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Revision 284 - Directory Listing
Modified Thu Dec 20 13:40:42 2007 UTC (10 years, 10 months ago) by lpetzo
... backslash at the end of the line doesn't work!
Revision 281 - Directory Listing
Modified Thu Dec 20 13:37:00 2007 UTC (10 years, 10 months ago) by lpetzo
... and also whitespace+backslash at the end of each line
Revision 278 - Directory Listing
Modified Thu Dec 20 13:28:18 2007 UTC (10 years, 10 months ago) by lpetzo
introducing line break in Class-path and putting a whitespace before each line helps to cope with long lines!
Revision 272 - Directory Listing
Modified Thu Dec 20 12:00:56 2007 UTC (10 years, 10 months ago) by lpetzo
getop lib was missing in the classpath
Revision 269 - Directory Listing
Modified Thu Dec 20 11:21:37 2007 UTC (10 years, 10 months ago) by lpetzo
adapted version information for version tag CMView-jung-0.1.2
Revision 267 - Directory Listing
Modified Wed Dec 19 16:36:41 2007 UTC (10 years, 10 months ago) by lpetzo
class Start:
minor change

class View:
- got rid of extra PyMol selection serial for nbh selections
- made pymolSelSerial static as it causes overwriting of previous selections when running more than one View instances
- adapted new naming convention for the nbh selection

class PyMolAdapter:
- implemented new function select(...) which takes the same list of arguments as the corresponding function in PyMol's python API
   -> replaces more or less function createSelectionObject(...) if used in combination with Interval.createSelectionString(TreeSet<Integer>)
   
file make-...:
added jung libraries to the classpath and the classpath as an argument to the javac command line
Revision 266 - Directory Listing
Modified Tue Dec 18 13:22:36 2007 UTC (10 years, 10 months ago) by duarte
Now disabling delete contacts in compare mode
Added getopt to class path in make script
Revision 265 - Directory Listing
Modified Tue Dec 18 11:21:00 2007 UTC (10 years, 10 months ago) by duarte
Fixed bug: CMview doesn't freeze anymore after a pymol connection is lost.
Fixed bug: loading structure into Pymol when pdb code was passed on command line wasn't working
Cleaned debugging output
Revision 264 - Directory Listing
Modified Mon Dec 17 17:33:49 2007 UTC (10 years, 10 months ago) by duarte
New feature: proper command line parameters
New feature: as many as 3 config files are now read from: system-wide file in current dir (as before), user dir and finally the one passed in command line
Now showing waiting cursors in Load dialogs (when clicking on get chains or get models or when clicking ok) and on Needleman-Wunsch sequence alignment
Revision 263 - Directory Listing
Modified Sat Dec 15 13:01:31 2007 UTC (10 years, 10 months ago) by lpetzo
added jung libraries to the class-path and the version to 0.1.1 according to the the CMView builds based on jung
Revision 261 - Directory Listing
Modified Fri Dec 14 16:38:59 2007 UTC (10 years, 10 months ago) by lpetzo
class View:
- even more changes due to the new naming convention for selections and groupings
- constructor increments a View instance counter, dispose() decrements it

class Start:
- instance counter for class View -> VIEW_INSTANCES
- only the real owner of the PyMol process is allowed to quit PyMol on exit if that is enabled
- resetting of the PyMol url in case the PyMol port differs from the default port

class PyMolAdaptor:
- added function setting the PyMol-server url
- added functionality to gather all commands in a command buffer and write them to a file at a certain time. PyMol load this file as logfile and executes the commands: flush() -> send commands to PyMol, PyMolAdapter(String,File) -> constructs adapter with url and dump-file
--> HOWEVER: this does not work! kept it for rather sentimental reason.
Revision 259 - Directory Listing
Modified Thu Dec 13 10:14:09 2007 UTC (10 years, 10 months ago) by lpetzo
changed handling of showing selected contacts in pymol. This includes:
- complete refactoring of function View.handleShowSelectedContact3D()
- new function in the PyMolAdapter to send distances, group selection and stuff
Revision 258 - Directory Listing
Modified Wed Dec 12 12:05:05 2007 UTC (10 years, 10 months ago) by stehr
adapted to changes in aglappe (Pdb objects now throwing only PdbLoadErrors instead of GetterErrors)
Revision 254 - Directory Listing
Modified Mon Dec 10 14:18:48 2007 UTC (10 years, 10 months ago) by lpetzo
comments
Revision 253 - Directory Listing
Modified Mon Dec 10 14:18:09 2007 UTC (10 years, 10 months ago) by lpetzo
class Start:
- method runPyMol(): determines port number after starting pymol in server mode. This is due to the fact that pymol tries different port numbers for running the server (starting with 9123 and so on ... )

