[biojava] Log of /biojava-live/trunk/biojava3-structure-gui

Revision 10099 - Directory Listing
Modified Wed Mar 20 00:41:31 2013 UTC (8 weeks, 3 days ago) by andreas

fixing broken print functionality

Revision 10098 - Directory Listing
Modified Tue Mar 19 23:39:21 2013 UTC (8 weeks, 3 days ago) by blivens

Reverting debugging statements introduced in r10020

Revision 10080 - Directory Listing
Modified Wed Mar 6 20:16:36 2013 UTC (2 months, 1 week ago) by andreas

cleaning up compile warnings

Revision 10079 - Directory Listing
Modified Wed Mar 6 20:16:04 2013 UTC (2 months, 1 week ago) by andreas

update to latest jmol in maven central: 13.0.12

Revision 10068 - Directory Listing
Modified Fri Mar 1 01:46:12 2013 UTC (2 months, 2 weeks ago) by blivens

Refactored RotationAxis & added documentation

Revision 10064 - Directory Listing
Modified Wed Feb 27 02:29:16 2013 UTC (2 months, 2 weeks ago) by andreas

new method to create jmol script

Revision 10037 - Directory Listing
Modified Sat Feb 23 04:26:22 2013 UTC (2 months, 3 weeks ago) by andreas

switching to latest Jmol from Maven central

Revision 10036 - Directory Listing
Modified Sat Feb 23 04:22:14 2013 UTC (2 months, 3 weeks ago) by andreas

upgrading to Jmol 13.0.13

Revision 10035 - Directory Listing
Modified Sat Feb 23 04:22:00 2013 UTC (2 months, 3 weeks ago) by andreas

upgrading to Jmol 13.0.13

Revision 10020 - Directory Listing
Modified Thu Feb 21 03:41:03 2013 UTC (2 months, 3 weeks ago) by blivens

RotatonAxis: Handle translational alignments (<5 deg)

Revision 10019 - Directory Listing
Modified Thu Feb 21 01:50:38 2013 UTC (2 months, 3 weeks ago) by blivens

Added constructor to RotationAxis

Revision 10018 - Directory Listing
Modified Thu Feb 21 01:00:22 2013 UTC (2 months, 3 weeks ago) by blivens

Added RotationAxis, which calculates (and displays) the axis of rotation for alignments.

Revision 10009 - Directory Listing
Modified Tue Feb 12 02:23:23 2013 UTC (3 months ago) by andreas

fixing problem with custom file uploads in UI

Revision 10002 - Directory Listing
Modified Mon Feb 11 19:01:18 2013 UTC (3 months ago) by andreas

refactoring DB search code to be independent of UI

Revision 9941 - Directory Listing
Modified Fri Nov 30 18:52:08 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9939 - Directory Listing
Modified Fri Nov 30 18:52:01 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.5

Revision 9901 - Directory Listing
Modified Tue Nov 20 01:29:17 2012 UTC (5 months, 3 weeks ago) by andreas

more docu and nice example

Revision 9886 - Directory Listing
Modified Sat Nov 10 18:04:28 2012 UTC (6 months ago) by andreas

update of url

Revision 9885 - Directory Listing
Modified Sat Nov 10 18:04:10 2012 UTC (6 months ago) by andreas

should take distribution config from parent

Revision 9801 - Directory Listing
Modified Tue Oct 23 19:07:18 2012 UTC (6 months, 3 weeks ago) by andreas

now with generic support for domain IDs

Revision 9800 - Directory Listing
Modified Tue Oct 23 19:06:55 2012 UTC (6 months, 3 weeks ago) by andreas

now with generic support for domain IDs

Revision 9799 - Directory Listing
Modified Tue Oct 23 19:06:22 2012 UTC (6 months, 3 weeks ago) by andreas

changing label

Revision 9741 - Directory Listing
Modified Fri Jun 29 20:56:04 2012 UTC (10 months, 2 weeks ago) by andreas

more demos for visualizing biological assemblies

Revision 9713 - Directory Listing
Modified Thu Jun 14 06:16:14 2012 UTC (11 months ago) by andreas

smarter UI behaviour for fetching suggestions

Revision 9712 - Directory Listing
Modified Thu Jun 14 01:41:27 2012 UTC (11 months ago) by andreas

Nicer loading animation and making sure there is no memory leak.

Revision 9691 - Directory Listing
Modified Wed Jun 6 00:42:30 2012 UTC (11 months, 1 week ago) by andreas

now printing some startup info

Revision 9683 - Directory Listing
Modified Tue Jun 5 21:57:42 2012 UTC (11 months, 1 week ago) by andreas

less verbose

Revision 9680 - Directory Listing
Modified Tue Jun 5 17:20:47 2012 UTC (11 months, 1 week ago) by andreas

catching a possible nullpointer exception

Revision 9677 - Directory Listing
Modified Tue Jun 5 17:08:36 2012 UTC (11 months, 1 week ago) by andreas

small cleanup

Revision 9671 - Directory Listing
Modified Wed May 30 21:56:06 2012 UTC (11 months, 2 weeks ago) by andreas

allows more manipulation of jmol from the outside...

