TZVanaalten [Fri, 1 Sep 2017 15:52:10 +0000 (16:52 +0100)]
JAL-2629 fix hmmbuild failing due to RF longer than alignment
TZVanaalten [Fri, 1 Sep 2017 14:19:39 +0000 (15:19 +0100)]
JAL-2629 fix hmmbuild validation failing if no AlignFrames present
TZVanaalten [Fri, 1 Sep 2017 14:18:09 +0000 (15:18 +0100)]
JAL-2629 manual curation of HMMs via reference annotation functional
TZVanaalten [Wed, 30 Aug 2017 16:43:38 +0000 (17:43 +0100)]
JAL-2616 HMM-Family alignments can now be filtered by residue counts
TZVanaalten [Wed, 30 Aug 2017 16:42:13 +0000 (17:42 +0100)]
JAL-2629 fix issue where HMM sequence would be longer than alignment
TZVanaalten [Wed, 30 Aug 2017 14:17:27 +0000 (15:17 +0100)]
JAL-2629 for multi-job hmmbuilds, group names are now the HMM names
osboxes [Tue, 29 Aug 2017 11:00:54 +0000 (07:00 -0400)]
JAL-2629 fix incorrect mapping between HMM and columns after move
osboxes [Tue, 29 Aug 2017 11:00:15 +0000 (07:00 -0400)]
JAL-2629 HMMs dropped on the alignment now map to the rf annotation
tzvanaalten [Mon, 28 Aug 2017 16:21:39 +0000 (17:21 +0100)]
JAL-2629 add option to set HMM Logo letter height to info content
TZVanaalten [Mon, 28 Aug 2017 11:13:13 +0000 (12:13 +0100)]
JAL-2629 add StringParameter
TZVanaalten [Mon, 28 Aug 2017 10:27:30 +0000 (11:27 +0100)]
JAL-2629 fix HMMER validation fail due to checking for HMM incorrectly
TZVanaalten [Mon, 28 Aug 2017 10:26:23 +0000 (11:26 +0100)]
JAL-2629 fix issue where HMM would not be added to alignment
TZVanaalten [Mon, 28 Aug 2017 10:25:44 +0000 (11:25 +0100)]
JAL-2629 HMMER alignment background colour scheme is functional
TZVanaalten [Fri, 25 Aug 2017 16:12:53 +0000 (17:12 +0100)]
JAL-2629 hmmsearch now adds the E-value as an annotation
TZVanaalten [Fri, 25 Aug 2017 16:11:17 +0000 (17:11 +0100)]
JAL-2629 hmmbuild runs on the alignment by default
TZVanaalten [Fri, 25 Aug 2017 16:10:28 +0000 (17:10 +0100)]
JAl-2629 add new HMMER colour scheme class
TZVanaalten [Fri, 25 Aug 2017 13:54:17 +0000 (14:54 +0100)]
JAL-2629 hmm annotation consensus characters are now upper case
TZVanaalten [Fri, 25 Aug 2017 13:53:58 +0000 (14:53 +0100)]
JAL-2629 fix for hmmbuild failing due to whitespace in the name
TZVanaalten [Fri, 25 Aug 2017 13:52:18 +0000 (14:52 +0100)]
Revert "jal-2629 fix for hmmbuild failing due to whitespace in the name"
This reverts commit
b0516b5aff64734bd343fe5b2178f64677c02863.
