 months ago) by lpetzo
Original Path: trunk/cmview/Start.java
File length: 21424 byte(s)
Diff to previous 198

Revision 198 - (view) (annotate) - [select for diffs]
Modified Wed Sep 19 14:24:30 2007 UTC (11 years, 7 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 21212 byte(s)
Diff to previous 193
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 193 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 14:13:25 2007 UTC (11 years, 7 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 21192 byte(s)
Diff to previous 191
always use Ca (or other single atom model specified in config file) for distance map calculation
Revision 191 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 10:13:53 2007 UTC (11 years, 7 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 21196 byte(s)
Diff to previous 190
added constants SHOW_ICON_BAR and ICON_BAR_FLOATABLE
Revision 190 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 08:46:31 2007 UTC (11 years, 7 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 20855 byte(s)
Diff to previous 186
updated version number to 0.8.5
Revision 186 - (view) (annotate) - [select for diffs]
Modified Thu Sep 13 16:08:14 2007 UTC (11 years, 7 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 20855 byte(s)
Diff to previous 167
New model PdbFtpModel to load from online PDB. Added to Load and Tools menu
Revision 167 - (view) (annotate) - [select for diffs]
Modified Mon Aug 13 10:40:01 2007 UTC (11 years, 8 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 20758 byte(s)
Diff to previous 166
added function call for saving to graph db, added 3 new options to config file, updated version number in Manifest
Revision 166 - (view) (annotate) - [select for diffs]
Modified Fri Aug 10 16:41:43 2007 UTC (11 years, 8 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19718 byte(s)
Diff to previous 163
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Revision 163 - (view) (annotate) - [select for diffs]
Modified Mon Aug 6 15:43:38 2007 UTC (11 years, 8 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19096 byte(s)
Diff to previous 159
printing version number of startup, added new color scheme for distance map, allow changing database in load dialogs for pdbase and msdsd
Revision 159 - (view) (annotate) - [select for diffs]
Modified Fri Jul 13 10:19:27 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19061 byte(s)
Diff to previous 151
added code to experiment with toolbar, statusbar and background loading of maps (all disabled by default)
Revision 151 - (view) (annotate) - [select for diffs]
Modified Fri Jul 6 13:06:06 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19061 byte(s)
Diff to previous 145
major code rearrangements in ContactMapPane, implemented buffering strategy for contact map and background maps, change mouse cursor to hourglass while calculating bg maps
Revision 145 - (view) (annotate) - [select for diffs]
Modified Mon Jul 2 09:45:49 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19064 byte(s)
Diff to previous 144
updated and simplified class comments (removed class,package,author,... clutter)
Revision 144 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 18:00:19 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19225 byte(s)
Diff to previous 143
made PyMolAdaptor independent of View, now a global PyMolAdaptor is created
in Start and used by all Views.
Revision 143 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 16:01:53 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 20189 byte(s)
Diff to previous 142
moved file chooser and color chooser to Start to remember last selected dir
Revision 142 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 15:29:41 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 19369 byte(s)
Diff to previous 140
added optional pymol shutdown on exit,
some cleanup of code and comments
Revision 140 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 13:11:46 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 15316 byte(s)
Diff to previous 139
still the same mac issue: try to getCanonicalPath() before running pymol executable
Revision 139 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 13:04:52 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 15312 byte(s)
Diff to previous 138
workaround for Mac: start pymol even though the executable seems not to exist
Revision 138 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 11:04:14 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 15150 byte(s)
Diff to previous 137
renamed constant DEFAULT_EDGETYPE to DEFAULT_CONTACT_TYPE and show default contact type in load dialogs
Revision 137 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 10:39:27 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 15127 byte(s)
Diff to previous 136
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 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 09:28:35 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 13928 byte(s)
Diff to previous 133
renamed file graph.py to cmview.py, renamed menu item "save config file"
Revision 133 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 15:44:23 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 13858 byte(s)
Diff to previous 132
Models catch new exceptions from Pdb and Graph classes, LoadDialog now checks user input
Revision 132 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 16:01:37 2007 UTC (11 years, 9 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 13859 byte(s)
Diff to previous 129
Now also catching SQLException for queries (as well as for connections) that were not thrown before