Revision 9669 - Directory Listing
Modified Wed May 30 18:28:39 2012 UTC (11 months, 2 weeks ago) by andreas

Demo how to access the biological assembly of a protein

Revision 9645 - Directory Listing
Modified Tue May 22 03:42:41 2012 UTC (11 months, 3 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9643 - Directory Listing
Modified Tue May 22 03:42:34 2012 UTC (11 months, 3 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.4

Revision 9629 - Directory Listing
Modified Thu May 3 17:21:04 2012 UTC (12 months, 2 weeks ago) by andreas

now correctly setting the structure name. This broke the XML export...

Revision 9613 - Directory Listing
Modified Wed Mar 28 06:52:52 2012 UTC (13 months, 3 weeks ago) by blivens

Added DemoAlignmentFromFasta, to show how to read a structural alignment from a fasta file.

Simplified DemoStructureFromFasta to make it more suitable for a cookbook recipe.

Revision 9608 - Directory Listing
Modified Tue Mar 27 21:34:42 2012 UTC (13 months, 3 weeks ago) by blivens

Added DemoStructureFromFasta.

Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.

Revision 9590 - Directory Listing
Modified Fri Mar 16 22:28:32 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9588 - Directory Listing
Modified Fri Mar 16 22:28:24 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.3

Revision 9520 - Directory Listing
Modified Fri Feb 3 22:54:57 2012 UTC (15 months, 1 week ago) by andreas

new gradient

Revision 9503 - Directory Listing
Modified Mon Jan 16 11:38:35 2012 UTC (16 months ago) by rthornton

Simplified boolean expressions.

Revision 9469 - Directory Listing
Modified Thu Dec 1 19:39:23 2011 UTC (17 months, 2 weeks ago) by andreas

colors were switched for multi block alignments

Revision 9300 - Directory Listing
Modified Thu Oct 6 15:55:49 2011 UTC (19 months, 1 week ago) by andreas

slowly starting to break this up in two classes - a UI class and a class for doing the actual DB scan.

Revision 9279 - Directory Listing
Modified Mon Sep 26 23:48:36 2011 UTC (19 months, 3 weeks ago) by andreas

now supports loading from a URL - for webstart

Revision 9278 - Directory Listing
Modified Mon Sep 26 23:48:05 2011 UTC (19 months, 3 weeks ago) by andreas

now supports loading from a URL - for webstart

Revision 9277 - Directory Listing
Modified Mon Sep 26 21:11:06 2011 UTC (19 months, 3 weeks ago) by andreas

adding support for description column

Revision 9276 - Directory Listing
Modified Mon Sep 26 21:10:56 2011 UTC (19 months, 3 weeks ago) by andreas

adding support for description column

Revision 9275 - Directory Listing
Modified Mon Sep 26 21:10:31 2011 UTC (19 months, 3 weeks ago) by andreas

adding support for description column

Revision 9273 - Directory Listing
Modified Mon Sep 26 20:35:24 2011 UTC (19 months, 3 weeks ago) by andreas

now writing some of the CE parameters into output files

Revision 9272 - Directory Listing
Modified Mon Sep 26 20:34:35 2011 UTC (19 months, 3 weeks ago) by andreas

now writing some of the CE parameters into output files

Revision 9267 - Directory Listing
Modified Sat Sep 24 22:36:37 2011 UTC (19 months, 3 weeks ago) by andreas

several improvements for better dealing with alignments of domains and fetching domain definitions from remote services.

Revision 9263 - Directory Listing
Modified Thu Sep 22 01:38:34 2011 UTC (19 months, 3 weeks ago) by andreas

simplifying example for how to show a structure in Jmol

Revision 9261 - Directory Listing
Modified Wed Sep 21 21:34:35 2011 UTC (19 months, 3 weeks ago) by andreas

now uses local PDP to suggest domains.

Revision 9258 - Directory Listing
Modified Wed Sep 21 21:17:37 2011 UTC (19 months, 3 weeks ago) by andreas

using the new auto-suggest panel for suggesting SCOP domains.

Revision 9257 - Directory Listing
Modified Wed Sep 21 21:16:52 2011 UTC (19 months, 3 weeks ago) by andreas

new CE parameter: run Ce while slightly preferring the alignment of sequence conserved residues

Revision 9256 - Directory Listing
Modified Wed Sep 21 21:16:13 2011 UTC (19 months, 3 weeks ago) by andreas

new %sequence ID column in DB search results

Revision 9255 - Directory Listing
Modified Wed Sep 21 21:15:38 2011 UTC (19 months, 3 weeks ago) by andreas

using the new auto-suggest panel for suggesting SCOP domains.

Revision 9254 - Directory Listing
Modified Wed Sep 21 21:15:04 2011 UTC (19 months, 3 weeks ago) by andreas

new %sequence ID column in DB search results

Revision 9253 - Directory Listing
Modified Wed Sep 21 21:13:52 2011 UTC (19 months, 3 weeks ago) by andreas

using the new auto-suggest panel for suggesting SCOP domains.

