------------------------------------------------------------------------ r391 | imilne | 2013-04-03 14:09:36 +0100 (Wed, 03 Apr 2013) | 2 lines - NEW: Minor UI tweaks for Windows versions. - NEW: Updated the installers to properly support the latest versions of Windows and OS X. ------------------------------------------------------------------------ r390 | imilne | 2009-07-31 11:53:57 +0100 (Fri, 31 Jul 2009) | 1 line - NEW: Changed the upper limit for number of generations on MrBayes jobs to be 20,000,000 (up from 1,000,000). ------------------------------------------------------------------------ r389 | imilne | 2009-06-16 15:50:24 +0100 (Tue, 16 Jun 2009) | 1 line - NEW: Quick edit to the last commit to deal with an unchecked operation (that was probably a typo). ------------------------------------------------------------------------ r388 | imilne | 2009-06-16 08:57:50 +0100 (Tue, 16 Jun 2009) | 1 line - NEW: (jprocter) - Improved cDNA recovery from a VAMSAS document. ------------------------------------------------------------------------ r387 | imilne | 2009-06-15 09:24:45 +0100 (Mon, 15 Jun 2009) | 1 line - NEW: The selection state of sequences within TOPALi (for manual or tree grouping selections) now generates a VAMSAS selection message. ------------------------------------------------------------------------ r386 | imilne | 2009-06-12 11:47:43 +0100 (Fri, 12 Jun 2009) | 1 line - NEW: The selection state of VAMSAS sequences (made in JalView) is now mirrored in TOPALi (but the inverse isn't (yet)). ------------------------------------------------------------------------ r385 | imilne | 2009-06-11 15:25:20 +0100 (Thu, 11 Jun 2009) | 3 lines - BUG: Importing TOPALi projects from a VAMSAS session was using the wrong parameters for the unmarshaller. - BUG: (Possibly a hack): VAMSAS alignments can have sequences with identical names, which is normally disallowed by TOPALi. The validity check for this has been disabled when importing VAMSAS data. - NEW: Added in the latest version of the VAMSAS client jar. ------------------------------------------------------------------------ r384 | imilne | 2009-04-15 14:38:23 +0100 (Wed, 15 Apr 2009) | 1 line - BUG: Fixed a bug that could cause a crash at project import time if CodeML hadn't completed its run correctly. ------------------------------------------------------------------------ r383 | imilne | 2009-01-26 11:39:41 +0000 (Mon, 26 Jan 2009) | 1 line NEW: Tagged public release of version 2.5 (09.01.26) ------------------------------------------------------------------------ r382 | imilne | 2009-01-26 11:30:53 +0000 (Mon, 26 Jan 2009) | 2 lines - BUG: Some of the cluster scripts were still wrong for Dominik's changed DSS analysis path. - CHG: Updated some web files ready for a new release. ------------------------------------------------------------------------ r381 | imilne | 2008-12-19 11:35:06 +0000 (Fri, 19 Dec 2008) | 4 lines - BUG: Fixed a problem with HMM TDS prediction when multiple identical sequences were included. - BUG: Fixed TOPALi bouncing VAMSAS mouse-over messages. - CHG: Updated the cluster scripts to assign more memory for Java. - CHG: Updated the Install4j file to include the latest JREs. ------------------------------------------------------------------------ r380 | imilne | 2008-12-17 11:26:41 +0000 (Wed, 17 Dec 2008) | 4 lines - BUG: Stopped TOPALi bouncing VAMSAS mouse messages by resending what it has already received. - CHG: Made the default size for the VAMSAS sessions dialog a little larger. - CHG: Reinstated the highlighting controls so VAMSAS mouse messages will display. - CHG: Updated vamsas-client.jar to the latest version. ------------------------------------------------------------------------ r379 | imilne | 2008-10-24 08:54:18 +0100 (Fri, 24 Oct 2008) | 1 line - CHG: Improved the look of the toolbar buttons when running on OS X. ------------------------------------------------------------------------ r378 | imilne | 2008-10-15 10:07:35 +0100 (Wed, 15 Oct 2008) | 1 line - BUG: Fixed problems with local runs of PhyML and ModelTest because the Windows batch files were not writing paths with spaces correctly. ------------------------------------------------------------------------ r377 | imilne | 2008-10-07 08:51:23 +0100 (Tue, 07 Oct 2008) | 1 line Tagged public release of version 2.5 (08.10.07) ------------------------------------------------------------------------ r376 | imilne | 2008-10-07 08:46:51 +0100 (Tue, 07 Oct 2008) | 3 lines - CHG: Modified the text displaying in the Model Selection dialog based on whether the alignment is DNA or Protein (and hence what programs the models can be generated for). - CHG: Modified the menu text for the phylogenetics analyses options. - CHG: Added download tracking to the google analytics code on the website. ------------------------------------------------------------------------ r375 | imilne | 2008-09-30 09:30:18 +0100 (Tue, 30 Sep 2008) | 1 line - BUG: Fixed the problem with combo boxes not drawing their outlines with the Office look and feel. ------------------------------------------------------------------------ r374 | imilne | 2008-09-25 13:39:33 +0100 (Thu, 25 Sep 2008) | 3 lines - CHG: Updated the build file to include debug information in the compiled classes. - NEW: Added Google Analytics JavaScript calls to the web pages. - CHG: The cluster.properties file can now include system environment variables in the paths (1st attempt). ------------------------------------------------------------------------ r373 | imilne | 2008-09-22 09:21:26 +0100 (Mon, 22 Sep 2008) | 1 line - NEW: Added in a couple of missing cluster SGE scripts that were missing for the UoD build. ------------------------------------------------------------------------ r372 | imilne | 2008-08-12 15:26:42 +0100 (Tue, 12 Aug 2008) | 3 lines - BUG: Reimplemented the translate-to-protein option that was removed in an earlier commit. - NEW: Fixed and improved some of the GUI text presented to the user. - NEW: TOPALi now checks to ensure protein alignments are NOT runnable by the codon position models of MrBayes and RaxML. ------------------------------------------------------------------------ r371 | imilne | 2008-07-30 09:18:29 +0100 (Wed, 30 Jul 2008) | 1 line Tagged public release of version 2.5 (08.07.30) ------------------------------------------------------------------------ r370 | imilne | 2008-07-30 09:17:39 +0100 (Wed, 30 Jul 2008) | 1 line Minor tweaks to some of the web pages and application text ready for a new release to the web. ------------------------------------------------------------------------ r369 | imilne | 2008-07-28 08:46:33 +0100 (Mon, 28 Jul 2008) | 1 line Updated the logs parser to output statistics on country and operating system. ------------------------------------------------------------------------ r368 | imilne | 2008-07-24 10:44:28 +0100 (Thu, 24 Jul 2008) | 3 lines Various text changes (spelling etc). Made the Analysis Results (info) dialog resizable to deal with some of the larger outputs (eg MrBayes). ------------------------------------------------------------------------ r367 | imilne | 2008-07-24 10:16:24 +0100 (Thu, 24 Jul 2008) | 4 lines Changed some of the text on the import dialog. Fixed some unicode display problems on the model selection results pane. Changed the maximum number of generations for a MrBayes tree to be 1,000,000 (up from 500,000). Limited the maximum number of bootstrap runs for certain job types (PDM, DSS, LRT, RaxML, and PhyML) when running on the cluster. ------------------------------------------------------------------------ r366 | imilne | 2008-07-24 09:48:07 +0100 (Thu, 24 Jul 2008) | 1 line Fixed a bug importing unaligned cDNA where a check for non-aligned data was not being made. ------------------------------------------------------------------------ r365 | imilne | 2008-07-11 15:19:04 +0100 (Fri, 11 Jul 2008) | 2 lines Committed 50% of an attempt to get the export alignment option working with the old partitions dialog. Still need to reinstate the convert-to-protein option which is currently not running (the exported alignment will still be DNA). ------------------------------------------------------------------------ r364 | imilne | 2008-07-11 14:48:36 +0100 (Fri, 11 Jul 2008) | 7 lines Reverted the AlignmentData code back to its original method of storing annotations. Have reinstated most of the functionality of the original Partitions dialog: - re-added code from revision 111 (and 259) to get the basic dialog working again - Dominik's code was missing various bits of state functionality - create quick tree from partition - new/edit partition Changes to the auto partition dialog and methods to support dropping back to the old style of annotations. ------------------------------------------------------------------------ r363 | imilne | 2008-07-11 08:56:12 +0100 (Fri, 11 Jul 2008) | 1 line Stopped the development builds from logging to the server at startup. ------------------------------------------------------------------------ r362 | imilne | 2008-07-10 14:21:32 +0100 (Thu, 10 Jul 2008) | 2 lines Minor edits to the web pages (to point at the change log from the front page). The install4j jar was missing from the manifest classpath in the ant build file. ------------------------------------------------------------------------ r361 | imilne | 2008-07-10 13:56:40 +0100 (Thu, 10 Jul 2008) | 1 line When displaying the quicktree dialog for Protein alignments, the option for transition/transversion ratio is now hidden from the user. ------------------------------------------------------------------------ r360 | imilne | 2008-07-10 13:51:05 +0100 (Thu, 10 Jul 2008) | 1 line Changed the popup windows for Model Selection to be properly modal (and so that only one can appear at a time). They are also now associated with the main TOPALi window. ------------------------------------------------------------------------ r359 | imilne | 2008-07-10 13:42:29 +0100 (Thu, 10 Jul 2008) | 1 line Edited and tidied up the Positive Selection (Site Model) dialog, also making it properly modal. ------------------------------------------------------------------------ r358 | imilne | 2008-07-10 12:00:21 +0100 (Thu, 10 Jul 2008) | 4 lines Tidied up the quick tree dialog. Added some help text to the MrBayes dialog. Fixed some bugs with the default model selection (due to the new 3 CP models). Various edits to the text (Frank lingo) in the dialogs. ------------------------------------------------------------------------ r357 | imilne | 2008-07-09 14:59:44 +0100 (Wed, 09 Jul 2008) | 4 lines Fake commit to deal with the previous one missing most of its comments. Split the Model Selection runs (for protein coding alignments) into three separate runs, one per codon position. Added separate codon-position based models to the alignment's SequenceSetProperties. Modified the MrBayes CDNA submission dialog to use the models from each position if available. ------------------------------------------------------------------------ r356 | imilne | 2008-07-09 14:55:39 +0100 (Wed, 09 Jul 2008) | 1 line Added separate codon-position based models to the alignment's SequenceSetProperties. ------------------------------------------------------------------------ r355 | imilne | 2008-07-08 15:28:58 +0100 (Tue, 08 Jul 2008) | 1 line Set the default font rendering to *not* be anti-aliased. ------------------------------------------------------------------------ r354 | imilne | 2008-07-08 15:28:30 +0100 (Tue, 08 Jul 2008) | 1 line Fixed a cut n paste typo that meant DSS reported errors with PDM when it failed. ------------------------------------------------------------------------ r353 | imilne | 2008-07-07 08:31:58 +0100 (Mon, 07 Jul 2008) | 3 lines Split the RaxML dialogs into two separate options. Improved the clean target of the Ant build file. Modified the Model Selection dialog to provide more information to the user about what its purpose is. ------------------------------------------------------------------------ r352 | imilne | 2008-06-25 10:15:39 +0100 (Wed, 25 Jun 2008) | 2 lines - Fixed an exception being thrown when attempting to load unaligned data files. - Split MrBayes dialog options into two separate dialogs (standard DNA and codon positions). ------------------------------------------------------------------------ r351 | imilne | 2008-05-30 14:18:27 +0100 (Fri, 30 May 2008) | 2 lines Modified the alignment handling code to use the remote ReadSeq service before any of the built-in TOPALi methods. Added new parse methods to the log readers to generate the information needed for geolocating countries. ------------------------------------------------------------------------ r350 | imilne | 2008-05-26 09:09:34 +0100 (Mon, 26 May 2008) | 1 line Tagged public