class View:
- construction of SADPDialog without preferences and start button
Revision 252 - Directory Listing
Modified Fri Dec 7 12:07:40 2007 UTC (10 years, 10 months ago) by lpetzo
class PdbFtpModel:
- added getter function for the cif filename
- added constructor taking a File object pointing to a local copy of the mmCIF file previously loaded from ftp
- new field: cifFile

class View:
- loading from ftp makes use local caching of mmCIF files (refers to changes in doLoadFromFtp() and handleLoadFromFtp() something)

class Start:
- changed type of pdbCode2Filename form <String (-> pdbCode),String (-> filename)> to <String (-> pdbCode),File (->filename)>
Revision 251 - Directory Listing
Modified Wed Dec 5 16:53:46 2007 UTC (10 years, 10 months ago) by lpetzo
added superpositioning for each alignment routine after computing the alignment and constructing the aligned models. the superpositioning is based on the set of common contacts as defined by the alignment.
Revision 250 - Directory Listing
Modified Tue Dec 4 15:29:32 2007 UTC (10 years, 10 months ago) by lpetzo
this class is already needed in revision 248!!!
Revision 249 - Directory Listing
Modified Tue Dec 4 15:27:58 2007 UTC (10 years, 10 months ago) by lpetzo
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 248 - Directory Listing
Modified Tue Dec 4 15:26:06 2007 UTC (10 years, 10 months ago) by lpetzo
class LoadDialog:
- chain code and model serial is implemented as combo box

class *Model:
- separated constructing the objects and loading the structures from the sources
- getChains() and getModels() determine all present chain codes and model serials in the sources

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

class SADPDialog:
- some changes in function main(...) due to the new loading scheme for models

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
Revision 242 - Directory Listing
Modified Wed Nov 28 15:25:08 2007 UTC (10 years, 10 months ago) by lpetzo
added mapping from pdb code to the filename of the local copy of the file containing the structure
Revision 241 - Directory Listing
Modified Wed Nov 28 13:07:53 2007 UTC (10 years, 10 months ago) by duarte
Refactoring of getNbhood methods to match new names in aglappe-jung
Revision 240 - Directory Listing
Modified Wed Nov 28 09:39:52 2007 UTC (10 years, 10 months ago) by duarte
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 - Directory Listing
Modified Wed Nov 28 09:00:54 2007 UTC (10 years, 10 months ago) by duarte
Copied from: trunk revision 238
Branching for development with new JUNG framework (in aglappe-jung branch)
Revision 238 - Directory Listing
Modified Tue Nov 27 15:31:58 2007 UTC (10 years, 10 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, 10 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 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, 11 months ago) by lpetzo
Original Path: trunk

Revision 210 - Directory Listing
Modified Thu Oct 25 15:02:04 2007 UTC (10 years, 11 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 (11 years 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 (11 years 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 (11 years 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 (11 years 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 (11 years 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 (11 years 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 (11 years, 1 month ago) by stehr
Original Path: trunk
added contact selection by color
Revision 201 - Directory Listing
Modified Thu Sep 20 14:54:43 2007 UTC (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month ago) by dinse
Original Path: trunk
changed colours of rulers
Revision 184 - Directory Listing
Modified Mon Sep 10 10:33:23 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk

Revision 183 - Directory Listing
Modified Thu Sep 6 13:54:21 2007 UTC (11 years, 1 month 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 (11 years, 1 month ago) by dinse
Original Path: trunk

Revision 181 - Directory Listing
Modified Thu Sep 6 08:05:07 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk
changed objectSelName - output to PyMol
Revision 180 - Directory Listing
Modified Tue Sep 4 13:20:16 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk

Revision 179 - Directory Listing
Modified Tue Sep 4 13:20:09 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk

Revision 178 - Directory Listing
Modified Tue Sep 4 13:19:55 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk
changed selections for comparing maps 
Revision 177 - Directory Listing
Modified Tue Sep 4 13:17:51 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk
changed viewer in comparing maps 
Revision 176 - Directory Listing
Modified Tue Sep 4 12:44:30 2007 UTC (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month ago) by dinse
Original Path: trunk
added alignStructure function
Revision 173 - Directory Listing
Modified Wed Aug 29 14:03:44 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk
changed for comparing contact maps
Revision 172 - Directory Listing
Modified Wed Aug 29 14:03:33 2007 UTC (11 years, 1 month ago) by dinse
Original Path: trunk
changed for comparing contact maps
Revision 171 - Directory Listing
Modified Wed Aug 29 14:03:02 2007 UTC (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 2 months ago) by stehr
Original Path: trunk
using new SecondaryStructure object
Revision 167 - Directory Listing
Modified Mon Aug 13 10:40:01 2007 UTC (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 months ago) by stehr
Original Path: trunk
using config file
Revision 127 - Directory Listing
Modified Tue Jun 26 17:11:38 2007 UTC (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 months ago) by stehr
Original Path: trunk
adding missing icon
Revision 119 - Directory Listing
Modified Mon Jun 25 14:27:38 2007 UTC (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 3 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 months ago) by duarte
Original Path: trunk
Minor clean up
Revision 109 - Directory Listing
Modified Wed Jun 20 11:54:33 2007 UTC (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 months ago) by duarte
Original Path: trunk
New feature: coloring edges
Revision 70 - Directory Listing
Modified Tue Jun 12 16:27:09 2007 UTC (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 months ago) by stehr
Original Path: trunk
updated javadoc comments
Revision 65 - Directory Listing
Modified Mon Jun 11 15:19:42 2007 UTC (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 months ago) by duarte
Original Path: trunk
Put everything into packages
Revision 50 - Directory Listing
Modified Fri May 25 12:39:49 2007 UTC (11 years, 4 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 (11 years, 4 months ago) by stehr
Original Path: trunk
changes classpath in Manifest
Revision 47 - Directory Listing
Modified Thu May 24 10:29:49 2007 UTC (11 years, 4 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 6 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 (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 20 - Directory Listing
Modified Fri Mar 30 13:02:24 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 19 - Directory Listing
Modified Fri Mar 30 13:02:10 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 18 - Directory Listing
Modified Thu Mar 29 15:15:01 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 17 - Directory Listing
Modified Thu Mar 29 12:57:35 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 16 - Directory Listing
Modified Thu Mar 29 12:57:18 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 15 - Directory Listing
Modified Thu Mar 29 11:51:06 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 14 - Directory Listing
Modified Thu Mar 29 11:50:56 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 13 - Directory Listing
Modified Wed Mar 28 13:40:49 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 12 - Directory Listing
Modified Wed Mar 28 13:40:39 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 11 - Directory Listing
Modified Wed Mar 28 08:07:32 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 10 - Directory Listing
Modified Tue Mar 27 12:46:15 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 9 - Directory Listing
Modified Tue Mar 27 12:46:05 2007 UTC (11 years, 6 months ago) by dinse
Original Path: trunk

Revision 8 - Directory Listing
Modified Thu Mar 22 09:16:14 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk

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

Revision 6 - Directory Listing
Modified Tue Mar 20 09:09:39 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk

Revision 5 - Directory Listing
Modified Mon Mar 19 08:27:34 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk

Revision 4 - Directory Listing
Modified Mon Mar 19 08:27:25 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk

Revision 3 - Directory Listing
Modified Mon Mar 19 08:27:16 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk

Revision 2 - Directory Listing
Modified Mon Mar 19 08:27:06 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk

Revision 1 - Directory Listing
Added Wed Mar 14 09:18:10 2007 UTC (11 years, 7 months ago) by dinse
Original Path: trunk
Initial import of the CM2PyMol project