Revision 9252 - Directory Listing
Modified Wed Sep 21 21:13:06 2011 UTC (19 months, 3 weeks ago) by andreas

new %sequence ID column in DB search results

Revision 9251 - Directory Listing
Modified Wed Sep 21 21:12:31 2011 UTC (19 months, 3 weeks ago) by andreas

adding a new panel that can do auto-suggestions

Revision 9237 - Directory Listing
Modified Wed Sep 14 19:01:35 2011 UTC (20 months ago) by andreas

don't overwrite the name that is assigned by AtomCache (unless there is no name)

Revision 9236 - Directory Listing
Modified Wed Sep 14 19:00:54 2011 UTC (20 months ago) by andreas

using the name that gets assigned by StructureTools.getSubRanges

Revision 9234 - Directory Listing
Modified Wed Sep 14 18:59:20 2011 UTC (20 months ago) by andreas

fixing a problem, that the name did not get written correctly in DB search results

Revision 9226 - Directory Listing
Modified Tue Sep 13 00:34:30 2011 UTC (20 months ago) by blivens

Modified the ParameterGUI to check both the getParameter and isParameter forms of getters, to better support booleans.

Revision 9221 - Directory Listing
Modified Mon Sep 12 21:03:00 2011 UTC (20 months ago) by blivens

Added comments to JMatrixPanel to clarify the orientation of the matrix.

Revision 9169 - Directory Listing
Modified Fri Sep 2 15:17:53 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9167 - Directory Listing
Modified Fri Sep 2 15:17:45 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.2

Revision 9164 - Directory Listing
Modified Wed Aug 31 18:23:41 2011 UTC (20 months, 2 weeks ago) by andreas

bean-ifying access methods

Revision 9151 - Directory Listing
Modified Wed Aug 31 06:05:45 2011 UTC (20 months, 2 weeks ago) by andreas

fixing all javadoc warnings in biojava-structure-gui

Revision 9130 - Directory Listing
Modified Wed Aug 31 04:22:13 2011 UTC (20 months, 2 weeks ago) by andreas

deleting files that should not be in svn

Revision 9126 - Directory Listing
Modified Wed Aug 31 04:04:31 2011 UTC (20 months, 2 weeks ago) by andreas

cleaning pom files, removing warnings.

Revision 9123 - Directory Listing
Modified Wed Aug 31 02:12:49 2011 UTC (20 months, 2 weeks ago) by blivens

Removed/suppressed some warnings

Revision 9122 - Directory Listing
Modified Wed Aug 31 02:08:52 2011 UTC (20 months, 2 weeks ago) by blivens

Refactored CeMain and CeCPMain to improve isolation of the circular permutation code. To check for CPs, use CeCPMain rather than setting a parameter to CeMain.

Revision 9115 - Directory Listing
Modified Tue Aug 30 17:57:56 2011 UTC (20 months, 2 weeks ago) by andreas

default config now comes from PDB_DIR env variable

Revision 9113 - Directory Listing
Modified Tue Aug 30 09:44:31 2011 UTC (20 months, 2 weeks ago) by blivens

Added default constructors for AtomCache and SCOPInstallation with reasonable file paths.

Revision 9079 - Directory Listing
Modified Wed Aug 24 19:07:14 2011 UTC (20 months, 3 weeks ago) by andreas

javadoc improvement

Revision 9078 - Directory Listing
Modified Wed Aug 24 19:06:39 2011 UTC (20 months, 3 weeks ago) by andreas

update to new Scop interfaces

Revision 9077 - Directory Listing
Modified Wed Aug 24 19:06:05 2011 UTC (20 months, 3 weeks ago) by andreas

update to new Scop interfaces

Revision 9076 - Directory Listing
Modified Wed Aug 24 19:05:07 2011 UTC (20 months, 3 weeks ago) by andreas

now support scop domain ids

Revision 9075 - Directory Listing
Modified Wed Aug 24 19:02:54 2011 UTC (20 months, 3 weeks ago) by andreas

cleanup

Revision 9074 - Directory Listing
Modified Wed Aug 24 19:02:30 2011 UTC (20 months, 3 weeks ago) by andreas

cleanup

Revision 9063 - Directory Listing
Modified Mon Aug 15 14:09:21 2011 UTC (21 months ago) by andreas

now checking if the groups have any atoms (can be the case in c-alpha only representation)