release of version 2.5 (08.05.26) ------------------------------------------------------------------------ r349 | imilne | 2008-05-26 09:07:35 +0100 (Mon, 26 May 2008) | 2 lines - Improved compatibility on Windows Vista. - Modified the tracking log to monitor locale and version number. ------------------------------------------------------------------------ r348 | imilne | 2008-05-22 12:02:16 +0100 (Thu, 22 May 2008) | 1 line Tagged public release of version 2.5 (08.05.22) ------------------------------------------------------------------------ r347 | imilne | 2008-05-22 11:55:51 +0100 (Thu, 22 May 2008) | 3 lines - Fixed the spacing of the radio buttons on the import options dialog. - Changed the new install4j update check to only run based on the user's update settings. - Modified the website for the new release. ------------------------------------------------------------------------ r346 | imilne | 2008-05-22 11:34:08 +0100 (Thu, 22 May 2008) | 7 lines - Removed the webstart version (it's too much effort to maintain). - Removed the signing data from all of the jar files to support this. - Removed the 'looks' look and feel from the linux version as the native ones are now good enough on support platforms. - Added an install4j build task to the main build.xml file. - Stopped the update dialog displaying at runtime every time (it should only appear if there is an actual update). - OSX: Fixed problems with some menu shortcuts still showing CTRL rather than CMD. - OSX: Added a proper appicon in OS X .icns format for dock. ------------------------------------------------------------------------ r345 | imilne | 2008-05-22 10:19:27 +0100 (Thu, 22 May 2008) | 1 line - Renamed the installer to match the actual installers it builds. ------------------------------------------------------------------------ r344 | imilne | 2008-05-22 09:49:34 +0100 (Thu, 22 May 2008) | 5 lines - Fixed more layout issues with the display settings, and removed some redundant options. - Removed the option to select language, and disabled German properties until we can catch up on translations. - Removed the source code from the ATV jar file to stop compiler warnings appearing for a TOPALi build. - Changed all references to TOPALi v2 to be v2.5 for a major step change. - Added install4j update facilities and removed all the old legacy TOPALi update code. ------------------------------------------------------------------------ r343 | imilne | 2008-04-02 15:42:35 +0100 (Wed, 02 Apr 2008) | 8 lines - Fixed mnemonics in the display settings dialog. - Fixed a bug with the OS X Window options causing crashes on non OS X systems because the menu items were still null. - Fixed (yet another) bug stoping the MrBayes dialog from opening. - Modified the jobs-in-front-of-you message to better reflect that it doesn't really know how many are actually on your queue. - Changed the settings files for SGE to submit to the new split serial/parallel queues on the SCRI cluster. - Fixed mnemonics in the menus. - Dialog buttons should all now be right-aligned with a minimum 75 pixel width. - Fixed the layout and formatting for the MrBayes settings dialog. ------------------------------------------------------------------------ r342 | imilne | 2008-03-31 11:59:03 +0100 (Mon, 31 Mar 2008) | 3 lines - Merging in the rest of Dominik's uncommitted changes. - Various classes have been moved into new folders. - Updates to the castor xml to cope with this. ------------------------------------------------------------------------ r341 | imilne | 2008-03-31 09:38:48 +0100 (Mon, 31 Mar 2008) | 1 line - Copied in Dominik's changes to topali.analyses ------------------------------------------------------------------------ r340 | imilne | 2008-03-31 09:32:51 +0100 (Mon, 31 Mar 2008) | 3 lines Updated scri-commons.jar Modified the web's version.txt to contain the correct version number for the next release. Copied over Dominik's latest translations and notes ready for merging. ------------------------------------------------------------------------ r339 | imilne | 2008-03-23 16:27:28 +0000 (Sun, 23 Mar 2008) | 16 lines - Fixed the layout and formatting for the PDM settings dialog. - Fixed the layout and formatting for the HMM settings dialog. - Fixed the layout and formatting for the DSS settings dialog. - Fixed the layout and formatting for the LRT settings dialog. - Added menu shortcut for Analysis->Show Annotations dialog. - Added default title (RegionDialog.title) to the Annotations dialog. - Upgraded scri-commons to the latest version. - OS X: Moved the menubar out of the TOPALi frame and onto the desktop. - OS X: Menu handlers mapped for About TOPALi, Preferences, and CMD-Q quit commands, and the Help->About, Analysis->Settings, and File->Exit therefore removed from the TOPALi menus. - OS X: Fixed toolbar spacing so the buttons look neater on the Mac. - OS X: Removed all menubar icons. - OS X: Remapped all shortcuts to be platform independant (CTRL to CMD). - The Annotations dialog wasn't modal attached to the main TOPALi window. - OS X: Added the Apple required Window menu with minimize, zoom, etc options. - Fixed a size/pack() problem with the MrBayes settings dialog. - Added keyboard shortcuts for the controls within the main settings dialog. ------------------------------------------------------------------------ r338 | imilne | 2008-02-28 08:36:30 +0000 (Thu, 28 Feb 2008) | 1 line Made some changes so that TOPALi can be properly compiled for 1.5 compatibility. ------------------------------------------------------------------------ r337 | dlindn | 2008-02-15 12:55:50 +0000 (Fri, 15 Feb 2008) | 2 lines - Improved alignment display buffering - Removed some unnecessary code ------------------------------------------------------------------------ r336 | dlindn | 2008-02-12 10:05:59 +0000 (Tue, 12 Feb 2008) | 1 line - Fixed broken I18N strings ------------------------------------------------------------------------ r335 | imilne | 2008-02-11 15:07:47 +0000 (Mon, 11 Feb 2008) | 1 line Removed redundant import. ------------------------------------------------------------------------ r334 | dlindn | 2008-02-11 14:43:29 +0000 (Mon, 11 Feb 2008) | 1 line - moved i18n texts back to res ------------------------------------------------------------------------ r333 | dlindn | 2008-02-11 14:36:42 +0000 (Mon, 11 Feb 2008) | 1 line - moved i18n texts back to res ------------------------------------------------------------------------ r332 | dlindn | 2008-02-11 14:21:40 +0000 (Mon, 11 Feb 2008) | 4 lines - Removed exportability/printability of Modeldiagram again (it was just not working properly) - Tables and Graphs are now also exportable as txt file. - Made AlignmentPanel scrolling more easy (removed extra Scroller thread) ------------------------------------------------------------------------ r331 | dlindn | 2008-02-08 15:22:18 +0000 (Fri, 08 Feb 2008) | 7 lines - Replaced MrBayes 3.1.1 with 3.1.2 (due to a bug in 3.1.1) - Had to move i18n stuff into src directory (otherwise NetBeans complains) - Implemented variable window sizes in DSS and LRT - If job entry gets removed (cancelled), the error info panel now also gets cleared. - Resultpanels: Again just one right-aligned toolbar (no separated toolbars for each graph etc. anymore) - Fixed: Printpreview just showed first page for multipage Printables - ModelDiagrams are now also exportable/printable (but still some problem with printing) ------------------------------------------------------------------------ r330 | dlindn | 2008-01-25 16:03:34 +0000 (Fri, 25 Jan 2008) | 1 line Tagged public release of version 2.19 ------------------------------------------------------------------------ r329 | dlindn | 2008-01-25 16:02:11 +0000 (Fri, 25 Jan 2008) | 2 lines - Repaired Castor.java - updated www docs ------------------------------------------------------------------------ r328 | dlindn | 2008-01-25 11:47:28 +0000 (Fri, 25 Jan 2008) | 4 lines - Moved all i18n texts in one file (i18n.properties) - Added language option in DisplaySettings dialog - Started translation to German - Fixed bug in Phyml sge-script ------------------------------------------------------------------------ r327 | dlindn | 2008-01-23 15:38:49 +0000 (Wed, 23 Jan 2008) | 1 line - deleted "classes" folder from repository ------------------------------------------------------------------------ r326 | dlindn | 2008-01-23 15:37:50 +0000 (Wed, 23 Jan 2008) | 1 line - ModeltestResults are now resubmittable ------------------------------------------------------------------------ r325 | dlindn | 2008-01-21 15:55:28 +0000 (Mon, 21 Jan 2008) | 10 lines - Extended ParamEstThread from DesktopThread (now it's cancellable) (therefore removed ParamEstDialog because now a DefaultWaitDialog is used instead) - Added "Estimate Parameters" option to QuickTreeDialog - Fixed DSS/LRT gap threshold (in case everything except less than 4 sequences are removed due to exceeding gap threshold) - Moved XML property settings from Castor.java to Topali.java, because of some XML serializer errors when saving projects (saving a Topali project does not instantiate Castor.java!) - Fixed bug: Phyml and MrBayes dialog throw error after parameter estimation - Fixed MrBayes job resubmission ------------------------------------------------------------------------ r324 | dlindn | 2008-01-18 09:53:26 +0000 (Fri, 18 Jan 2008) | 1 line - Removed doe.jar ------------------------------------------------------------------------ r323 | dlindn | 2008-01-18 09:29:27 +0000 (Fri, 18 Jan 2008) | 2 lines - Removed xerces.jar - Replaced sbrn-commons with scri-commons ------------------------------------------------------------------------ r322 | dlindn | 2008-01-16 16:15:10 +0000 (Wed, 16 Jan 2008) | 2 lines - Separated (variable) user preferences and (fixed) system preferences - Did some cleanup ------------------------------------------------------------------------ r321 | dlindn | 2008-01-15 15:13:45 +0000 (Tue, 15 Jan 2008) | 5 lines - Fixed bug in LRT: LRT.getLikelihood(): JC and F84 were interchanged LRTAnalysis: alpha and tRatio were always -1 Gap removal caused Exception - If a alignment has duplicate seq. names, the user now get's told which seq. these are. ------------------------------------------------------------------------ r320 | dlindn | 2008-01-11 16:06:03 +0000 (Fri, 11 Jan 2008) | 3 lines - Added XSLT file for 2.18-2.19 transformation (doesn't do anything yet) - Fixed bug: RaxML result (field: anlysis info) contained an invalid character (therefore project.xml will now be checked when loaded) ------------------------------------------------------------------------ r319 | imilne | 2008-01-09 09:36:28 +0000 (Wed, 09 Jan 2008) | 2 lines Added "friendlier" error messages for when jobs fail. Added the ability to detect when a cluster-side job has been killed outside of TOPALi's control (eg by an admin or by exceeding SGE's queue limits). ------------------------------------------------------------------------ r318 | dlindn | 2007-12-13 15:59:34 +0000 (Thu, 13 Dec 2007) | 7 lines - AlignmentPanel: Cursor is now crosshair cursor if mouse over highlighting is enabled - DSS ans LRT: Added option for ignoring sequences, if they exceed a certain gap threshold - Removed "Emp. Freq." choice from RaxMl cdna panel - Wait dialog will be displayed while alignment display buffer is created - Antialiasing for alignment display is now optional - Run, Cancel, ... buttons are now again layout in GridLayout ------------------------------------------------------------------------ r317 | imilne | 2007-12-13 11:49:08 +0000 (Thu, 13 Dec 2007) | 2 lines Modified the installer for 2.18. Optimised the alignment overview so it doesn't need to draw rows/cols of data that would just be overdrawn anyway. ------------------------------------------------------------------------ r316 | imilne | 2007-12-13 09:08:54 +0000 (Thu, 13 Dec 2007) | 1 line Tagged public release of version 2.18 ------------------------------------------------------------------------ r315 | dlindn | 2007-12-12 15:45:20 +0000 (Wed, 12 Dec 2007) | 5 lines - Fixed RaxML bootstrapping - Added "copy to clipboard" button to analysis info dialog - Fixed: PhyML partition was ignored - Export tree as PNG: Size of the image = size of the actual window - DNAModelDiagram: Fixed loss of rate 'bubbles' when rates are extremly high ------------------------------------------------------------------------ r314 | dlindn | 2007-12-07 16:16:16 +0000 (Fri, 07 Dec 2007) | 17 lines - Alignment display: Each nucleotid rectangle is now pre-painted and copied into the actual display canvas (instead of repainted again and again) Sequence and paritition dimming as well as mouse over highlighting is now done by transparent overlaying (instead of repainting the panel