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Revision 249 - (view) (annotate) - [select for diffs]
Modified Tue Dec 4 15:27:58 2007 UTC (11 years, 10 months ago) by lpetzo
File length: 126461 byte(s)
Diff to previous 240
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 240 - (view) (annotate) - [select for diffs]
Modified Wed Nov 28 09:39:52 2007 UTC (11 years, 10 months ago) by duarte
File length: 121738 byte(s)
Diff to previous 239
First working version of CMView using the new JUNG framework. Needs more testing. Known bug: showing contacts in 3D in compare mode not working properly.
Fixed 2 bugs/feature requests: computation of common neighborhood sizes now fast (thanks JUNG) and residue types are now shown even for unobserved residues (when sequence is known)
Revision 239 - (view) (annotate) - [select for diffs]
Modified Wed Nov 28 09:00:54 2007 UTC (11 years, 10 months ago) by duarte
File length: 121602 byte(s)
Diff to previous 238
Branching for development with new JUNG framework (in aglappe-jung branch)
Revision 238 - (view) (annotate) - [select for diffs]
Modified Tue Nov 27 15:31:58 2007 UTC (11 years, 10 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 121602 byte(s)
Diff to previous 235
removed tbShowSel3D from the set of buttons to be disabled in function compareModeButtonAccessibility()
Revision 235 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 11:46:56 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 121633 byte(s)
Diff to previous 230
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 230 - (view) (annotate) - [select for diffs]
Modified Mon Nov 19 09:40:06 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 120741 byte(s)
Diff to previous 227
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 227 - (view) (annotate) - [select for diffs]
Modified Mon Nov 12 16:24:06 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 121632 byte(s)
Diff to previous 226
class View:
- deleted some output stuff for debugging
Revision 226 - (view) (annotate) - [select for diffs]
Modified Mon Nov 12 15:57:04 2007 UTC (11 years, 11 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 122053 byte(s)
Diff to previous 222
new feature: pairwise sequence alignment for comparison
Revision 222 - (view) (annotate) - [select for diffs]
Modified Wed Nov 7 18:21:36 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 119050 byte(s)
Diff to previous 214
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 214 - (view) (annotate) - [select for diffs]
Modified Fri Nov 2 18:03:28 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 103865 byte(s)
Diff to previous 211
- 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 211 - (view) (annotate) - [select for diffs]
Modified Wed Oct 31 10:19:00 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/cmview/View.java
File length: 91754 byte(s)
Diff to previous 206