Revision 9015 - Directory Listing
Modified Fri Jun 24 22:17:32 2011 UTC (22 months, 3 weeks ago) by andreas

moved a utility method from DisplayAFP to AFPAlignmentDisplay

Revision 9010 - Directory Listing
Modified Thu Jun 23 23:50:08 2011 UTC (22 months, 3 weeks ago) by andreas

new method for accessing jmolscript for alignment blocks

Revision 9009 - Directory Listing
Modified Thu Jun 23 23:49:46 2011 UTC (22 months, 3 weeks ago) by andreas

now using ScopDatabase interface

Revision 8954 - Directory Listing
Modified Wed May 18 17:57:33 2011 UTC (2 years ago) by andreas

remove white spaces from user input

Revision 8941 - Directory Listing
Modified Mon May 16 21:44:40 2011 UTC (2 years ago) by andreas

now can deal with custom user provided PDB files (and chain Id) via URLs

Revision 8924 - Directory Listing
Modified Tue May 10 02:29:47 2011 UTC (2 years ago) by andreas

adding a new Gradient 0..100

Revision 8923 - Directory Listing
Modified Tue May 10 02:28:54 2011 UTC (2 years ago) by andreas

providing access method for JFrame

Revision 8896 - Directory Listing
Modified Mon Apr 25 23:14:25 2011 UTC (2 years ago) by andreas

now a static method

Revision 8895 - Directory Listing
Modified Mon Apr 25 23:13:52 2011 UTC (2 years ago) by andreas

new utility method for creating fake structure objects

Revision 8894 - Directory Listing
Modified Mon Apr 25 22:56:38 2011 UTC (2 years ago) by andreas

fixing an error if no scop domains are found

Revision 8893 - Directory Listing
Modified Mon Apr 25 22:55:38 2011 UTC (2 years ago) by andreas

workaround for out of index error

Revision 8831 - Directory Listing
Modified Wed Mar 9 20:06:17 2011 UTC (2 years, 2 months ago) by andreas

demo how to show a structure in jmol

Revision 8828 - Directory Listing
Modified Sun Mar 6 22:57:39 2011 UTC (2 years, 2 months ago) by blivens

Added additional gradients to ScaleableMatrixPanel, and fixed a few bugs.

Revision 8808 - Directory Listing
Modified Wed Feb 23 23:47:45 2011 UTC (2 years, 2 months ago) by blivens

Added a gradient selector to the top of dot plots

Revision 8789 - Directory Listing
Modified Fri Feb 18 22:22:54 2011 UTC (2 years, 2 months ago) by blivens

Improved DotPlot coloring.

 - Added structure.gui.util.color package, which includes methods for calculating gradients and mapping colors to values
 - Moved ColorUtils class into color package
 - Improve ScaleableMatrixPanel to allow non-integer amounts of scaling. This sometimes introduces artifacts into the display due to a bug in JMatrixPanel, but leads to smoother zooming.
 

For examples of generating gradients, see the main method of GradientMapper.

Revision 8778 - Directory Listing
Modified Tue Feb 15 05:29:36 2011 UTC (2 years, 3 months ago) by andreas

fixing dependency on previous version of core

Revision 8752 - Directory Listing
Modified Mon Feb 14 04:49:52 2011 UTC (2 years, 3 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8750 - Directory Listing
Modified Mon Feb 14 04:49:40 2011 UTC (2 years, 3 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.1

Revision 8715 - Directory Listing
Modified Thu Feb 3 06:06:44 2011 UTC (2 years, 3 months ago) by andreas

fix for structures with more than 6 domains

Revision 8671 - Directory Listing
Modified Mon Jan 17 19:50:37 2011 UTC (2 years, 4 months ago) by andreas

cleanup of non UTF characters

Revision 8670 - Directory Listing
Modified Mon Jan 17 07:39:56 2011 UTC (2 years, 4 months ago) by andreas

now depends on 3.0.1-SNAPSHOT

Revision 8668 - Directory Listing
Modified Mon Jan 17 07:36:33 2011 UTC (2 years, 4 months ago) by andreas

fixing jmol script errors for single chain scop domains

Revision 8667 - Directory Listing
Modified Mon Jan 17 07:22:10 2011 UTC (2 years, 4 months ago) by andreas

now can show SCOP and PDP domains

Revision 8666 - Directory Listing
Modified Mon Jan 17 07:21:50 2011 UTC (2 years, 4 months ago) by andreas

now can show SCOP and PDP domains

Revision 8648 - Directory Listing
Modified Tue Dec 28 17:33:53 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8646 - Directory Listing
Modified Tue Dec 28 17:33:41 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0

Revision 8627 - Directory Listing
Modified Sun Dec 19 10:37:20 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8625 - Directory Listing
Modified Sun Dec 19 10:37:07 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta4

Revision 8621 - Directory Listing
Modified Sun Dec 19 10:14:01 2010 UTC (2 years, 4 months ago) by andreas

javadoc

Revision 8620 - Directory Listing
Modified Sun Dec 19 10:12:30 2010 UTC (2 years, 4 months ago) by andreas

 javadoc

Revision 8619 - Directory Listing
Modified Sun Dec 19 08:49:12 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

Revision 8618 - Directory Listing
Modified Sun Dec 19 08:45:52 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

Revision 8617 - Directory Listing
Modified Sun Dec 19 08:44:53 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

Revision 8616 - Directory Listing
Modified Sun Dec 19 08:41:28 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

Revision 8606 - Directory Listing
Modified Sat Dec 18 13:19:44 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

Revision 8605 - Directory Listing
Modified Sat Dec 18 13:17:53 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

Revision 8604 - Directory Listing
Modified Sat Dec 18 13:17:16 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warnings

Revision 8603 - Directory Listing
Modified Sat Dec 18 13:14:38 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