or buffer on each action) Also added a light color gradient to the nuc. rectangles - Fixed update checker (version.txt in /www, upload to webserver with next release) (already done in previous svn commit) - Fixed a bug in "remove bootstrap value" dialog - Added ToolTips to various table headers - Removed some unneccessary System.out.println()s - Added RF tree distances to model selection webservice - Quick Tree Estimation: Now allows setting of ts/tv and alpha parameter - Fixed bug in model test: AIC2 and BIC score was wrong - Removed 'Optimize...' checkboxes from phyml dialog (not needed at the moment) - Fixed bug: AA sub. models have 0 degress of freedom not 19 - Updated treedist to newer version (needed for model test) ------------------------------------------------------------------------ r313 | dlindn | 2007-11-29 13:02:37 +0000 (Thu, 29 Nov 2007) | 3 lines - Added facility to remove/replace bootstrap values from trees. - Model selection results now also show trees - Improved alignment diplay by using offscreen buffering ------------------------------------------------------------------------ r312 | dlindn | 2007-11-19 16:52:38 +0000 (Mon, 19 Nov 2007) | 7 lines - Updated help texts - Updated "what's new" part for topali website - Created a little "framework" for running small threads (e.g. quick tree estimation) locally on the desktop ("killable" thread class, showing "please wait" dialogs, etc.) (package var.threads) - Created workaround for loosing bootstrap values when midpoint rooting trees with PAL. - Improved ModelDiagram graphics ------------------------------------------------------------------------ r311 | dlindn | 2007-11-14 17:17:03 +0000 (Wed, 14 Nov 2007) | 7 lines - Fixed: After quick tree is created, view should automatically be switched to tree pane - Fixed: Codon position models can now just be selected if there is a dna alignment and sequence length is dividable by 3. - Bootstrapping now also possible with quick F84/WAG+G tree (ported the relevant code from Topali v1) - Creation of quick tree can now also be cancelled - Fixed a problem with FastML (was writting tree with real seq names) ------------------------------------------------------------------------ r310 | dlindn | 2007-11-12 16:56:32 +0000 (Mon, 12 Nov 2007) | 2 lines Deleted (previous accidently committed) topali installer ------------------------------------------------------------------------ r309 | dlindn | 2007-11-12 16:54:37 +0000 (Mon, 12 Nov 2007) | 1 line Deleted res/images directory again, as it is not needed anymore ------------------------------------------------------------------------ r308 | dlindn | 2007-11-12 16:51:27 +0000 (Mon, 12 Nov 2007) | 3 lines - Added on-the-fly generation of protein model diagramms - Added new webservice RaxML - Split former TreeDialog into several submenus in the analysis menu ------------------------------------------------------------------------ r307 | imilne | 2007-11-09 16:12:28 +0000 (Fri, 09 Nov 2007) | 1 line Model generator dialog now appears at the correct position (aligned to the main window). ------------------------------------------------------------------------ r306 | dlindn | 2007-11-08 08:35:15 +0000 (Thu, 08 Nov 2007) | 1 line Deleted (accidentely committed) topali.jar again :) ------------------------------------------------------------------------ r305 | imilne | 2007-11-08 08:35:14 +0000 (Thu, 08 Nov 2007) | 1 line Fixed a bug on nav-panel tree selection when loading older projects that would sometimes cause an exception. ------------------------------------------------------------------------ r304 | imilne | 2007-11-08 08:30:40 +0000 (Thu, 08 Nov 2007) | 1 line Changes to the website to correct left-over BioSS code, add images, and fix Gràinne's name. ------------------------------------------------------------------------ r303 | imilne | 2007-11-08 08:19:17 +0000 (Thu, 08 Nov 2007) | 1 line Removed jar files (again!). ------------------------------------------------------------------------ r302 | dlindn | 2007-11-05 16:41:49 +0000 (Mon, 05 Nov 2007) | 4 lines - Replaced fixed model images with ModelDiagram and RateHetDiagram to visualize substitution models - TreeResult now also holds log likelihood (lnl) - Modified PhyML parser to read lnl - Modified MrBayes parser to read lnl (not working yet) ------------------------------------------------------------------------ r301 | dlindn | 2007-10-31 16:22:23 +0000 (Wed, 31 Oct 2007) | 9 lines - Added ModelTestProcess extends StoppableProcess (MT local jobs can now be properly cancelled) - MrBayes Summary is now added to "Analysis Info". - MrBayes: User will be warned if a PSRF value is greater than 1.2 - MrBayes and PhyML settings will now be stored in Preferences - Replaced PhyML with PhyML-aLRT (because PhyML won't do bootstrapping with custom models) - Added some images showing model details, gamma dist. and inv. sites to ModelInfoPanel - Alignment can be splitted into 3, according to codon positions (already added some time ago) - Wrote unit test for MathUtils class (already added some time ago) ------------------------------------------------------------------------ r300 | dlindn | 2007-10-23 15:58:41 +0100 (Tue, 23 Oct 2007) | 5 lines - Autoselect Model: After Modeltest finishes, the best BIC model will be selected automatically. - The currently selected model will now be marked in the Modeltest table (bold font) - Implemented a unit test for Modeltest job - Added XSLT mechanism for backward compatibility (V. 2.16 projects will now be transformed to be 2.17 compatible) ------------------------------------------------------------------------ r299 | dlindn | 2007-10-22 09:50:36 +0100 (Mon, 22 Oct 2007) | 2 lines - Added new model testing webservice based on phyml (removed modelgenerator from the menu) - Added highlighting/tooltip functionality to CustomTable ------------------------------------------------------------------------ r298 | dlindn | 2007-10-08 15:52:48 +0100 (Mon, 08 Oct 2007) | 1 line Improved TrackingLogParser ------------------------------------------------------------------------ r297 | dlindn | 2007-10-05 14:22:33 +0100 (Fri, 05 Oct 2007) | 5 lines - Added static boolean "debug" to TOPALi to enable/disable extensive logging - Fixed vamsas sequence duplication bug - Fixed table printing issues - Extended modelgenerator parser to include best hlrt, aic1, aic2 and bic models - Added a parser for the tracking log file ------------------------------------------------------------------------ r296 | imilne | 2007-09-28 14:34:34 +0100 (Fri, 28 Sep 2007) | 1 line Modified the histogram panel in the PDM results window so that it looks a little less Toys R Us. ------------------------------------------------------------------------ r295 | imilne | 2007-09-28 10:05:44 +0100 (Fri, 28 Sep 2007) | 1 line Tagged public release of version 2.17 ------------------------------------------------------------------------ r294 | imilne | 2007-09-28 10:02:31 +0100 (Fri, 28 Sep 2007) | 3 lines Fixed null frame references in several dialog boxes. Implemented maximum number of sequences limits on the cluster jobs (and provided more detail in the related error messages). Set a 2.5 hr hard time limit on cluster jobs. ------------------------------------------------------------------------ r293 | imilne | 2007-09-27 12:47:51 +0100 (Thu, 27 Sep 2007) | 1 line Modified the way the example alignment is loaded so it can be read from topali.jar ------------------------------------------------------------------------ r292 | dlindn | 2007-09-27 12:17:20 +0100 (Thu, 27 Sep 2007) | 3 lines Fixed missing icons in CMLSitePanel Fixed a typo in estimate_tree help ------------------------------------------------------------------------ r291 | imilne | 2007-09-27 10:29:45 +0100 (Thu, 27 Sep 2007) | 1 line Tagged public release of version 2.16 ------------------------------------------------------------------------ r290 | imilne | 2007-09-27 10:28:59 +0100 (Thu, 27 Sep 2007) | 3 lines The ant deploy task was not copying version.txt to the server. Removed the "Import example dataset" option until we can make it work via the jar file. Updated the web server for the final release of 2.16. ------------------------------------------------------------------------ r289 | dlindn | 2007-09-27 10:03:45 +0100 (Thu, 27 Sep 2007) | 2 lines Added some help information Added Codeml site table coloring ------------------------------------------------------------------------ r288 | dlindn | 2007-09-27 08:59:03 +0100 (Thu, 27 Sep 2007) | 4 lines Fixed: Tree, including branchlengths was given to FastML, which caused FastML to fail. Edited CodeML settings, so that just the selection of the model groups is possible. Added LRT to Codeml site result panel. ------------------------------------------------------------------------ r287 | imilne | 2007-09-26 15:51:06 +0100 (Wed, 26 Sep 2007) | 1 line Signed all of the jar files with the new certificate. ------------------------------------------------------------------------ r286 | imilne | 2007-09-26 14:11:23 +0100 (Wed, 26 Sep 2007) | 4 lines More changes to the website in preparation for release: - Added another screenshot - Removed the version history and provided a pointer to the output from the svn log instead (generated hourly via a cron job) - version.html renamed to version.txt yet again with just the release number included so TOPALi clients can check for updates. ------------------------------------------------------------------------ r285 | imilne | 2007-09-26 13:36:37 +0100 (Wed, 26 Sep 2007) | 1 line Moved doc/web folder to the top level, renaming it to www. ------------------------------------------------------------------------ r284 | imilne | 2007-09-26 11:43:58 +0100 (Wed, 26 Sep 2007) | 1 line Provided a more detailed error message for when a project fails to load. ------------------------------------------------------------------------ r283 | imilne | 2007-09-26 11:36:24 +0100 (Wed, 26 Sep 2007) | 2 lines Changed the import dialog's text. Set the alignment-highlighting to off by default. ------------------------------------------------------------------------ r282 | imilne | 2007-09-26 11:23:20 +0100 (Wed, 26 Sep 2007) | 1 line Public jobs at SCRI are now submitted to public.q on SGE. ------------------------------------------------------------------------ r281 | imilne | 2007-09-26 10:39:46 +0100 (Wed, 26 Sep 2007) | 1 line Added GradientPanel headers to the results panels (some still need titles). ------------------------------------------------------------------------ r280 | dlindn | 2007-09-26 10:10:39 +0100 (Wed, 26 Sep 2007) | 8 lines Dominik: - REMOVED (not working properly): When F84 tree job finishes, Topali now again automatically switches to tree view - Modified icons - Cleaned up "Omega start values" dialog - CodeMLSite dialog: run button now has default focus - Updated license information in Topali help section (ModelGenerator license still missing!) Iain: - Extensive GUI clean up ------------------------------------------------------------------------ r279 | imilne | 2007-09-26 08:36:08 +0100 (Wed, 26 Sep 2007) | 1 line Removed two ancient and redundant files that had no source in them (they made Ant complain). ------------------------------------------------------------------------ r278 | dlindn | 2007-09-25 11:18:34 +0100 (Tue, 25 Sep 2007) | 1 line Removed topali.jar again, added updated vamsas-client.jar. ------------------------------------------------------------------------ r277 | dlindn | 2007-09-24 17:48:03 +0100 (Mon, 24 Sep 2007) | 6 lines - Modified icons again - When F84 tree job finishes, Topali now again automatically switches to tree view - Fixed Codeml Site/Branch job resubmission and anaylsis info display - Fixed: Default button was not working for every job settings dialog - Added application details and literature references to jobs' analysis info - Repacked ATV library (forester.jar), now includes source code ------------------------------------------------------------------------ r276 | imilne | 2007-09-24 08:56:11 +0100 (Mon, 24 Sep 2007) | 1 line Latest changes to logging and the website. ------------------------------------------------------------------------ r275 | dlindn | 2007-09-21 15:19:47 +0100 (Fri, 21 Sep 2007) | 6 lines - cleaned up phyml settings dialog - modified some icons (not yet finished) - modified codeml webservice, so that single failed sub-jobs don't break the whole job anymore. - simplified CMLModel class (had to change topali.xml therefore again) ------------------------------------------------------------------------ r274 | imilne | 2007-09-21 11:20:17 +0100 (Fri, 21 Sep 2007) | 1 line The jobs panel will now identify known remote clusters and display them to the user, so you know which cluster your job is