Revision 206 - (view) (annotate) - [select for diffs]
Modified Thu Oct 11 12:52:48 2007 UTC (12 years ago) by duarte
Original Path: trunk/cmview/View.java
File length: 81060 byte(s)
Diff to previous 204
Added '...' to menus that open dialogs
Revision 204 - (view) (annotate) - [select for diffs]
Modified Thu Oct 4 13:28:44 2007 UTC (12 years ago) by dinse
Original Path: trunk/cmview/View.java
File length: 81006 byte(s)
Diff to previous 202
changed View and PyMolAdaptor for grouping in PyMol
changed colors on the ruler again
Revision 202 - (view) (annotate) - [select for diffs]
Modified Thu Sep 20 16:01:36 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 73261 byte(s)
Diff to previous 200
added contact selection by color
Revision 200 - (view) (annotate) - [select for diffs]
Modified Thu Sep 20 11:01:14 2007 UTC (12 years, 1 month ago) by dinse
Original Path: trunk/cmview/View.java
File length: 71364 byte(s)
Diff to previous 199
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 - (view) (annotate) - [select for diffs]
Modified Wed Sep 19 16:51:57 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 70756 byte(s)
Diff to previous 198
added menu item 'select by residue number'
Revision 198 - (view) (annotate) - [select for diffs]
Modified Wed Sep 19 14:24:30 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 69935 byte(s)
Diff to previous 197
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 - (view) (annotate) - [select for diffs]
Modified Wed Sep 19 12:04:13 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 69312 byte(s)
Diff to previous 196
now, selection mode buttons are also being updated when the mode is changed from somewhere else (main- or popup menu)
Revision 196 - (view) (annotate) - [select for diffs]
Modified Wed Sep 19 10:56:09 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 68372 byte(s)
Diff to previous 195
rearranged selection mode menu items and made toggle buttons for them
Revision 195 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 15:27:42 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 68123 byte(s)
Diff to previous 193
added menu items for selecting various contacts between secondary structure objects, changed title of main window when comparing
Revision 193 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 14:13:25 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 66213 byte(s)
Diff to previous 192
always use Ca (or other single atom model specified in config file) for distance map calculation
Revision 192 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 13:59:04 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 66607 byte(s)
Diff to previous 191
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 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 10:13:53 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 68238 byte(s)
Diff to previous 189
added constants SHOW_ICON_BAR and ICON_BAR_FLOATABLE
Revision 189 - (view) (annotate) - [select for diffs]
Modified Tue Sep 18 08:45:58 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 68187 byte(s)
Diff to previous 187
added difference distance map in comparison mode, updated Manifest to v0.8.5
Revision 187 - (view) (annotate) - [select for diffs]
Modified Mon Sep 17 14:25:50 2007 UTC (12 years, 1 month ago) by dinse
Original Path: trunk/cmview/View.java
File length: 66401 byte(s)
Diff to previous 186
view: inserted new icons in toolbar for contact map comparison
cmPane: adapted contact map comparison changes
PyMolAdaptor: changed edgeSelection method

Revision 186 - (view) (annotate) - [select for diffs]
Modified Thu Sep 13 16:08:14 2007 UTC (12 years, 1 month ago) by duarte
Original Path: trunk/cmview/View.java
File length: 61967 byte(s)
Diff to previous 184
New model PdbFtpModel to load from online PDB. Added to Load and Tools menu
Revision 184 - (view) (annotate) - [select for diffs]
Modified Mon Sep 10 10:33:23 2007 UTC (12 years, 1 month ago) by dinse
Original Path: trunk/cmview/View.java
File length: 59652 byte(s)
Diff to previous 177