Revision 8602 - Directory Listing
Modified Sat Dec 18 13:12:57 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

Revision 8601 - Directory Listing
Modified Sat Dec 18 13:12:12 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

Revision 8600 - Directory Listing
Modified Sat Dec 18 13:11:12 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

Revision 8589 - Directory Listing
Modified Fri Dec 17 12:12:02 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8587 - Directory Listing
Modified Fri Dec 17 12:11:49 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta3

Revision 8577 - Directory Listing
Modified Sun Nov 28 23:47:56 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

Revision 8576 - Directory Listing
Modified Sun Nov 28 22:07:07 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

Revision 8500 - Directory Listing
Modified Wed Nov 24 01:51:29 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8498 - Directory Listing
Modified Wed Nov 24 01:51:21 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta1

Revision 8496 - Directory Listing
Modified Wed Nov 24 01:46:28 2010 UTC (2 years, 5 months ago) by andreas

fixing bad character

Revision 8495 - Directory Listing
Modified Wed Nov 24 01:45:19 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] rollback the release of biojava-3.0-beta1

Revision 8494 - Directory Listing
Modified Wed Nov 24 01:32:29 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8492 - Directory Listing
Modified Wed Nov 24 01:32:21 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta1

Revision 8489 - Directory Listing
Modified Wed Nov 24 01:26:58 2010 UTC (2 years, 5 months ago) by andreas

setting correct project version

Revision 8471 - Directory Listing
Modified Mon Nov 22 18:37:10 2010 UTC (2 years, 5 months ago) by andreas
Copied from: biojava-live/trunk/structure-gui revision 8470

proper biojava3 namespace now

Revision 8450 - Directory Listing
Modified Mon Nov 22 17:38:51 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8448 - Directory Listing
Modified Mon Nov 22 17:38:42 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha6

Revision 8447 - Directory Listing
Modified Fri Nov 19 23:29:42 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

small UI improvements

Revision 8445 - Directory Listing
Modified Fri Nov 19 23:18:08 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

enabling saving of state

Revision 8444 - Directory Listing
Modified Fri Nov 19 23:17:47 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

enabling saving of state

Revision 8441 - Directory Listing
Modified Fri Nov 19 22:01:40 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Upgrade to latest Jmol (12.0.22)

Revision 8440 - Directory Listing
Modified Fri Nov 19 22:01:18 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding more options to the Jmol display

Revision 8431 - Directory Listing
Modified Fri Nov 19 00:37:58 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

This color scheme is more friendly for color blind.

Revision 8418 - Directory Listing
Modified Sat Nov 13 18:47:35 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8416 - Directory Listing
Modified Sat Nov 13 18:47:27 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha5

Revision 8388 - Directory Listing
Modified Sat Oct 30 10:46:37 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8386 - Directory Listing
Modified Sat Oct 30 10:46:28 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha4

Revision 8383 - Directory Listing
Modified Fri Oct 29 22:23:15 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8381 - Directory Listing
Modified Fri Oct 29 22:23:07 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha3

Revision 8353 - Directory Listing
Modified Fri Oct 22 17:35:31 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8351 - Directory Listing
Modified Fri Oct 22 17:35:22 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha2

Revision 8339 - Directory Listing
Modified Thu Oct 21 22:11:27 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now with correct artifact version nr

Revision 8314 - Directory Listing
Modified Sat Oct 16 02:44:51 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8312 - Directory Listing
Modified Sat Oct 16 02:44:43 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha1

Revision 8310 - Directory Listing
Modified Sat Oct 16 02:37:32 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] rollback the release of biojava-3.0-alpha1

Revision 8308 - Directory Listing
Modified Sat Oct 16 02:07:11 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha1

Revision 8307 - Directory Listing
Modified Sat Oct 16 01:44:19 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8304 - Directory Listing
Modified Sat Oct 16 00:49:02 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] rollback the release of biojava-3.0-alpha1

Revision 8303 - Directory Listing
Modified Sat Oct 16 00:11:55 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare for next development iteration

Revision 8293 - Directory Listing
Modified Fri Oct 15 22:51:13 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

[maven-release-plugin] prepare release biojava-3.0-alpha1

Revision 8236 - Directory Listing
Modified Thu Sep 9 18:01:22 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

slightly better looking input form

Revision 8235 - Directory Listing
Modified Thu Sep 9 18:00:48 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

new menu item for showing PDB ids

Revision 8208 - Directory Listing
Modified Sat Aug 14 01:23:06 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

replacing core dependency with new biojava3-core and biojava3-alignment dependencies

Revision 8189 - Directory Listing
Modified Wed Aug 11 01:54:25 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

starting to depend on new biojava3-core

Revision 8186 - Directory Listing
Modified Wed Aug 11 01:51:08 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

better multi-threaded execution of structure alignments triggered via the user interface

Revision 8108 - Directory Listing
Modified Fri Jul 16 21:53:06 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now antialias is on by default

Revision 8107 - Directory Listing
Modified Fri Jul 16 21:52:16 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now antialias is on by default

Revision 8106 - Directory Listing
Modified Fri Jul 16 21:43:55 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding a dialog for fetching structures by their IDs

Revision 8105 - Directory Listing
Modified Fri Jul 16 21:43:40 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding a dialog for fetching structures by their IDs

Revision 8065 - Directory Listing
Modified Wed Jun 30 23:55:44 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding support for SCOP also to user interface

Revision 8064 - Directory Listing
Modified Wed Jun 30 23:55:29 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding support for SCOP also to user interface

Revision 8063 - Directory Listing
Modified Wed Jun 30 23:55:12 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding support for SCOP also to user interface

Revision 8040 - Directory Listing
Modified Mon Jun 28 22:16:21 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

making sure test passes...