running on (SCRI or Dundee for now). ------------------------------------------------------------------------ r273 | imilne | 2007-09-20 10:39:47 +0100 (Thu, 20 Sep 2007) | 2 lines Changed some of the logging so that the CLIENT logs what used to be server messages TO the SERVER (see topali.gui.Tracker). Restored version.html as a static file for version checking, and made tracking.jsp just for the logging. Both these are deployed to tomcat. ------------------------------------------------------------------------ r272 | imilne | 2007-09-19 16:04:58 +0100 (Wed, 19 Sep 2007) | 3 lines Binaries for locally running jobs will now be distributed with the installers. Modified the help text for local jobs. Removed the src folder from the installers - we've made the svn public so that should be enough for gnu compliance. ------------------------------------------------------------------------ r271 | imilne | 2007-09-19 15:39:24 +0100 (Wed, 19 Sep 2007) | 1 line Edited some of the tips text. ------------------------------------------------------------------------ r270 | imilne | 2007-09-19 15:39:10 +0100 (Wed, 19 Sep 2007) | 1 line Added our locally (gruffalo) compiled linux executables into svn. Other users will still need to recompile before use unless they have identical Intel Xeon hardware (I think). ------------------------------------------------------------------------ r269 | imilne | 2007-09-19 10:35:42 +0100 (Wed, 19 Sep 2007) | 1 line Fixed a problem with the build file that meant certain files were not been updated when copied into the build directory. The Ant tasks now do a clean beforehand to ensure the correct files are always copied over. ------------------------------------------------------------------------ r268 | imilne | 2007-09-19 10:30:38 +0100 (Wed, 19 Sep 2007) | 1 line Modifications to support everything now being hosted via www.topali.org rather than gruffalo. ------------------------------------------------------------------------ r267 | imilne | 2007-09-18 15:13:49 +0100 (Tue, 18 Sep 2007) | 2 lines Made new settings for internal and public TOPALi deployments to tomcat. Modified TOPALi's resource broker settings to query either a serial or a parallel resource broker depending on the job type. ------------------------------------------------------------------------ r266 | imilne | 2007-09-18 12:06:31 +0100 (Tue, 18 Sep 2007) | 1 line Modified the download page so that we maintain a log file of downloads (by linking to the jsp tracking file and using its log). ------------------------------------------------------------------------ r265 | imilne | 2007-09-18 11:28:33 +0100 (Tue, 18 Sep 2007) | 3 lines Changes to the GUIs for trees. Changed the deployment directory on gruffalo. Added some more whatsnew text and images. ------------------------------------------------------------------------ r264 | dlindn | 2007-09-17 15:30:28 +0100 (Mon, 17 Sep 2007) | 1 line - Modified build.scri.properties ------------------------------------------------------------------------ r263 | dlindn | 2007-09-17 14:12:32 +0100 (Mon, 17 Sep 2007) | 2 lines - VAMSAS: Removed mapper serialization again, replaced it with a "ID mechanism for all DataObjects" - Connecting to vamsas session does not clear the current project anymore ------------------------------------------------------------------------ r262 | dlindn | 2007-09-12 16:25:48 +0100 (Wed, 12 Sep 2007) | 5 lines - Created (empty) html pages for help menu, linked to help buttons - Moved "Run,Cancel,Default,Help" button panel creation to one single method in utils class - Cleaned up codonw dialog - before running codeml it's now checked if the selected partition is a multiple of 3 and does not contain stop codons - fixed codeml ------------------------------------------------------------------------ r261 | dlindn | 2007-09-11 12:02:45 +0100 (Tue, 11 Sep 2007) | 10 lines - fixed vamsas mouseover bug - fixed vamsas "writing non-finished result to vamsas" bug - cleaned up branch model dialog layout - fixed Project.merge() method - added Button to hide non-supported models from the modelgenerator table - tided up partitions dialog - fixed "atv still running after closing dialog" bug - added "atv starting up" message INFO: Updated vamsas-lib. ------------------------------------------------------------------------ r260 | dlindn | 2007-09-07 13:44:33 +0100 (Fri, 07 Sep 2007) | 1 line ------------------------------------------------------------------------ r259 | dlindn | 2007-09-07 11:42:09 +0100 (Fri, 07 Sep 2007) | 3 lines - Fixed tree dialog layout. - Moved all job settings dialogs in a new package (topali.gui.dialog.jobs) - Currently working on Codeml dialog layout ------------------------------------------------------------------------ r258 | dlindn | 2007-09-06 10:47:25 +0100 (Thu, 06 Sep 2007) | 1 line Removed unused class definitions from topali.xml ------------------------------------------------------------------------ r257 | dlindn | 2007-09-06 10:43:12 +0100 (Thu, 06 Sep 2007) | 2 lines Implemented ObjectMapper serializiation, storing/loading complete Topali project to Vamsas appdata is working now. ------------------------------------------------------------------------ r256 | imilne | 2007-09-06 10:06:02 +0100 (Thu, 06 Sep 2007) | 1 line The "tracking" progress bar for jobs that can't be tracked is now the same size as other job types. ------------------------------------------------------------------------ r255 | imilne | 2007-09-06 09:29:35 +0100 (Thu, 06 Sep 2007) | 1 line Updates to the web documentation pages for deployment to the new www.topali.org domain. ------------------------------------------------------------------------ r254 | imilne | 2007-09-06 08:20:19 +0100 (Thu, 06 Sep 2007) | 1 line Added our short-term todo list. ------------------------------------------------------------------------ r253 | dlindn | 2007-08-31 10:35:34 +0100 (Fri, 31 Aug 2007) | 1 line - activated "writing/reading to vamsas appdata" in VamsasManager.java (just for testing purposes); ------------------------------------------------------------------------ r252 | dlindn | 2007-08-30 15:02:32 +0100 (Thu, 30 Aug 2007) | 1 line - Just added some comments to VamsasManager ------------------------------------------------------------------------ r251 | dlindn | 2007-08-30 13:54:12 +0100 (Thu, 30 Aug 2007) | 4 lines - Further worked on topali<->vamsas - Added a vamsas session selection dialog - New vamsas library - New castor library ------------------------------------------------------------------------ r250 | dlindn | 2007-08-30 13:53:42 +0100 (Thu, 30 Aug 2007) | 5 lines - Further worked on topali<->vamsas - Added a vamsas session selection dialog - New vamsas library - New castor library ------------------------------------------------------------------------ r249 | imilne | 2007-08-21 08:40:46 +0100 (Tue, 21 Aug 2007) | 1 line Fixed the naming of the SGE script for a MrBayes analysis (and the name of the class that is called by the script). ------------------------------------------------------------------------ r248 | imilne | 2007-08-20 09:17:12 +0100 (Mon, 20 Aug 2007) | 1 line Added a new property "user.topali.dir" into the build file to allow an alternate location to be specified for finding TOPALi's files (for Jim's situation where the child nodes can't see the webapps dir). ------------------------------------------------------------------------ r247 | imilne | 2007-08-20 09:00:41 +0100 (Mon, 20 Aug 2007) | 1 line Removed some tips text that was out of date. ------------------------------------------------------------------------ r246 | dlindn | 2007-08-20 08:34:51 +0100 (Mon, 20 Aug 2007) | 1 line ------------------------------------------------------------------------ r245 | dlindn | 2007-08-17 10:22:04 +0100 (Fri, 17 Aug 2007) | 2 lines - Fixed a bug in nexus file writer (which produced a corrupt file, when selecting partitions of size n%50==0) - Worked on vamsas stuff reimplementation (still in progress) ------------------------------------------------------------------------ r244 | imilne | 2007-08-16 08:37:17 +0100 (Thu, 16 Aug 2007) | 1 line An SGE script for fastml had never been added to the Dundee Uni scripts directory. ------------------------------------------------------------------------ r243 | imilne | 2007-08-16 08:15:35 +0100 (Thu, 16 Aug 2007) | 1 line Added cluster.properties.template that was missing from the repo! ------------------------------------------------------------------------ r242 | imilne | 2007-08-15 10:19:02 +0100 (Wed, 15 Aug 2007) | 1 line Merged in the changes from the branch: revisions 222 (-1?) to 241. ------------------------------------------------------------------------ r241 | imilne | 2007-08-15 09:40:59 +0100 (Wed, 15 Aug 2007) | 1 line Yet another attempt at fixing the windows/linux file-format incompatibility that is stopping the script from being used (on linux). ------------------------------------------------------------------------ r240 | imilne | 2007-08-14 15:25:48 +0100 (Tue, 14 Aug 2007) | 1 line Made multiple build.CLUSTER.properties files for each location and added the ability for ant to use each of the files by passing it a -Dprops=filename option. ------------------------------------------------------------------------ r239 | imilne | 2007-08-14 14:03:15 +0100 (Tue, 14 Aug 2007) | 1 line Modifications to the Dundee scripts after meeting with Jim. ------------------------------------------------------------------------ r238 | imilne | 2007-08-14 09:44:06 +0100 (Tue, 14 Aug 2007) | 1 line Modified the default location of the resource broker. ------------------------------------------------------------------------ r237 | imilne | 2007-08-14 09:36:23 +0100 (Tue, 14 Aug 2007) | 1 line Delete deploy.sh which isn't really needed any more. ------------------------------------------------------------------------ r236 | imilne | 2007-08-14 09:28:15 +0100 (Tue, 14 Aug 2007) | 2 lines Modified the installer for the new directory layout. Removed the Build Tree installer, as we'll just offer out the SVN repo from now one, rather than a downloadable source tree. ------------------------------------------------------------------------ r235 | imilne | 2007-08-14 09:03:41 +0100 (Tue, 14 Aug 2007) | 2 lines Reduced logging requirements in build.properties to just the directory path, rather than explicit paths for each log file. Added tracking.jsp into the WAR file and used the same logging template to determine its log location. ------------------------------------------------------------------------ r234 | imilne | 2007-08-14 08:44:13 +0100 (Tue, 14 Aug 2007) | 1 line Reorganization of the binaries location, and fixes for locally running jobs. ------------------------------------------------------------------------ r233 | imilne | 2007-08-13 15:56:43 +0100 (Mon, 13 Aug 2007) | 4 lines Changes to the directory structures (again). Ant task now copies entire binaries directory to server, but leaves it at /binaries rather than /WEB-INF/binaries Comments added to the build.properties file. Compiled location for classes stays at the top level now. ------------------------------------------------------------------------ r232 | imilne | 2007-08-13 11:27:03 +0100 (Mon, 13 Aug 2007) | 1 line First attempt at configuring the server-side logging via Ant. Might not work, but I need to check it in to maintain a clean directory-repository. ------------------------------------------------------------------------ r231 | imilne | 2007-08-13 11:10:41 +0100 (Mon, 13 Aug 2007) | 1 line Linux/Windows file-format edit to ensure the script can be run. ------------------------------------------------------------------------ r230 | dlindn | 2007-08-13 08:40:14 +0100 (Mon, 13 Aug 2007) | 1 line - Quick hack for ISMB: commented out writing MGResults to VAMSAS document ------------------------------------------------------------------------ r229 | imilne | 2007-07-26 15:35:29 +0100 (Thu, 26 Jul 2007) | 1 line Checking in modifications at the end of Thursday. ------------------------------------------------------------------------ r228 | imilne | 2007-07-26 15:31:39 +0100 (Thu, 26 Jul 2007) | 1 line Moved phyml directory into the binaries source folder. ------------------------------------------------------------------------ r227 | imilne | 2007-07-26 11:22:44 +0100 (Thu, 26 Jul 2007) | 1 line Added initial Tomcat deployment tasks and modified the build.properties files to include the parameters required for this. ------------------------------------------------------------------------ r226 | imilne | 2007-07-26 11:19:49 +0100 (Thu, 26 Jul 2007) | 1 line Used the default template server-config.wsdd file from Axis to pre-generate the file for use on the cluster. If it is deployed as is, then Axis does not need any further configuration (or use of deploy.wsdd files). ------------------------------------------------------------------------ r225 | imilne | 2007-07-26 08:55:17 +0100 (Thu, 26 Jul 2007) | 2 lines Initial work on the WAR task started. Required files are copied into the build directory and the .war built from that. All previous WEB-INF files are now in a new folder called config. ------------------------------------------------------------------------ r224 | imilne | 2007-07-25 14:12:25 +0100 (Wed, 25 Jul 2007) | 1 line Folder restructuring. ------------------------------------------------------------------------ r223 | imilne | 2007-07-25 11:42:33 +0100 (Wed, 25 Jul 2007) | 1 line Creating a branch to experiment with full Ant install/deploy tasks (which will probably require major folder reorganization). ------------------------------------------------------------------------ r222 | imilne | 2007-07-25 11:40:44 +0100 (Wed, 25 Jul 2007) | 1 line Changes to build script. ------------------------------------------------------------------------ r221 | imilne | 2007-07-25 08:32:24 +0100 (Wed, 25 Jul 2007) | 2 lines Deleted the unused logs directory. Created a new directory for development-time libs, that is, libs that are only needed to compile or deploy TOPALi - they're not needed at runtime or by tomcat. ------------------------------------------------------------------------ r220 | imilne | 2007-07-25 08:25:38 +0100 (Wed, 25 Jul 2007) | 1 line Minor edit to show the user ID we generate in the Help->About dialog box. ------------------------------------------------------------------------ r219 | dlindn | 2007-07-13 16:09:34 +0100 (Fri, 13 Jul 2007) | 1 line - Final commit before the VAMSAS demo ------------------------------------------------------------------------ r218 | dlindn | 2007-07-12 18:57:36 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r217 | dlindn | 2007-07-12 18:18:39 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r216 | dlindn | 2007-07-12 18:04:47 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r215 | dlindn | 2007-07-12 17:57:49 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r214 | dlindn | 2007-07-12 17:36:43 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r213 | dlindn | 2007-07-12 17:05:52 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r212 | dlindn | 2007-07-12 17:05:42 +0100 (Thu, 12 Jul 2007) | 1 line ------------------------------------------------------------------------ r211 | dlindn | 2007-07-12 16:45:17 +0100 (Thu, 12 Jul 2007) | 1 line - Changed the way, Topali reads/writes CodeMLResult to the vamsas document ------------------------------------------------------------------------ r210 | dlindn | 2007-07-12 12:24:07 +0100 (Thu, 12 Jul 2007) | 2 lines - Worked on FastML - Changed some things in MenuBar (Names, etc.) ------------------------------------------------------------------------ r209 | imilne | 2007-07-10 18:11:34 +0100 (Tue, 10 Jul 2007) | 1 line Tagged copy of the public release of version 2.15 ------------------------------------------------------------------------ r208 | dlindn | 2007-07-10 14:24:52 +0100 (Tue, 10 Jul 2007) | 4 lines - Improved FastML to support models and gamma - Removed possibility to run DSS and LRT with non-DNA seq. - Commented out the different recomb. method buttons on the toolbar - Commented out the icons for the recomb. methods ------------------------------------------------------------------------ r207 | dlindn | 2007-07-06 17:05:26 +0100 (Fri, 06 Jul 2007) | 2 lines -Added FastML webservice for ancestral sequence creation (still very buggy!) ------------------------------------------------------------------------ r206 | dlindn | 2007-06-28 16:31:42 +0100 (Thu, 28 Jun 2007) | 1 line ------------------------------------------------------------------------ r205 | dlindn | 2007-06-28 16:31:16 +0100 (Thu, 28 Jun 2007) | 4 lines - Implemented fast WAG/NJ tree for protein alignments - Changed webservice limit from total number of bases to number of sequences - Added "Load example alignment" option to "Import alignment" dialog - Added MrBayes cDNA tree estimation ------------------------------------------------------------------------ r204 | dlindn | 2007-06-28 16:30:46 +0100 (Thu, 28 Jun 2007) | 1 line ------------------------------------------------------------------------ r203 | imilne | 2007-06-25 08:38:05 +0100 (Mon, 25 Jun 2007) | 1 line Minor edits to the web pages to reflect the 2.15 version's problems with Castor and Java 1.6 ------------------------------------------------------------------------ r202 | dlindn | 2007-06-20 16:48:27 +0100 (Wed, 20 Jun 2007) | 5 lines - Extended MrBayes Webservice to support more parameters - Implemented Phyml Webservice - Added midpoint routing option to TreePanel - Did a "Clean up import statements" in Eclipse (by accident...) ------------------------------------------------------------------------ r201 | dlindn | 2007-06-15 16:17:09 +0100 (Fri, 15 Jun 2007) | 1 line - Extended MrBayes Webservice to support more parameters ------------------------------------------------------------------------ r200 | dlindn | 2007-06-12 16:13:35 +0100 (Tue, 12 Jun 2007) | 3 lines - Replaced JC tree construction with F84+G (needs to be tested!) - Added a VAMSAS icon to the toolbar, to connect to/synchronize a VAMSAS session ------------------------------------------------------------------------ r199 | dlindn | 2007-06-12 08:31:12 +0100 (Tue, 12 Jun 2007) | 1 line ------------------------------------------------------------------------ r198 | dlindn | 2007-06-12 08:30:55 +0100 (Tue, 12 Jun 2007) | 1 line ------------------------------------------------------------------------ r197 | imilne | 2007-06-11 16:07:33 +0100 (Mon, 11 Jun 2007) | 1 line Fixed a log problem that had the access and info logs from the cluster code logging into the tracking log from the JSP check-for-updates page. ------------------------------------------------------------------------ r196 | imilne | 2007-06-11 14:54:21 +0100 (Mon, 11 Jun 2007) | 2 lines Changed cluster-side logging to use log4j (and single logfile output). access-log.txt will now write request and result data (ie, what was asked for and (if) it worked, when it was sent back). ------------------------------------------------------------------------ r195 | dlindn | 2007-06-11 13:40:26 +0100 (Mon, 11 Jun 2007) | 4 lines - Extended DocumentHandler to also read/write the various job parameters (pdm_burnin, etc.) as Vamsas provencance entry. - Modified NavPanel, so that it automatically updates when a new Result has been added. ------------------------------------------------------------------------ r194 | dlindn | 2007-06-06 16:49:32 +0100 (Wed, 06 Jun 2007) | 1 line ------------------------------------------------------------------------ r193 | dlindn | 2007-06-06 16:49:19 +0100 (Wed, 06 Jun 2007) | 1 line ------------------------------------------------------------------------ r192 | dlindn | 2007-06-06 16:44:29 +0100 (Wed, 06 Jun 2007) | 1 line ------------------------------------------------------------------------ r191 | dlindn | 2007-06-06 16:43:25 +0100 (Wed, 06 Jun 2007) | 4 lines - Added vamsas read/write support for TOPALi annotations (Partitions, Coding Regions) - Made MrBayes and Modelgenerator Webservice progress trackable - Implemented a basic server side limit mechanism (limited alignment size) - Added "Load example alignment" to help menu ------------------------------------------------------------------------ r190 | dlindn | 2007-05-28 16:26:59 +0100 (Mon, 28 May 2007) | 1 line ------------------------------------------------------------------------ r189 | dlindn | 2007-05-28 16:26:39 +0100 (Mon, 28 May 2007) | 5 lines - Alignments, analysis results and annotations (partitions) can now be exported and imported to/from a VAMSAS session (but a proper update mechanism is still missing) ------------------------------------------------------------------------ r188 | imilne | 2007-05-25 15:10:09 +0100 (Fri, 25 May 2007) | 1 line Updated the installer config file. ------------------------------------------------------------------------ r187 | imilne | 2007-05-25 14:12:51 +0100 (Fri, 25 May 2007) | 1 line Updated the RemoteJob.java code to use the more up-to-date SBRN resource broker. ------------------------------------------------------------------------ r186 | imilne | 2007-05-25 14:12:24 +0100 (Fri, 25 May 2007) | 1 line Updated tracking and version code to log who/when each time TOPALi checks for updates. ------------------------------------------------------------------------ r185 | dlindn | 2007-05-25 11:35:42 +0100 (Fri, 25 May 2007) | 1 line Updated version.jsp ------------------------------------------------------------------------ r184 | imilne | 2007-05-24 14:22:33 +0100 (Thu, 24 May 2007) | 1 line Added more accurate percentage tracking feedback for jobs in the progress bars. ------------------------------------------------------------------------ r183 | imilne | 2007-05-24 14:22:03 +0100 (Thu, 24 May 2007) | 1 line A failed cluster job is now cancelled (in the SGE queues) as soon as the monitor is notified of the exception. Updated code. ------------------------------------------------------------------------ r182 | imilne | 2007-05-24 14:12:18 +0100 (Thu, 24 May 2007) | 1 line A failed cluster job is now cancelled (in the SGE queues) as soon as the monitor is notified of the exception. ------------------------------------------------------------------------ r181 | imilne | 2007-05-24 12:27:43 +0100 (Thu, 24 May 2007) | 1 line Fixed the warning messages about the Sun BASE64 encoder/decoder. ------------------------------------------------------------------------ r180 | imilne | 2007-05-24 09:19:16 +0100 (Thu, 24 May 2007) | 3 lines Updated the cluster scripts to increase the JVM max memory to 256MB. Added some of Dominik's newer scripts to the Dundee University directory. Added a hostname command at the start of each script so that the SGE output logs will show the name of the node that is running the job. ------------------------------------------------------------------------ r179 | dlindn | 2007-05-22 17:35:12 +0100 (Tue, 22 May 2007) | 7 lines - Alignments and Sequences can now be written and read to/from a VAMSAS document (topali.gui) - Added PropertyChangeListener support to Project.java (GUI componentes should register to the project to receive data update events) (topali.vamsas) ------------------------------------------------------------------------ r178 | dlindn | 2007-05-21 16:19:02 +0100 (Mon, 21 May 2007) | 1 line VAMSAS DocumentHandler: Writing to file now works. ------------------------------------------------------------------------ r177 | imilne | 2007-05-19 11:45:30 +0100 (Sat, 19 May 2007) | 4 lines Changes from the Friday of the meeting. Initial attempts at using the new vamsas API to do document updates (api is currently bugged and although TOPALi code is ok, the functionality isn't working). New class DocumentHandler now does all the store/load operations. New class ObjectMapper maintains hashtable mappings between TOPALi objects and vamsas object IDs. ------------------------------------------------------------------------ r176 | imilne | 2007-05-19 11:43:50 +0100 (Sat, 19 May 2007) | 1 line Deleted more vamsas classes that won't be used. ------------------------------------------------------------------------ r175 | imilne | 2007-05-19 11:43:02 +0100 (Sat, 19 May 2007) | 1 line Renamed more vamsas classes that won't be used. ------------------------------------------------------------------------ r174 | imilne | 2007-05-17 18:08:22 +0100 (Thu, 17 May 2007) | 7 lines Many changes from the May 17th (Thursday) vamsas meeting at Dundee Uni. The topali.vamsas package has had several classes removed (renamed to .bak for now) that are no longer valid. VamsasManager.java is now the main class for handling vamsas communication. Renamed PickHandler.java to VamsasMsgHandler.java Added a new topali.gui class - VasmasEvents - to deal with pick related messages and to act as an gopher between VamsasManager and TOPALi's GUI classes. The vamsas code now contains JimP's new client initialization routines and registers various handlers for document updates. Pick message code reimplemented in TOPALi. ------------------------------------------------------------------------ r173 | imilne | 2007-05-17 18:04:45 +0100 (Thu, 17 May 2007) | 1 line Deleted the vamsas jar files from the repository. Similar to topali.jar they are rebuilt often and shouldn't be under version control. ------------------------------------------------------------------------ r172 | imilne | 2007-05-17 18:03:32 +0100 (Thu, 17 May 2007) | 1 line Modified the various TOPALi launchers so they contain the correct library jar