Revision 177 - (view) (annotate) - [select for diffs]
Modified Tue Sep 4 13:17:51 2007 UTC (12 years, 1 month ago) by dinse
Original Path: trunk/cmview/View.java
File length: 54783 byte(s)
Diff to previous 176
changed viewer in comparing maps 
Revision 176 - (view) (annotate) - [select for diffs]
Modified Tue Sep 4 12:44:30 2007 UTC (12 years, 1 month ago) by dinse
Original Path: trunk/cmview/View.java
File length: 53544 byte(s)
Diff to previous 169
added specific functions and altered existing ones to show and work with the compared maps (2 different structures at the same time) 
Revision 169 - (view) (annotate) - [select for diffs]
Modified Mon Aug 27 14:30:31 2007 UTC (12 years, 1 month ago) by stehr
Original Path: trunk/cmview/View.java
File length: 42332 byte(s)
Diff to previous 168
added console message when saving to graph db
Revision 168 - (view) (annotate) - [select for diffs]
Modified Tue Aug 14 10:03:58 2007 UTC (12 years, 2 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 42310 byte(s)
Diff to previous 166
using new SecondaryStructure object
Revision 166 - (view) (annotate) - [select for diffs]
Modified Fri Aug 10 16:41:43 2007 UTC (12 years, 2 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 42303 byte(s)
Diff to previous 165
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Revision 165 - (view) (annotate) - [select for diffs]
Modified Thu Aug 9 13:48:45 2007 UTC (12 years, 2 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 42208 byte(s)
Diff to previous 163
added menu item "Save to graph db" (but implementation in Graph still missing)
Revision 163 - (view) (annotate) - [select for diffs]
Modified Mon Aug 6 15:43:38 2007 UTC (12 years, 2 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 41455 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 41462 byte(s)
Diff to previous 157
added code to experiment with toolbar, statusbar and background loading of maps (all disabled by default)
Revision 157 - (view) (annotate) - [select for diffs]
Modified Tue Jul 10 10:19:12 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 41566 byte(s)
Diff to previous 156
updated Manifest files and make scripts to include vecmath.jar
Revision 156 - (view) (annotate) - [select for diffs]
Modified Mon Jul 9 17:29:37 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 41824 byte(s)
Diff to previous 155
added dragging in ruler, started implementing tool bar (currently disabled)
Revision 155 - (view) (annotate) - [select for diffs]
Modified Mon Jul 9 15:37:26 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 39116 byte(s)
Diff to previous 153
added secondary structure selection, changes to background loading but still disabled and not really working
Revision 153 - (view) (annotate) - [select for diffs]
Modified Fri Jul 6 17:12:18 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 38754 byte(s)
Diff to previous 151
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 151 - (view) (annotate) - [select for diffs]
Modified Fri Jul 6 13:06:06 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 39178 byte(s)
Diff to previous 148
major code rearrangements in ContactMapPane, implemented buffering strategy for contact map and background maps, change mouse cursor to hourglass while calculating bg maps
Revision 148 - (view) (annotate) - [select for diffs]
Modified Wed Jul 4 13:55:03 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 37088 byte(s)
Diff to previous 145
added zoom command when showing triangles in pymol, extracted constants for (action) menu item labels, renamed icon variables
Revision 145 - (view) (annotate) - [select for diffs]
Modified Mon Jul 2 09:45:49 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35907 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35900 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35901 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 36246 byte(s)
Diff to previous 138
added optional pymol shutdown on exit,
some cleanup of code and comments
Revision 138 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 11:04:14 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 36713 byte(s)
Diff to previous 136
renamed constant DEFAULT_EDGETYPE to DEFAULT_CONTACT_TYPE and show default contact type in load dialogs
Revision 136 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 09:28:35 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 36512 byte(s)
Diff to previous 129
renamed file graph.py to cmview.py, renamed menu item "save config file"
Revision 129 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 13:35:12 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 36520 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35905 byte(s)
Diff to previous 125
using config file
Revision 125 - (view) (annotate) - [select for diffs]
Modified Tue Jun 26 17:04:47 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35624 byte(s)
Diff to previous 122
warning dialogs in view now have consistent look
Revision 122 - (view) (annotate) - [select for diffs]
Modified Tue Jun 26 14:27:26 2007 UTC (12 years, 3 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 35593 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35976 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 (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35845 byte(s)
Diff to previous 117
new context menu function: show current residue pair as edge in pymol
Revision 117 - (view) (annotate) - [select for diffs]
Modified Mon Jun 25 13:01:24 2007 UTC (12 years, 3 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 35244 byte(s)
Diff to previous 113
added constant USE_PYMOL to enable/disable pymol related menu items
Revision 113 - (view) (annotate) - [select for diffs]
Modified Fri Jun 22 09:22:52 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 33135 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 (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 32175 byte(s)
Diff to previous 111
delete temp pdb files on exit,
cleaned up constants in Start
Revision 111 - (view) (annotate) - [select for diffs]
Modified Wed Jun 20 15:45:40 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 32128 byte(s)
Diff to previous 109
Now dealing with cases when pdb is null in the Model object. 
Using new method has3DCoordinates for that
Revision 109 - (view) (annotate) - [select for diffs]
Modified Wed Jun 20 11:54:33 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 31788 byte(s)
Diff to previous 107
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 107 - (view) (annotate) - [select for diffs]
Modified Tue Jun 19 17:10:47 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 31720 byte(s)
Diff to previous 106
pretty icons for 'View' and 'Color' menu
Revision 106 - (view) (annotate) - [select for diffs]
Modified Tue Jun 19 13:34:03 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 29718 byte(s)
Diff to previous 101
bug fix: toggle rulers won't resize window
implemented component resize listener
Revision 101 - (view) (annotate) - [select for diffs]
Modified Tue Jun 19 09:22:37 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 29674 byte(s)
Diff to previous 100
few minor changes for 0.7 release
Revision 100 - (view) (annotate) - [select for diffs]
Modified Mon Jun 18 17:42:52 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 29606 byte(s)
Diff to previous 94
New feature: showing of color graded distance matrix (only single atom models)
Revision 94 - (view) (annotate) - [select for diffs]
Modified Mon Jun 18 15:30:09 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 28553 byte(s)
Diff to previous 93
new function: show contact density
Revision 93 - (view) (annotate) - [select for diffs]
Modified Mon Jun 18 09:44:27 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 28041 byte(s)
Diff to previous 92
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 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 17:13:44 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 27252 byte(s)
Diff to previous 91
added some experimental code to show multiple contact maps in one window
(currently commented out)
Revision 91 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 16:01:58 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 26712 byte(s)
Diff to previous 90
added draw contacts as crosses and draw contacts as arcs
turned out to be not useful, so they are commented out
Revision 90 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 15:28:13 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 26241 byte(s)
Diff to previous 89
NEW FEATURE: delete selected edges
Revision 89 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 14:51:48 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 25579 byte(s)
Diff to previous 88
made the way the icon files are accessed compliant with jar packaging
Revision 88 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 14:42:29 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 25613 byte(s)
Diff to previous 87
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 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 13:42:35 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 25143 byte(s)
Diff to previous 86
added SelectAll menu item, color chooser now without ugly preview panel,
selection now being reset after coloring
Revision 86 - (view) (annotate) - [select for diffs]
Modified Fri Jun 15 09:55:07 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 24399 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 (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 23977 byte(s)
Diff to previous 83
Back to no letters ruler. Last missing tick now shown
Rulers optional (new in View menu)
Updates for 0.6 release
Revision 83 - (view) (annotate) - [select for diffs]
Modified Thu Jun 14 13:27:25 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 22858 byte(s)
Diff to previous 82
Painting residue types in rulers, not very useful
Revision 82 - (view) (annotate) - [select for diffs]
Modified Thu Jun 14 10:48:37 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 22823 byte(s)
Diff to previous 81
Now repainting ResidueRuler after node neighbourhood selection
New color menu, renamed the actions
Revision 81 - (view) (annotate) - [select for diffs]
Modified Thu Jun 14 10:03:08 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 22573 byte(s)
Diff to previous 79
Added selection of node neighbours, both from ruler and contact map
Revision 79 - (view) (annotate) - [select for diffs]
Modified Thu Jun 14 08:01:30 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 22015 byte(s)
Diff to previous 78
added grid and tickmarks (currently commented out)
Revision 78 - (view) (annotate) - [select for diffs]
Modified Wed Jun 13 16:57:42 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 22000 byte(s)
Diff to previous 73
First very basic implementation of rulers: 
new class ResidueRuler and adding 2 more panes to the View frame
Revision 73 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 18:13:41 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 21600 byte(s)
Diff to previous 72
warning screen (no contact map loaded yet) for more functions (hopefully all now)
Revision 72 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 18:07:18 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 21340 byte(s)
Diff to previous 71
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 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 17:14:51 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 19628 byte(s)
Diff to previous 70
New feature: coloring edges
Revision 70 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 16:27:09 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 18801 byte(s)
Diff to previous 68
NEW FEATURE: highlight of common neighbours by size