Revision 8038 - Directory Listing
Modified Sat Jun 26 20:22:57 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

having problems with cruisecontrol in headless mode with this test. disabling for now

Revision 8037 - Directory Listing
Modified Sat Jun 26 20:22:13 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

having problems with cruisecontrol in headless mode with this test. disabling for now

Revision 8028 - Directory Listing
Modified Fri Jun 25 04:11:28 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

this tests cant be run in headless mode, adding check for that

Revision 8025 - Directory Listing
Modified Thu Jun 24 23:25:48 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

this tests cant be run in headless mode, adding check for that

Revision 8020 - Directory Listing
Modified Thu Jun 24 01:42:14 2010 UTC (2 years, 10 months ago) by blivens
Original Path: biojava-live/trunk/structure-gui

Introduced a "View Aligned Pairs" menu option in the alignment GUI, which formats an alignment as a list of equivalent residues. It can be called programmatically from AfpChainWriter.toAlignedPairs().

Revision 8017 - Directory Listing
Modified Wed Jun 23 02:43:00 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

these tests cant be run in headless mode, adding check for that

Revision 8013 - Directory Listing
Modified Tue Jun 22 23:48:30 2010 UTC (2 years, 10 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

mini cleanup

Revision 7977 - Directory Listing
Modified Thu Jun 17 17:23:14 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

support for config of new parameters

Revision 7976 - Directory Listing
Modified Thu Jun 17 17:15:46 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

New FileParsingParameter class

Revision 7862 - Directory Listing
Modified Sat May 29 07:51:36 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now shorter...

Revision 7861 - Directory Listing
Modified Sat May 29 06:52:14 2010 UTC (2 years, 11 months ago) by blivens
Original Path: biojava-live/trunk/structure-gui

minor change: removed user-specific path from DotPlotPanel

Revision 7853 - Directory Listing
Modified Fri May 28 21:31:23 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

demo for how to run a web start client

Revision 7847 - Directory Listing
Modified Thu May 27 23:02:34 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

some cleanup

Revision 7827 - Directory Listing
Modified Wed May 26 21:01:36 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing problem if alignment too short

Revision 7815 - Directory Listing
Modified Tue May 25 21:23:26 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

better display of multi block alignments

Revision 7806 - Directory Listing
Modified Thu May 20 17:13:37 2010 UTC (2 years, 11 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

coloring the 2nd chain slightly lighter

Revision 7805 - Directory Listing
Modified Wed May 19 00:16:57 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

more display issues fixed...

Revision 7804 - Directory Listing
Modified Tue May 18 21:12:14 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Cleanup in 3D alignment display, fixed issues with CE-CP and fatcat flexible

Revision 7773 - Directory Listing
Modified Fri May 7 02:12:05 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing a rotation problem

Revision 7772 - Directory Listing
Modified Fri May 7 02:11:16 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

cleanup warning

Revision 7771 - Directory Listing
Modified Fri May 7 02:10:18 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now with support for coloring multi blocks

Revision 7756 - Directory Listing
Modified Wed May 5 07:38:37 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now with support to upload to biojava maven repository

Revision 7722 - Directory Listing
Modified Tue May 4 03:52:12 2010 UTC (3 years ago) by blivens
Original Path: biojava-live/trunk/structure-gui

Adding the new scoring strategy to the alignment GUI

Revision 7720 - Directory Listing
Modified Mon May 3 23:51:02 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now with antialiasing

Revision 7719 - Directory Listing
Modified Mon May 3 22:24:58 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

nicer colors

Revision 7718 - Directory Listing
Modified Mon May 3 22:24:42 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

nicer colors

Revision 7716 - Directory Listing
Modified Mon May 3 22:01:56 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

try to load alignments from central server

Revision 7715 - Directory Listing
Modified Mon May 3 22:01:00 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding view as FATCAT menu

Revision 7714 - Directory Listing
Modified Mon May 3 22:00:33 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now correct color display of alignments with multiple blocks

Revision 7713 - Directory Listing
Modified Mon May 3 22:00:16 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now correct color display of alignments with multiple blocks

Revision 7711 - Directory Listing
Modified Mon May 3 21:59:24 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now correct color display of alignments with multiple blocks

Revision 7710 - Directory Listing
Modified Mon May 3 20:39:07 2010 UTC (3 years ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now also shift ligands of 2nd structure, if alignment has more than 1 block. Rotation to be applied is the one of block 0...