files. ------------------------------------------------------------------------ r171 | imilne | 2007-05-16 18:04:47 +0100 (Wed, 16 May 2007) | 1 line Deleted topali.jar from the repository. (It should never be added as it gets rebuilt all the time). ------------------------------------------------------------------------ r170 | dlindn | 2007-05-16 17:23:04 +0100 (Wed, 16 May 2007) | 7 lines - Implemented CodonW webservice - Implemented Modelgenerator webservice - Modified MrBayes webservice (to take several options) - Implemented Vamsas2Topali methods moved all x2x methods to VamsasMapper.java - misc. small changes ------------------------------------------------------------------------ r169 | dlindn | 2007-04-16 12:03:02 +0100 (Mon, 16 Apr 2007) | 1 line Just some minor changes ------------------------------------------------------------------------ r168 | dlindn | 2007-04-16 08:49:10 +0100 (Mon, 16 Apr 2007) | 1 line ------------------------------------------------------------------------ r167 | dlindn | 2007-04-13 10:08:25 +0100 (Fri, 13 Apr 2007) | 1 line Changed the client side logging from java logging to log4j. ------------------------------------------------------------------------ r166 | imilne | 2007-04-12 14:31:58 +0100 (Thu, 12 Apr 2007) | 1 line Header code for the start of logging in version.jsp ------------------------------------------------------------------------ r165 | dlindn | 2007-04-12 13:53:21 +0100 (Thu, 12 Apr 2007) | 1 line Restored HistogramPanel ------------------------------------------------------------------------ r164 | imilne | 2007-04-12 09:42:27 +0100 (Thu, 12 Apr 2007) | 1 line Initial files for moving update checking (and logging) to gruffalo. ------------------------------------------------------------------------ r163 | imilne | 2007-04-12 09:15:57 +0100 (Thu, 12 Apr 2007) | 1 line Added a results icon for the codeml jobs. ------------------------------------------------------------------------ r162 | imilne | 2007-03-29 14:59:47 +0100 (Thu, 29 Mar 2007) | 1 line Working dist for Iain, plus added the jar files into SVN (finally). ------------------------------------------------------------------------ r161 | dlindn | 2007-03-29 14:44:45 +0100 (Thu, 29 Mar 2007) | 2 lines - Small changes on LogHandler - Commented some classes ------------------------------------------------------------------------ r160 | dlindn | 2007-03-28 16:48:48 +0100 (Wed, 28 Mar 2007) | 1 line ------------------------------------------------------------------------ r159 | dlindn | 2007-03-28 16:48:27 +0100 (Wed, 28 Mar 2007) | 1 line ------------------------------------------------------------------------ r158 | dlindn | 2007-03-28 16:48:10 +0100 (Wed, 28 Mar 2007) | 1 line ------------------------------------------------------------------------ r157 | dlindn | 2007-03-28 16:47:40 +0100 (Wed, 28 Mar 2007) | 1 line ------------------------------------------------------------------------ r156 | dlindn | 2007-03-28 16:44:48 +0100 (Wed, 28 Mar 2007) | 3 lines - Worked on client side logging - Removed unused fields from CodeMLModel - Fixed Chi2 calculation in CMLBranchResultPanel ------------------------------------------------------------------------ r155 | dlindn | 2007-03-26 09:42:37 +0100 (Mon, 26 Mar 2007) | 5 lines - Fixed CodeML branch model analysis. - Worked on ATV integration - Overworked all result panels - Implemented a log handler for the client side (and replaced System.out.println's with logging statements) ------------------------------------------------------------------------ r154 | dlindn | 2007-03-08 09:03:30 +0000 (Thu, 08 Mar 2007) | 1 line Added a directory for junit tests ------------------------------------------------------------------------ r153 | dlindn | 2007-03-08 09:02:41 +0000 (Thu, 08 Mar 2007) | 1 line ------------------------------------------------------------------------ r152 | dlindn | 2007-03-08 09:01:34 +0000 (Thu, 08 Mar 2007) | 1 line ------------------------------------------------------------------------ r151 | dlindn | 2007-03-08 09:00:51 +0000 (Thu, 08 Mar 2007) | 5 lines - Added CodeML branch model job (not yet working properly) - Implemented CodeML site model settings dialog. - Added CodeML branch model settings dialog. ------------------------------------------------------------------------ r150 | dlindn | 2007-02-27 15:44:06 +0000 (Tue, 27 Feb 2007) | 1 line ------------------------------------------------------------------------ r149 | dlindn | 2007-02-27 12:29:14 +0000 (Tue, 27 Feb 2007) | 1 line ------------------------------------------------------------------------ r148 | dlindn | 2007-02-27 12:28:54 +0000 (Tue, 27 Feb 2007) | 4 lines - Merged the different codeml model and result classes to just one class called CMLModel - Added a extra data class for positive selected sites (PSSite) and changed the codeml parsers accordingly - Added CodeMLResultPanel (graphical representation of the codeml results) ------------------------------------------------------------------------ r147 | imilne | 2007-02-22 16:02:34 +0000 (Thu, 22 Feb 2007) | 1 line Checked in first attempt at displaying the number of jobs that are in the queue in front of you. ------------------------------------------------------------------------ r146 | imilne | 2007-02-21 08:57:38 +0000 (Wed, 21 Feb 2007) | 1 line Modified the preferences to make gruffalo the default web service machine (and also to default to using it in broker mode rather than direct mode). ------------------------------------------------------------------------ r145 | dlindn | 2007-02-13 08:28:00 +0000 (Tue, 13 Feb 2007) | 1 line -Added CodeMLRunCount to topali.xml ------------------------------------------------------------------------ r144 | dlindn | 2007-02-12 16:57:30 +0000 (Mon, 12 Feb 2007) | 2 lines Did some small changes: Code formatted, removed unused variables, etc. ------------------------------------------------------------------------ r143 | dlindn | 2007-02-08 09:10:19 +0000 (Thu, 08 Feb 2007) | 4 lines -Modified CMLResultParsers, so that they now also parse PSS information. -Added PSS information to CodeMLModel (just a String), see also topali.xml -Changed Model<->Run, was M1a=Run4, M2a=Run5, is now M1a=Run2, M2a=Run3 ------------------------------------------------------------------------ r142 | imilne | 2007-02-07 10:24:17 +0000 (Wed, 07 Feb 2007) | 1 line License and copyright updates. Now 2003-2007, and with Dominik included. ------------------------------------------------------------------------ r141 | dlindn | 2007-02-06 16:23:28 +0000 (Tue, 06 Feb 2007) | 1 line Added primitive JTable to CodeMLResultsPanel. ------------------------------------------------------------------------ r140 | imilne | 2007-02-06 15:50:45 +0000 (Tue, 06 Feb 2007) | 1 line Job monitoring for CodeML now complete, and the parsers return the full set of results for each model. ------------------------------------------------------------------------ r139 | imilne | 2007-02-06 14:48:41 +0000 (Tue, 06 Feb 2007) | 2 lines Modified parsers to use CodeMLModel classes. Added basic results panel for a CodeML run. ------------------------------------------------------------------------ r138 | imilne | 2007-02-06 14:10:34 +0000 (Tue, 06 Feb 2007) | 1 line Added CodeMLModel.java to the topali.data.CodeMLResult class so that the data received back from each model run can be held in a proper OO structure. ------------------------------------------------------------------------ r137 | dlindn | 2007-02-06 13:57:54 +0000 (Tue, 06 Feb 2007) | 1 line ------------------------------------------------------------------------ r136 | dlindn | 2007-02-06 13:43:20 +0000 (Tue, 06 Feb 2007) | 1 line ------------------------------------------------------------------------ r135 | dlindn | 2007-02-06 13:25:05 +0000 (Tue, 06 Feb 2007) | 1 line ------------------------------------------------------------------------ r134 | dlindn | 2007-02-06 13:20:35 +0000 (Tue, 06 Feb 2007) | 1 line ------------------------------------------------------------------------ r133 | imilne | 2007-02-06 11:57:55 +0000 (Tue, 06 Feb 2007) | 1 line The CodeML analysis now returns a basic status string that can be used by the job tracker. ------------------------------------------------------------------------ r132 | imilne | 2007-02-06 09:17:13 +0000 (Tue, 06 Feb 2007) | 1 line Modified the remote web services code to use the new resource broker methods. ------------------------------------------------------------------------ r131 | dlindn | 2007-02-05 14:00:01 +0000 (Mon, 05 Feb 2007) | 1 line Made JobsPanelEntry abstract, implemented subtypes for different purposes. ------------------------------------------------------------------------ r130 | imilne | 2007-02-05 13:39:04 +0000 (Mon, 05 Feb 2007) | 1 line Changed the web services so that they return a JobStatus instance in their getPercentageComplete() methods (rather than a simple float), allowing us finer tracking of the job's status. ------------------------------------------------------------------------ r129 | imilne | 2007-02-05 09:10:17 +0000 (Mon, 05 Feb 2007) | 1 line Running an "ant tomcat" will now restart the remote server in addition to copying over the topali.jar file. ------------------------------------------------------------------------ r128 | imilne | 2007-02-02 13:55:56 +0000 (Fri, 02 Feb 2007) | 1 line Final mods (for now) to server-config code. Now we just have WEB-INF/cluster and the SGE scripts go in there, along with a simple cluster.properties file. Most of what used to be in scri/dundee.properties is now determined dynamically. ------------------------------------------------------------------------ r127 | imilne | 2007-02-02 13:39:27 +0000 (Fri, 02 Feb 2007) | 1 line Updates to properties files due to server-config simplification (Jim is ok with these settings for Dundee). ------------------------------------------------------------------------ r126 | imilne | 2007-01-31 09:04:00 +0000 (Wed, 31 Jan 2007) | 1 line Simplified the cluster-side settings file for logs, going from two separate entries to a single path. ------------------------------------------------------------------------ r125 | imilne | 2007-01-31 08:55:20 +0000 (Wed, 31 Jan 2007) | 1 line Removed the (useless) server-status panel from the jobs panel. It would make no sense in a resource-broker environment where each job could go to a different cluster in the pool. ------------------------------------------------------------------------ r124 | dlindn | 2007-01-24 15:48:54 +0000 (Wed, 24 Jan 2007) | 1 line Modified LRT to provide more accurate progress information ------------------------------------------------------------------------ r123 | imilne | 2007-01-24 11:45:36 +0000 (Wed, 24 Jan 2007) | 3 lines First attempt at improving DSS job monitoring with per-subjob percentage tracking (NOT working yet). Renamed binaries/src back to binaries/unix. Modified cluster-side properties files so that only a single "bin-path" exists, with actual paths to the binaries worked out in each methods WebService code. ------------------------------------------------------------------------ r122 | imilne | 2007-01-24 09:54:40 +0000 (Wed, 24 Jan 2007) | 1 line Minor vamsas mod to AlignmentPanel.java ------------------------------------------------------------------------ r121 | dlindn | 2007-01-24 09:54:10 +0000 (Wed, 24 Jan 2007) | 1 line ------------------------------------------------------------------------ r120 | dlindn | 2007-01-24 09:47:22 +0000 (Wed, 24 Jan 2007) | 1 line ------------------------------------------------------------------------ r119 | imilne | 2007-01-24 09:24:36 +0000 (Wed, 24 Jan 2007) | 1 line Changed the location of where logs are stored on gruffalo. ------------------------------------------------------------------------ r118 | imilne | 2007-01-24 09:24:19 +0000 (Wed, 24 Jan 2007) | 1 line Latest version.txt ------------------------------------------------------------------------ r117 | imilne | 2007-01-24 09:13:09 +0000 (Wed, 24 Jan 2007) | 1 line Rename binaries/src back to binaries/unix ------------------------------------------------------------------------ r116 | imilne | 2007-01-24 08:47:28 +0000 (Wed, 24 Jan 2007) | 1 line Updated vamsas code. ------------------------------------------------------------------------ r115 | imilne | 2007-01-24 08:43:39 +0000 (Wed, 24 Jan 2007) | 1 line Removed file/folder ------------------------------------------------------------------------ r114 | imilne | 2007-01-24 08:42:15 +0000 (Wed, 24 Jan 2007) | 1 line New web settings files for the updated gruffalo configuration at SCRI. ------------------------------------------------------------------------ r113 | dlindn | 2007-01-19 12:23:50 +0000 (Fri, 19 Jan 2007) | 1 line ------------------------------------------------------------------------ r112 | dlindn | 2007-01-19 12:16:06 +0000 (Fri, 19 Jan 2007) | 1 line ------------------------------------------------------------------------ r111 | dlindn | 2007-01-19 12:12:47 +0000 (Fri, 19 Jan 2007) | 5 lines -Fixed mouse highlighting/selection -Added CDSAnnotations -Replaced PartitionDialog with the more general RegionDialog ------------------------------------------------------------------------ r110 | dlindn | 2007-01-12 09:00:20 +0000 (Fri, 12 Jan 2007) | 1 line Initial (Dominik) commit with pre/post Christmas changes from vamsas meeting. ------------------------------------------------------------------------ r109 | imilne | 2007-01-12 08:36:30 +0000 (Fri, 12 Jan 2007) | 1 line Post Christmas commit with several changes (vamsas code from the meeting, additional positive selection code). ------------------------------------------------------------------------ r108 | imilne | 2006-11-23 13:04:25 +0000 (Thu, 23 Nov 2006) | 1 line Updates to the web services connecting code to first query for a server status HTML file that is displayed in the GUI while jobs are running. ------------------------------------------------------------------------ r107 | imilne | 2006-11-21 10:02:40 +0000 (Tue, 21 Nov 2006) | 1 line Changes to the XML format - 2D arrays are now saved as strings (using methods from SBRN Commons). This negates the Java 1.6 problems with Castor but has made the project format different from earlier versions. ------------------------------------------------------------------------ r106 | imilne | 2006-11-21 10:01:49 +0000 (Tue, 21 Nov 2006) | 1 line Minor change to the text shown on progress bars in the job monitoring screen. ------------------------------------------------------------------------ r105 | imilne | 2006-11-15 16:27:28 +0000 (Wed, 15 Nov 2006) | 1 line Cleaned up logging statements and refactored cluster job code based on the new CodeML stuff. ------------------------------------------------------------------------ r104 | imilne | 2006-11-15 14:37:15 +0000 (Wed, 15 Nov 2006) | 1 line Improved logging setup for cluster side runs. There are now two log files - one for accesses only, and another for more details logging that used to go to catalina.out (and probably still does, but it goes to a TOPALi-specific file now too). ------------------------------------------------------------------------ r103 | imilne | 2006-11-15 13:46:21 +0000 (Wed, 15 Nov 2006) | 1 line Updated the timer thread for JobPanel repaints so that indeterminate progress bars animate properly. ------------------------------------------------------------------------ r102 | imilne | 2006-11-15 13:36:16 +0000 (Wed, 15 Nov 2006) | 1 line Fixed typo in the job description shell script. ------------------------------------------------------------------------ r101 | imilne | 2006-11-15 11:55:39 +0000 (Wed, 15 Nov 2006) | 1 line Updated Axis deployment file for the renamed job packages. ------------------------------------------------------------------------ r100 | imilne | 2006-11-15 11:53:10 +0000 (Wed, 15 Nov 2006) | 1 line Trees moved to topali.cluster.jobs.trees ------------------------------------------------------------------------ r99 | imilne | 2006-11-15 11:51:33 +0000 (Wed, 15 Nov 2006) | 1 line PDM2 moved to topali.cluster.jobs.pdm2 ------------------------------------------------------------------------ r98 | imilne | 2006-11-15 11:48:52 +0000 (Wed, 15 Nov 2006) | 1 line PDM moved to topali.cluster.jobs.pdm ------------------------------------------------------------------------ r97 | imilne | 2006-11-15 11:44:42 +0000 (Wed, 15 Nov 2006) | 1 line LRT moved to topali.cluster.jobs.lrt ------------------------------------------------------------------------ r96 | imilne | 2006-11-15 11:42:48 +0000 (Wed, 15 Nov 2006) | 1 line HMM moved to topali.cluster.jobs.hmm ------------------------------------------------------------------------ r95 | imilne | 2006-11-15 11:20:43 +0000 (Wed, 15 Nov 2006) | 1 line DSS moved to topali.cluster.jobs.dss ------------------------------------------------------------------------ r94 | imilne | 2006-11-15 11:16:41 +0000 (Wed, 15 Nov 2006) | 1 line CML moved to topali.cluster.jobs.cml ------------------------------------------------------------------------ r93 | imilne | 2006-11-15 11:15:39 +0000 (Wed, 15 Nov 2006) | 1 line CML moved to topali.cluster.jobs.cml ------------------------------------------------------------------------ r92 | imilne | 2006-11-15 10:27:10 +0000 (Wed, 15 Nov 2006) | 1 line ReadSeq code added to version control (it had been forgotten!) ------------------------------------------------------------------------ r91 | imilne | 2006-11-15 10:08:59 +0000 (Wed, 15 Nov 2006) | 1 line Code refactoring for the codeml analysis package. ------------------------------------------------------------------------ r90 | imilne | 2006-11-14 13:02:38 +0000 (Tue, 14 Nov 2006) | 1 line Moved the ThreadManager and MultiThread classes into the SBRN commons package (renaming them) and then reintegrated the code into TOPALi via jar imports. ------------------------------------------------------------------------ r89 | imilne | 2006-11-13 15:04:02 +0000 (Mon, 13 Nov 2006) | 1 line Basic dialog for starting codeml jobs. ------------------------------------------------------------------------ r88 | imilne | 2006-11-13 11:51:25 +0000 (Mon, 13 Nov 2006) | 2 lines First attempt at the CODEML webservice. Source files for codeml added to repo. ------------------------------------------------------------------------ r87 | imilne | 2006-11-13 10:28:07 +0000 (Mon, 13 Nov 2006) | 1 line Basic runnable version of CODEML working. Results sent to working directory (not processed yet). ------------------------------------------------------------------------ r86 | imilne | 2006-11-10 09:58:11 +0000 (Fri, 10 Nov 2006) | 1 line Updated the export options so that an alignment can now be created/exported by concatenating together one or more of the selected partitions. ------------------------------------------------------------------------ r85 | imilne | 2006-11-09 14:06:04 +0000 (Thu, 09 Nov 2006) | 1 line Started added support for codeml positive selection analyses. Basic framework added, but no method as yet. ------------------------------------------------------------------------ r84 | imilne | 2006-11-09 11:58:49 +0000 (Thu, 09 Nov 2006) | 1 line Messing about with reading start/stop codons (nothing that works). ------------------------------------------------------------------------ r83 | imilne | 2006-11-09 11:58:31 +0000 (Thu, 09 Nov 2006) | 1 line Put the ReadSeq handling code *after* PAL loading code as it just doesn't work for many cases. Will use it as a last resort only. ------------------------------------------------------------------------ r82 | imilne | 2006-11-08 11:39:04 +0000 (Wed, 08 Nov 2006) | 1 line Updated help files. ------------------------------------------------------------------------ r81 | imilne | 2006-11-08 11:38:36 +0000 (Wed, 08 Nov 2006) | 1 line Modified ant and webstart scripts for updated library jar files. ------------------------------------------------------------------------ r80 | imilne | 2006-11-02 16:20:19 +0000 (Thu, 02 Nov 2006) | 1 line JFreeChart now uses back buffering to improve performance. ------------------------------------------------------------------------ r79 | imilne | 2006-10-30 11:31:34 +0000 (Mon, 30 Oct 2006) | 1 line Updated comments. ------------------------------------------------------------------------ r78 | imilne | 2006-10-26 16:20:20 +0100 (Thu, 26 Oct 2006) | 2 lines Cleaned up the batch file for easier library editing. TOPALi prints version of JRE upon launch (start of 1.6 testing). ------------------------------------------------------------------------ r77 | imilne | 2006-10-26 13:45:44 +0100 (Thu, 26 Oct 2006) | 1 line Attempts at changing the JFreeChart code for graph back-highlighting (not in use). ------------------------------------------------------------------------ r76 | imilne | 2006-09-27 11:23:12 +0100 (Wed, 27 Sep 2006) | 1 line Added a monitoring dialog to inform the user of status during alignment loading/conversion via ReadSeq. ------------------------------------------------------------------------ r75 | imilne | 2006-09-25 16:34:57 +0100 (Mon, 25 Sep 2006) | 1 line Used the new sbrn-sequtils.jar ReadSeq program so that TOPALi can deal with more sequence formats. Reading only so far - writing out these formats is still to be done. ------------------------------------------------------------------------ r74 | imilne | 2006-09-18 14:24:28 +0100 (Mon, 18 Sep 2006) | 1 line Fixed a layout bug with the new swing-layout package that affected border sizes. ------------------------------------------------------------------------ r73 | imilne | 2006-09-18 10:26:18 +0100 (Mon, 18 Sep 2006) | 3 lines Release 2.15. New installer to distribute a build tree version. Changed swing-layout.jar to latest version. ------------------------------------------------------------------------ r72 | imilne | 2006-09-15 17:09:15 +0100 (Fri, 15 Sep 2006) | 1 line Added a missing vamsas source file (which means prior commits won't work unless this file is included). ------------------------------------------------------------------------ r71 | imilne | 2006-09-15 14:35:51 +0100 (Fri, 15 Sep 2006) | 2 lines Added support for writing out graph annotation data. Fixes for not being able to have two or more TOPALi instances connected to the same VAMSAS session. ------------------------------------------------------------------------ r70 | imilne | 2006-09-14 13:52:24 +0100 (Thu, 14 Sep 2006) | 1 line More updates on TOPALi->VAMSAS code. Hopefully legit VAMSAS xml being written now. ------------------------------------------------------------------------ r69 | imilne | 2006-09-13 11:16:20 +0100 (Wed, 13 Sep 2006) | 1 line Added options to the Web Settings dialog so the user can select between using the resource broker and having a direct connection to a cluster. ------------------------------------------------------------------------ r68 | imilne | 2006-09-11 17:02:26 +0100 (Mon, 11 Sep 2006) | 2 lines Minor changes to the web site's index.html file. Added some images that were missing from version control. ------------------------------------------------------------------------ r67 | imilne | 2006-09-11 16:35:30 +0100 (Mon, 11 Sep 2006) | 1 line Annotations are now written out to VAMSAS xml (partitions for now). ------------------------------------------------------------------------ r66 | imilne | 2006-09-08 11:55:10 +0100 (Fri, 08 Sep 2006) | 1 line Got (very) basic TOPALi->VAMSAS data serialization working again. Sequences only, no alignments or anything fancy yet. ------------------------------------------------------------------------ r65 | imilne | 2006-09-06 14:15:56 +0100 (Wed, 06 Sep 2006) | 1 line Modified repository so it supports trunk/branches/tags folders. ------------------------------------------------------------------------ r64 | imilne | 2006-09-06 14:10:19 +0100 (Wed, 06 Sep 2006) | 1 line Added some files that were missing from version control. ------------------------------------------------------------------------ r63 | imilne | 2006-08-31 09:51:40 +0100 (Thu, 31 Aug 2006) | 1 line Modified web services initialization to rely upon a remote resource broker to return a valid URL for further job submission. ------------------------------------------------------------------------ r62 | imilne | 2006-08-24 14:08:39 +0100 (Thu, 24 Aug 2006) | 1 line Clicking on the Results folder in the treeview will now give a proper indication of result status (how many, and how many completed/in progress). ------------------------------------------------------------------------ r61 | imilne | 2006-08-24 10:24:50 +0100 (Thu, 24 Aug 2006) | 1 line Added javadoc task to Ant. ------------------------------------------------------------------------ r60 | imilne | 2006-08-24 10:23:49 +0100 (Thu, 24 Aug 2006) | 1 line Batch file put back the way it was until issues with -Djava.ext.dirs is resolved (classpath to Castor topali.xml file and the fact that topali.jar in the libs directory gets picked up before the working-copy located in the classes directory). ------------------------------------------------------------------------ r59 | imilne | 2006-08-18 16:28:14 +0100 (Fri, 18 Aug 2006) | 1 line Added shorthand version of j.bat that uses -Djava.ext.dirs to set the jar classpath. ------------------------------------------------------------------------ r58 | imilne | 2006-08-18 15:45:14 +0100 (Fri, 18 Aug 2006) | 1 line Release 2.14 ------------------------------------------------------------------------ r57 | imilne | 2006-08-18 15:40:41 +0100 (Fri, 18 Aug 2006) | 1 line Fixed a bug that was stopping the tree clustering