Revision 68 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 13:35:20 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 17803 byte(s)
Diff to previous 66
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 66 - (view) (annotate) - [select for diffs]
Modified Tue Jun 12 10:25:58 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 17194 byte(s)
Diff to previous 60
updated javadoc comments
Revision 60 - (view) (annotate) - [select for diffs]
Modified Mon Jun 11 14:02:54 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 16901 byte(s)
Diff to previous 59
Made version a constant in Start
Revision 59 - (view) (annotate) - [select for diffs]
Modified Mon Jun 11 14:00:23 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 16887 byte(s)
Diff to previous 54
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 54 - (view) (annotate) - [select for diffs]
Modified Fri Jun 8 13:55:38 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 17750 byte(s)
Diff to previous 53
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 - (view) (annotate) - [select for diffs]
Modified Thu Jun 7 16:35:57 2007 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 17773 byte(s)
Diff to previous 52
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 - (view) (annotate) - [select for diffs]
Modified Fri May 25 15:14:29 2007 UTC (12 years, 4 months ago) by stehr
Original Path: trunk/cmview/View.java
File length: 17731 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 (12 years, 4 months ago) by duarte
Original Path: trunk/cmview/View.java
File length: 17659 byte(s)
Copied from: trunk/View.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 (12 years, 4 months ago) by duarte
Original Path: trunk/View.java
File length: 19978 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 20760 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 8296 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 8277 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 8285 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 8197 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 5250 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 5472 byte(s)
Diff to previous 32
Structure is now loaded automatically when contact map windows opens
Revision 32 - (view) (annotate) - [select for diffs]
Modified Mon May 7 10:39:50 2007 UTC (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 5667 byte(s)
Diff to previous 31
Added some icons for the context menu
Revision 31 - (view) (annotate) - [select for diffs]
Modified Mon May 7 10:25:27 2007 UTC (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 5240 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 5118 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 (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 4000 byte(s)
Diff to previous 25
Fixed problems with null chain codes
Revision 25 - (view) (annotate) - [select for diffs]
Modified Thu Apr 26 13:52:01 2007 UTC (12 years, 5 months ago) by stehr
Original Path: trunk/View.java
File length: 3808 byte(s)
Diff to previous 23
Read user name from environment and run pymol automatically.
Revision 23 - (view) (annotate) - [select for diffs]
Modified Wed Apr 11 14:05:18 2007 UTC (12 years, 6 months ago) by stehr
Original Path: trunk/View.java
File length: 3812 byte(s)
Diff to previous 21
Constants for accessing the database and the pymol server can now be set globally in the Start class
Revision 21 - (view) (annotate) - [select for diffs]
Modified Fri Mar 30 13:29:00 2007 UTC (12 years, 6 months ago) by dinse
Original Path: trunk/View.java
File length: 3698 byte(s)
Diff to previous 18