Revision 7686 - Directory Listing
Modified Thu Apr 15 17:24:02 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

removing AStex dependency

Revision 7685 - Directory Listing
Modified Wed Apr 14 06:46:02 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

more docu for javaws.jar

Revision 7684 - Directory Listing
Modified Wed Apr 14 06:44:11 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

no need to keep docu for astex at the moment

Revision 7683 - Directory Listing
Modified Tue Apr 13 23:17:56 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing unit test, now it passes

Revision 7682 - Directory Listing
Modified Tue Apr 13 23:17:26 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

disabling prototype-fail

Revision 7681 - Directory Listing
Modified Tue Apr 13 23:17:04 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

disabling prototype-fail

Revision 7680 - Directory Listing
Modified Tue Apr 13 23:16:42 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

disabling Astex for now until we can host it on a public MVN server

Revision 7679 - Directory Listing
Modified Tue Apr 13 23:16:32 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

test speedup and prevent auto-failing

Revision 7678 - Directory Listing
Modified Tue Apr 13 23:15:43 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

disabling Astex for now until we can host it on a public MVN server

Revision 7640 - Directory Listing
Modified Thu Apr 8 00:02:34 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding tmScore to display

Revision 7633 - Directory Listing
Modified Wed Apr 7 23:10:25 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

incrementing version in docu

Revision 7632 - Directory Listing
Modified Wed Apr 7 23:09:12 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Heavily improved alignment UI

Revision 7612 - Directory Listing
Modified Wed Mar 31 01:52:12 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

no more stand alone DB search GUI...

Revision 7611 - Directory Listing
Modified Wed Mar 31 01:51:30 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

User interface has been massively improved, in particular DB searches...

Revision 7607 - Directory Listing
Modified Fri Mar 26 18:30:15 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding new demo for Smith Waterman based 3D structure overlay

Revision 7605 - Directory Listing
Modified Fri Mar 26 16:20:30 2010 UTC (3 years, 1 month ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing nullpointer exception

Revision 7589 - Directory Listing
Modified Thu Mar 18 21:30:11 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding property file for jfatcat

Revision 7575 - Directory Listing
Modified Wed Mar 17 19:34:42 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now showing parameters in Jmol frame title

Revision 7574 - Directory Listing
Modified Wed Mar 17 19:34:20 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

correct display of new parameter config

Revision 7570 - Directory Listing
Modified Tue Mar 16 22:47:20 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

boolean arguments are now displayed nicer

Revision 7568 - Directory Listing
Modified Tue Mar 16 16:46:08 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now displaying ligands for CE again

Revision 7566 - Directory Listing
Modified Mon Mar 15 23:35:49 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

two examples of how to use the new structure alignment algorithms

Revision 7565 - Directory Listing
Modified Mon Mar 15 23:33:35 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

new convenience method for easier display of structure alignments

Revision 7563 - Directory Listing
Modified Fri Mar 12 00:52:56 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now supports config of string array parameters

Revision 7559 - Directory Listing
Modified Thu Mar 11 22:20:02 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

removing deprecated class

Revision 7558 - Directory Listing
Modified Thu Mar 11 22:19:37 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

declaring deprecated

Revision 7557 - Directory Listing
Modified Thu Mar 11 22:18:38 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

removing warnings

Revision 7556 - Directory Listing
Modified Thu Mar 11 22:17:49 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

no need to wrap FATCAT algorithms with reflection any longer.

Revision 7555 - Directory Listing
Modified Thu Mar 11 22:15:51 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

no need to wrap FATCAT algorithms with reflection any longer.

Revision 7554 - Directory Listing
Modified Thu Mar 11 22:15:14 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

new example for how to run a structure alignment

Revision 7550 - Directory Listing
Modified Thu Mar 11 22:03:36 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Revision 7545 - Directory Listing
Modified Wed Mar 10 23:07:13 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

added acknowledgment of FATCAT origin.

Revision 7543 - Directory Listing
Modified Wed Mar 10 02:20:24 2010 UTC (3 years, 2 months ago) by blivens
Original Path: biojava-live/trunk/structure-gui

Merging the circular_permutations branch back into trunk.
This adds a new alignment algorithm, 'jCE-CP', and additional parameters to
the existing 'jCE' algorithm which allow CE to search for circular permutations
between compared structures. See CeMain and CeCPMain classes for more info.

An additional feature included is the ability to view dot plots of any alignments in the
AlignmentGUI. Finally, this commit sets svn:ignore properties for eclipse target directories.

Revision 7540 - Directory Listing
Modified Tue Mar 9 22:46:35 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

moving method to AFPTwister in biojava

Revision 7514 - Directory Listing
Modified Fri Feb 19 23:19:35 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

small fix

Revision 7509 - Directory Listing
Modified Fri Feb 19 04:19:54 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

cleanup

Revision 7505 - Directory Listing
Modified Fri Feb 19 04:05:46 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

better display again...

Revision 7504 - Directory Listing
Modified Fri Feb 19 03:19:49 2010 UTC (3 years, 2 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

correctly displaying jFatCat-flexible alignments again...