from selecting the correct sequences. ------------------------------------------------------------------------ r56 | imilne | 2006-08-17 09:25:29 +0100 (Thu, 17 Aug 2006) | 1 line Added a help section for the Analysis Settings dialog. ------------------------------------------------------------------------ r55 | imilne | 2006-08-17 09:24:25 +0100 (Thu, 17 Aug 2006) | 1 line Removed the .jws Axis mapping that isn't needed. ------------------------------------------------------------------------ r54 | imilne | 2006-08-04 16:43:38 +0100 (Fri, 04 Aug 2006) | 2 lines Release 2.13. Added a new tab to the settings dialog to allow for basic local job settings. ------------------------------------------------------------------------ r53 | imilne | 2006-08-04 11:59:43 +0100 (Fri, 04 Aug 2006) | 1 line Modified ThreadManager to be statically global so that all locally running jobs will request CPU resource from the same manager - this means only 2 jobs will run concurrently on a 2 CPU machine, rather than [n] jobs. ------------------------------------------------------------------------ r52 | imilne | 2006-07-27 09:50:59 +0100 (Thu, 27 Jul 2006) | 2 lines Release 2.12. Modified Topology Defining Sites code (HMM) so that it's impossible to have the first region "ending" at position 1. ------------------------------------------------------------------------ r51 | imilne | 2006-07-13 16:52:10 +0100 (Thu, 13 Jul 2006) | 1 line Release 2.11 ------------------------------------------------------------------------ r50 | imilne | 2006-07-10 10:54:07 +0100 (Mon, 10 Jul 2006) | 1 line PDM1 method has been modified to allows calculate a threshold via bootstrapping (which will run in parallel). ------------------------------------------------------------------------ r49 | imilne | 2006-07-05 16:09:46 +0100 (Wed, 05 Jul 2006) | 1 line Removed BambeInfile.java's reliance on the SequenceSet object which although not wrong isn't suitable for simulated alignments that haven't had parameters estimated. ------------------------------------------------------------------------ r48 | imilne | 2006-07-05 09:52:19 +0100 (Wed, 05 Jul 2006) | 1 line More PDM2 modifications. ------------------------------------------------------------------------ r47 | imilne | 2006-06-28 10:20:58 +0100 (Wed, 28 Jun 2006) | 1 line Modified Help->About dialog. ------------------------------------------------------------------------ r46 | imilne | 2006-06-27 17:04:33 +0100 (Tue, 27 Jun 2006) | 3 lines PDM2 analysis now complete, but not finished :-) Graphs and thresholds available but further tweaking needed before Frank is happy with the method. Bug exists somewhere in the code that checks the number of "percent" directory files - it's not always counting every file even when they all exist. ------------------------------------------------------------------------ r45 | imilne | 2006-06-20 11:30:10 +0100 (Tue, 20 Jun 2006) | 1 line More work on PDMPostAnalysis.java ------------------------------------------------------------------------ r44 | imilne | 2006-06-16 17:38:20 +0100 (Fri, 16 Jun 2006) | 3 lines Changed PDMPostAnalysis back to being part of the main analysis (but running last). Not working yet... The win file reading of PDMPostAnalysis now sorts directory and file names so that 1, 2, 10 ordering is used rather than 1, 10, 2. PDM2 partitioning now goes into a nodes/run[n] subfolder so that the nodes directory only contains other directories and not the additional top-level crap like .SGE_ID, run scripts, or output files. ------------------------------------------------------------------------ r43 | imilne | 2006-06-15 13:57:15 +0100 (Thu, 15 Jun 2006) | 1 line Modified PDM2 method to run an additional (PDM2PostAnalysis.java) class at the end of the main analysis run. This is cluster-node submitted, but does not (and can not) run in parallel with the rest of the job. ------------------------------------------------------------------------ r42 | imilne | 2006-06-09 11:47:55 +0100 (Fri, 09 Jun 2006) | 3 lines Initial infrastructure for importing and displaying multiple, multiple alignments. New class AlignmentFileStat that contains summary data on a single alignment import (file reference), and AlignmentData modified to contain a list of these references if needed. FileListPanel added for display in WinMain along with associated navigation classes in topali.gui.nav ------------------------------------------------------------------------ r41 | imilne | 2006-05-11 14:00:02 +0100 (Thu, 11 May 2006) | 1 line Release 2.09 ------------------------------------------------------------------------ r40 | imilne | 2006-05-10 15:04:10 +0100 (Wed, 10 May 2006) | 1 line Modified the SGE scripts so that separate files exist for different clusters, rather than trying to share the same file (it was getting too complicated). ------------------------------------------------------------------------ r39 | imilne | 2006-05-10 14:02:18 +0100 (Wed, 10 May 2006) | 3 lines PDMInitializer.java now writes windows per job, rather than regions per job (in preparation for variable sites). Proxy problems fixed for now, but axis 1.2RC2 MUST be used. Updated what's new documentation. ------------------------------------------------------------------------ r38 | imilne | 2006-05-04 16:26:41 +0100 (Thu, 04 May 2006) | 1 line Added the classes directory (but not its contents). ------------------------------------------------------------------------ r37 | imilne | 2006-05-04 09:44:54 +0100 (Thu, 04 May 2006) | 1 line Modified the way qstat runs to work around a segmentation fault with it at Dundee Uni. ------------------------------------------------------------------------ r36 | imilne | 2006-04-28 14:49:50 +0100 (Fri, 28 Apr 2006) | 2 lines More development on PDM2. Changes to the way PDM1 and HMM track job percentages. ------------------------------------------------------------------------ r35 | imilne | 2006-04-24 11:49:02 +0100 (Mon, 24 Apr 2006) | 1 line Code tidyup (Eclipse). ------------------------------------------------------------------------ r34 | imilne | 2006-04-21 15:42:05 +0100 (Fri, 21 Apr 2006) | 1 line Added makeNA code for merging cDNA and guide protein on alignment import. ------------------------------------------------------------------------ r33 | imilne | 2006-04-20 11:08:07 +0100 (Thu, 20 Apr 2006) | 1 line Added options dialog at alignment import to decide how a file should be imported. ------------------------------------------------------------------------ r32 | imilne | 2006-04-19 11:14:35 +0100 (Wed, 19 Apr 2006) | 1 line Updated overview documentation. ------------------------------------------------------------------------ r31 | imilne | 2006-04-17 15:05:43 +0100 (Mon, 17 Apr 2006) | 2 lines Still working on proxy authentication (not working with Dundee Univ at present). Finished TOPALi v1 support for tree clustering. ------------------------------------------------------------------------ r30 | imilne | 2006-04-14 11:36:11 +0100 (Fri, 14 Apr 2006) | 1 line ------------------------------------------------------------------------ r29 | imilne | 2006-04-14 11:35:23 +0100 (Fri, 14 Apr 2006) | 1 line Changes to classpath so that client-config.wsdd is found when running within a JAR distribution. ------------------------------------------------------------------------ r28 | imilne | 2006-04-14 11:33:21 +0100 (Fri, 14 Apr 2006) | 4 lines Added items remotely D:\Projects\BBSRC Visualization\mrbayes ------------------------------------------------------------------------ r27 | imilne | 2006-04-14 11:23:22 +0100 (Fri, 14 Apr 2006) | 1 line Trying to cleanup mrbayes repository problems (Removed file/folder) ------------------------------------------------------------------------ r26 | imilne | 2006-04-13 16:56:51 +0100 (Thu, 13 Apr 2006) | 1 line Added client-config.wsdd for NTLM proxy support. ------------------------------------------------------------------------ r25 | imilne | 2006-04-13 16:56:03 +0100 (Thu, 13 Apr 2006) | 4 lines Added authenticating proxy support (GUI modified). Added encryption/decryption of proxy password. Changed preferences to store empty/null strings properly. ------------------------------------------------------------------------ r24 | imilne | 2006-04-11 16:57:42 +0100 (Tue, 11 Apr 2006) | 2 lines Alignments sent to Barce are now checked for compatibility. Default setting of 0 for web proxy port was too low for the spinner control. ------------------------------------------------------------------------ r23 | imilne | 2006-04-11 12:18:14 +0100 (Tue, 11 Apr 2006) | 2 lines Removed compression code until we understand more. Start of work on proxy authentication in TOPALi.java ------------------------------------------------------------------------ r22 | imilne | 2006-04-07 16:57:44 +0100 (Fri, 07 Apr 2006) | 2 lines Release 2.08 Modified doe.jar to match Windows colour schemes. ------------------------------------------------------------------------ r21 | imilne | 2006-04-06 13:29:32 +0100 (Thu, 06 Apr 2006) | 1 line ------------------------------------------------------------------------ r20 | imilne | 2006-04-06 13:27:11 +0100 (Thu, 06 Apr 2006) | 2 lines Source code for external binaries moved to binaries/src. All local jobs can be cancelled. ------------------------------------------------------------------------ r19 | imilne | 2006-04-06 13:26:14 +0100 (Thu, 06 Apr 2006) | 1 line binaries/unix deleted. ------------------------------------------------------------------------ r18 | imilne | 2006-04-05 17:13:12 +0100 (Wed, 05 Apr 2006) | 1 line Release version 2.06 ------------------------------------------------------------------------ r17 | imilne | 2006-04-05 17:09:59 +0100 (Wed, 05 Apr 2006) | 2 lines added gzip compression support to the client. changes to web documentation. ------------------------------------------------------------------------ r16 | imilne | 2006-04-04 14:59:17 +0100 (Tue, 04 Apr 2006) | 5 lines Web documentation ("what's new") added. Lots of logging messages added to the cluster code. The start of PDM2 implementation (hidden in client). 90% of the work required to bring back the tree clustering (hidden). DRMMA code disabled and qstat -xml checking done instead. ------------------------------------------------------------------------ r15 | imilne | 2006-03-22 15:52:06 +0000 (Wed, 22 Mar 2006) | 1 line HelpAbout moved to UpdateChecker.java so all update/version tracking is in a single class. ------------------------------------------------------------------------ r14 | imilne | 2006-03-22 11:45:38 +0000 (Wed, 22 Mar 2006) | 1 line Folder cleanup (removing JCreator files from version control). ------------------------------------------------------------------------ r13 | imilne | 2006-03-22 11:41:58 +0000 (Wed, 22 Mar 2006) | 1 line Removing .lib files from version control. ------------------------------------------------------------------------ r12 | imilne | 2006-03-22 11:33:49 +0000 (Wed, 22 Mar 2006) | 1 line Added a file remotely ------------------------------------------------------------------------ r11 | imilne | 2006-03-22 11:33:43 +0000 (Wed, 22 Mar 2006) | 1 line Added a file remotely ------------------------------------------------------------------------ r10 | imilne | 2006-03-22 11:33:38 +0000 (Wed, 22 Mar 2006) | 1 line Added a file remotely ------------------------------------------------------------------------ r9 | imilne | 2006-03-22 11:33:22 +0000 (Wed, 22 Mar 2006) | 1 line Created folder remotely ------------------------------------------------------------------------ r8 | imilne | 2006-03-22 11:31:03 +0000 (Wed, 22 Mar 2006) | 1 line Removed file/folder ------------------------------------------------------------------------ r7 | imilne | 2006-03-22 11:30:58 +0000 (Wed, 22 Mar 2006) | 1 line Removed file/folder ------------------------------------------------------------------------ r6 | imilne | 2006-03-22 11:30:56 +0000 (Wed, 22 Mar 2006) | 1 line Removed file/folder ------------------------------------------------------------------------ r5 | imilne | 2006-03-22 11:29:23 +0000 (Wed, 22 Mar 2006) | 1 line Removed file/folder ------------------------------------------------------------------------ r4 | imilne | 2006-03-22 11:26:39 +0000 (Wed, 22 Mar 2006) | 1 line ------------------------------------------------------------------------ r3 | imilne | 2006-03-22 11:25:33 +0000 (Wed, 22 Mar 2006) | 1 line ------------------------------------------------------------------------ r2 | imilne | 2006-03-09 17:14:18 +0000 (Thu, 09 Mar 2006) | 1 line Release version 2.05 ------------------------------------------------------------------------ r1 | imilne | 2006-03-07 16:58:49 +0000 (Tue, 07 Mar 2006) | 1 line ------------------------------------------------------------------------