Revision 18 - (view) (annotate) - [select for diffs]
Modified Thu Mar 29 15:15:01 2007 UTC (12 years, 6 months ago) by dinse
Original Path: trunk/View.java
File length: 3700 byte(s)
Diff to previous 15

Revision 15 - (view) (annotate) - [select for diffs]
Modified Thu Mar 29 11:51:06 2007 UTC (12 years, 6 months ago) by dinse
Original Path: trunk/View.java
File length: 3557 byte(s)
Diff to previous 10

Revision 10 - (view) (annotate) - [select for diffs]
Modified Tue Mar 27 12:46:15 2007 UTC (12 years, 6 months ago) by dinse
Original Path: trunk/View.java
File length: 3450 byte(s)
Diff to previous 8

Revision 8 - (view) (annotate) - [select for diffs]
Modified Thu Mar 22 09:16:14 2007 UTC (12 years, 7 months ago) by dinse
Original Path: trunk/View.java
File length: 3287 byte(s)
Diff to previous 6

Revision 6 - (view) (annotate) - [select for diffs]
Modified Tue Mar 20 09:09:39 2007 UTC (12 years, 7 months ago) by dinse
Original Path: trunk/View.java
File length: 3227 byte(s)
Diff to previous 5

Revision 5 - (view) (annotate) - [select for diffs]
Modified Mon Mar 19 08:27:34 2007 UTC (12 years, 7 months ago) by dinse
Original Path: trunk/View.java
File length: 3229 byte(s)
Diff to previous 1

Revision 1 - (view) (annotate) - [select for diffs]
Added Wed Mar 14 09:18:10 2007 UTC (12 years, 7 months ago) by dinse
Original Path: trunk/View.java
File length: 2968 byte(s)
Initial import of the CM2PyMol project

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