Revision 129 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 13:35:12 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 13929 byte(s)
Diff to previous 128
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 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 12:39:16 2007 UTC (11 years, 9 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 14096 byte(s)
Diff to previous 122
using config file
Revision 122 - (view) (annotate) - [select for diffs]
Modified Tue Jun 26 14:27:26 2007 UTC (11 years, 9 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 9406 byte(s)
Diff to previous 121
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 - (view) (annotate) - [select for diffs]
Modified Tue Jun 26 12:06:31 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 8578 byte(s)
Diff to previous 119
check for database and pymol connection on startup,
some minor rearrangements in Start
Revision 119 - (view) (annotate) - [select for diffs]
Modified Mon Jun 25 14:27:38 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 6129 byte(s)
Diff to previous 118
new context menu function: show current residue pair as edge in pymol
Revision 118 - (view) (annotate) - [select for diffs]
Modified Mon Jun 25 13:27:04 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 6147 byte(s)
Diff to previous 117
using new pymol version with localhost as server
Revision 117 - (view) (annotate) - [select for diffs]
Modified Mon Jun 25 13:01:24 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 6626 byte(s)
Diff to previous 115
added constant USE_PYMOL to enable/disable pymol related menu items
Revision 115 - (view) (annotate) - [select for diffs]
Modified Mon Jun 25 10:09:00 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 6562 byte(s)
Diff to previous 113
graph.py now being loaded from subdir 'recources'
Revision 113 - (view) (annotate) - [select for diffs]
Modified Fri Jun 22 09:22:52 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 4779 byte(s)
Diff to previous 112
proper error handling for loading models
Revision 112 - (view) (annotate) - [select for diffs]
Modified Thu Jun 21 14:54:28 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 4548 byte(s)
Diff to previous 106
delete temp pdb files on exit,
cleaned up constants in Start
Revision 106 - (view) (annotate) - [select for diffs]
Modified Tue Jun 19 13:34:03 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 4129 byte(s)
Diff to previous 104
bug fix: toggle rulers won't resize window
implemented component resize listener
Revision 104 - (view) (annotate) - [select for diffs]
Modified Tue Jun 19 12:26:30 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 4025 byte(s)
Diff to previous 101
now showing residue numbers when mouse is in ruler
updated version number for 0.7.1
Revision 101 - (view) (annotate) - [select for diffs]
Modified Tue Jun 19 09:22:37 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 4023 byte(s)
Diff to previous 86
few minor changes for 0.7 release
Revision 86 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 09:55:07 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 4599 byte(s)
Diff to previous 84
added option to restrict max seq sep when loading (many files changed)
Revision 84 - (view) (annotate) - [select for diffs]
Modified Thu Jun 14 14:42:52 2007 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 3739 byte(s)
Diff to previous 67
Back to no letters ruler. Last missing tick now shown
Rulers optional (new in View menu)
Updates for 0.6 release
Revision 67 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 12:42:35 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 3739 byte(s)
Diff to previous 66
Fixed null pointer exception in Start class when running without command line parameters.
Added functionality to select and deselect single contacts.
Revision 66 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 10:25:58 2007 UTC (11 years, 10 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 3738 byte(s)
Diff to previous 65
updated javadoc comments
Revision 65 - (view) (annotate) - [select for diffs]
Modified Mon Jun 11 15:19:42 2007 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 3589 byte(s)
Diff to previous 60
Fixed bug: taking accession code and chain code from command line now works correctly
Revision 60 - (view) (annotate) - [select for diffs]
Modified Mon Jun 11 14:02:54 2007 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 3493 byte(s)
Diff to previous 56
Made version a constant in Start
Revision 56 - (view) (annotate) - [select for diffs]
Modified Fri Jun 8 15:51:41 2007 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 3443 byte(s)
Diff to previous 52
NEW FEATURE: Now Start can take pdbCode and chainCode from command line and display default contact map for it
Revision 52 - (view) (annotate) - [select for diffs]
Modified Fri May 25 15:14:29 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/cmview/Start.java
File length: 2955 byte(s)
Diff to previous 51
removed menu item "Load Structure in Pymol",
hide crosshair when mouse is leaving contact map window
Revision 51 - (view) (annotate) - [select for diffs]
Modified Fri May 25 12:57:53 2007 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/cmview/Start.java
File length: 2827 byte(s)
Copied from: trunk/Start.java revision 50
Diff to previous 50
Put everything into packages
Revision 50 - (view) (annotate) - [select for diffs]
Modified Fri May 25 12:39:49 2007 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/Start.java
File length: 2861 byte(s)
Diff to previous 47
Got rid of OldModel, PaintController (now ContactMapPane)
Renamed MyTestPyMol to PymolAdaptor
Start is now the starting point again. Contains strictly only static methods