Revision 7486 - Directory Listing
Modified Fri Feb 12 01:06:09 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

more panel size fixes

Revision 7485 - Directory Listing
Modified Fri Feb 12 00:18:05 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing some display bugs for precalculated alignments. probably created during the refactoring...

Revision 7484 - Directory Listing
Modified Fri Feb 12 00:10:03 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing some display bugs for precalculated alignments. probably created during the refactoring...

Revision 7483 - Directory Listing
Modified Fri Feb 12 00:09:12 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding new wrapper for JFatCAt algorithm related stuff

Revision 7482 - Directory Listing
Modified Fri Feb 12 00:07:27 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now with larger box for showing mouse over coords

Revision 7481 - Directory Listing
Modified Thu Feb 11 22:56:44 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

I am trying to keep the structure modules compile with 1.5 for now

Revision 7466 - Directory Listing
Modified Tue Feb 9 03:31:37 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now correct displaying alignment

Revision 7461 - Directory Listing
Modified Mon Feb 8 23:03:36 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

use system temp dir rather than local dir if no filePath specified

Revision 7440 - Directory Listing
Modified Thu Feb 4 01:38:48 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixed incorrect arguments size check

Revision 7435 - Directory Listing
Modified Wed Feb 3 23:45:30 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now using /tmp as default location

Revision 7428 - Directory Listing
Modified Wed Feb 3 01:50:30 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

making method public

Revision 7427 - Directory Listing
Modified Wed Feb 3 01:49:52 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

more general approach to build up jmol script

Revision 7426 - Directory Listing
Modified Wed Feb 3 01:49:20 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

now server location is a parameter

Revision 7415 - Directory Listing
Modified Wed Jan 27 03:05:00 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

making the server location in the JFatCatClient optional

Revision 7372 - Directory Listing
Modified Thu Jan 21 17:47:15 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

incremental progress on selections

Revision 7370 - Directory Listing
Modified Thu Jan 21 17:33:36 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding new unit test for AtomInfo

Revision 7368 - Directory Listing
Modified Thu Jan 21 15:41:58 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

fixing unit test

Revision 7367 - Directory Listing
Modified Thu Jan 21 15:31:04 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

small demo

Revision 7366 - Directory Listing
Modified Thu Jan 21 15:23:36 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

changing package name of new stuff

Revision 7365 - Directory Listing
Modified Thu Jan 21 15:23:16 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

adding a demo

Revision 7364 - Directory Listing
Modified Thu Jan 21 15:23:01 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

changing package name of new stuff

Revision 7362 - Directory Listing
Modified Thu Jan 21 14:41:59 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

updating package name

Revision 7355 - Directory Listing
Modified Thu Jan 21 12:18:10 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

new and renamed modules

Revision 7352 - Directory Listing
Modified Thu Jan 21 12:07:43 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Revision 7351 - Directory Listing
Modified Thu Jan 21 11:58:11 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

moving out all GUI code to the GUI module

Revision 7349 - Directory Listing
Modified Thu Jan 21 11:00:33 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Revision 7348 - Directory Listing
Modified Thu Jan 21 10:59:35 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

explaining how to manually install all dependencies

Revision 7347 - Directory Listing
Modified Thu Jan 21 10:59:11 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

latest dependcies

Revision 7337 - Directory Listing
Modified Wed Jan 20 16:38:45 2010 UTC (3 years, 3 months ago) by jacobsen
Original Path: biojava-live/trunk/structure-gui

removed specific junit version declaration as this was overriding the project managed version.

Revision 7336 - Directory Listing
Modified Wed Jan 20 16:34:03 2010 UTC (3 years, 3 months ago) by jacobsen
Original Path: biojava-live/trunk/structure-gui

Moved Andreas' BioJavaJmol implementation over into the new JmolViewerImpl and added the first 'test'

Revision 7332 - Directory Listing
Modified Wed Jan 20 16:12:05 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

Major new feature: biojava-structure-gui now can display results of the Combinatorial Extension (CE) algorithm

Revision 7322 - Directory Listing
Modified Tue Jan 19 17:51:37 2010 UTC (3 years, 3 months ago) by jacobsen
Original Path: biojava-live/trunk/structure-gui

added RenderStyle enum

Revision 7321 - Directory Listing
Modified Tue Jan 19 17:50:47 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui

changing artifact ID

Revision 7319 - Directory Listing
Modified Tue Jan 19 17:30:29 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/structure-gui
Copied from: biojava-live/trunk/biojava-structure-gui revision 7318

renaming

Revision 7316 - Directory Listing
Modified Tue Jan 19 17:22:08 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/trunk/biojava-structure-gui
Copied from: biojava-live/biojava-structure-gui revision 7315

oops wrong path

Revision 7315 - Directory Listing
Modified Tue Jan 19 17:20:25 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/biojava-structure-gui

Revision 7314 - Directory Listing
Added Tue Jan 19 17:19:22 2010 UTC (3 years, 3 months ago) by andreas
Original Path: biojava-live/biojava-structure-gui

Creating a new module for 3D related GUI hooks