Revision 47 - (view) (annotate) - [select for diffs]
Modified Thu May 24 10:29:49 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 16097 byte(s)
Diff to previous 46
New version with many changes. The contact map window can now be opened directly using the main function in View.
Revision 46 - (view) (annotate) - [select for diffs]
Modified Tue May 15 14:05:56 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 15834 byte(s)
Diff to previous 45
Created different contact map data model classes
Revision 45 - (view) (annotate) - [select for diffs]
Modified Mon May 14 11:15:08 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 14899 byte(s)
Diff to previous 44
Renamed ModelTemp to Model, now it is how i wanted it to be :)
Revision 44 - (view) (annotate) - [select for diffs]
Modified Mon May 14 11:12:56 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 14903 byte(s)
Diff to previous 43
Temporary commit, extracted Interface from class Model but couldn't call it model again
Revision 43 - (view) (annotate) - [select for diffs]
Modified Mon May 14 09:03:24 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 15360 byte(s)
Diff to previous 34
Some code cleanup, added dummy menu bar
Revision 34 - (view) (annotate) - [select for diffs]
Modified Thu May 10 14:41:50 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 15286 byte(s)
Diff to previous 33
Updated version number before tagging
Revision 33 - (view) (annotate) - [select for diffs]
Modified Mon May 7 14:05:46 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 18153 byte(s)
Diff to previous 31
Structure is now loaded automatically when contact map windows opens
Revision 31 - (view) (annotate) - [select for diffs]
Modified Mon May 7 10:25:27 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 18280 byte(s)
Diff to previous 30
Changes to all classes. Now, multiple contact maps can be opened and modified in the same pymol session.
Revision 30 - (view) (annotate) - [select for diffs]
Modified Thu May 3 14:50:55 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 18175 byte(s)
Diff to previous 27
New functionality: context menu, see selection rectangle and coordinates while dragging
Revision 27 - (view) (annotate) - [select for diffs]
Modified Mon Apr 30 14:29:10 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 17802 byte(s)
Diff to previous 26
Fixed problems with null chain codes
Revision 26 - (view) (annotate) - [select for diffs]
Modified Fri Apr 27 11:13:41 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/Start.java
File length: 17357 byte(s)
Diff to previous 25
Made selecting structures nicer: Now combo boxes with preselection in the startup dialog
Revision 25 - (view) (annotate) - [select for diffs]
Modified Thu Apr 26 13:52:01 2007 UTC (12 years ago) by stehr
Original Path: trunk/Start.java
File length: 15511 byte(s)
Diff to previous 24
Read user name from environment and run pymol automatically.
Revision 24 - (view) (annotate) - [select for diffs]
Modified Thu Apr 26 08:27:53 2007 UTC (12 years ago) by duarte
Original Path: trunk/Start.java
File length: 15058 byte(s)
Diff to previous 23
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 - (view) (annotate) - [select for diffs]
Modified Wed Apr 11 14:05:18 2007 UTC (12 years ago) by stehr
Original Path: trunk/Start.java
File length: 15196 byte(s)
Diff to previous 19
Constants for accessing the database and the pymol server can now be set globally in the Start class
Revision 19 - (view) (annotate) - [select for diffs]
Modified Fri Mar 30 13:02:10 2007 UTC (12 years ago) by dinse
Original Path: trunk/Start.java
File length: 14473 byte(s)
Diff to previous 18

Revision 18 - (view) (annotate) - [select for diffs]
Modified Thu Mar 29 15:15:01 2007 UTC (12 years ago) by dinse
Original Path: trunk/Start.java
File length: 13120 byte(s)
Diff to previous 16

Revision 16 - (view) (annotate) - [select for diffs]
Added Thu Mar 29 12:57:18 2007 UTC (12 years ago) by dinse
Original Path: trunk/Start.java
File length: 12343 byte(s)

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