TZVanaalten [Fri, 25 Aug 2017 13:51:03 +0000 (14:51 +0100)]
jal-2629 fix for hmmbuild failing due to whitespace in the name
TZVanaalten [Fri, 25 Aug 2017 13:37:20 +0000 (14:37 +0100)]
JAL-2629 add multiple options for running hmmbuild on alignment/groups
TZVanaalten [Thu, 24 Aug 2017 15:49:34 +0000 (16:49 +0100)]
JAL-2629 add adjustable parameters to hmmbuild
TZVanaalten [Thu, 24 Aug 2017 14:41:40 +0000 (15:41 +0100)]
JAL-2629 adjust log parameter slightly and reduce granularity
TZVanaalten [Thu, 24 Aug 2017 14:08:39 +0000 (15:08 +0100)]
JAL-2629 fix issue where Stockholm file would print two terminators
TZVanaalten [Thu, 24 Aug 2017 14:08:02 +0000 (15:08 +0100)]
JAL-2629 hmmsearch no longer throws an error if no sequences are found
TZVanaalten [Thu, 24 Aug 2017 14:07:36 +0000 (15:07 +0100)]
JAL-2629 adjust parameter min and max to better suit HMMER ranges
TZVanaalten [Thu, 24 Aug 2017 13:19:31 +0000 (14:19 +0100)]
JAL-2629 hmmsearch/build/align no longer run after cancelling
TZVanaalten [Thu, 24 Aug 2017 13:13:30 +0000 (14:13 +0100)]
JAL-2629 fix for NPE caused by incorrect initiation of HMM annotation
TZVanaalten [Thu, 24 Aug 2017 13:12:45 +0000 (14:12 +0100)]
JAL-2629 hmmsearch now works for different databases
TZVanaalten [Thu, 24 Aug 2017 11:24:46 +0000 (12:24 +0100)]
JAL-2629 add ability to add and select a DB for hmmsearch
TZVanaalten [Thu, 24 Aug 2017 09:21:15 +0000 (10:21 +0100)]
JAL-2629 remove sequence and group HMMER options
TZVanaalten [Thu, 24 Aug 2017 09:20:28 +0000 (10:20 +0100)]
JAL-2629 add basic parameter adjustment to hmmsearch/align
tzvanaalten [Wed, 23 Aug 2017 14:39:03 +0000 (15:39 +0100)]
JAL-2629 selected HMM is now a sequence, not a HMM
tzvanaalten [Wed, 23 Aug 2017 14:36:07 +0000 (15:36 +0100)]
JAL-2629 fix for addHMMConsensus failing if no HMM sequences found
tzvanaalten [Wed, 23 Aug 2017 14:33:47 +0000 (15:33 +0100)]
JAL-2629 add logarithmic parameter for logarithmic slider
TZVanaalten [Tue, 22 Aug 2017 15:32:36 +0000 (16:32 +0100)]
JAL-2629 add hmmsearch class
TZVanaalten [Mon, 21 Aug 2017 13:53:14 +0000 (14:53 +0100)]
Merge remote-tracking branch 'origin/releases/Release_2_10_2_Branch' into features/hmmer
TZVanaalten [Mon, 21 Aug 2017 13:52:02 +0000 (14:52 +0100)]
Merge remote-tracking branch 'origin/releases/Release_2_10_2_Branch' into features/hmmer
Jim Procter [Mon, 21 Aug 2017 13:47:22 +0000 (14:47 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 21 Aug 2017 13:46:45 +0000 (14:46 +0100)]
JAL-2675 typo in what's new href
TZVanaalten [Mon, 21 Aug 2017 08:22:03 +0000 (09:22 +0100)]
JAL-2668 fix failing tests caused by HMMER-related functions
TZVanaalten [Fri, 18 Aug 2017 16:29:38 +0000 (17:29 +0100)]
Merge branch 'develop' into features/hmmer
Conflicts:
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/JalviewColourScheme.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/AlignCalcManager.java
TZVanaalten [Fri, 18 Aug 2017 13:49:38 +0000 (14:49 +0100)]
JAL-2668 add tests for HMMER commands, annotation and io
TZVanaalten [Fri, 18 Aug 2017 13:47:49 +0000 (14:47 +0100)]
JAL-2668 HMMFile export method moved to print method
Jim Procter [Fri, 18 Aug 2017 13:17:50 +0000 (14:17 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:15:40 +0000 (14:15 +0100)]
JAL-2675 bump version for branch to 2.10.2b1
Jim Procter [Fri, 18 Aug 2017 13:14:17 +0000 (14:14 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:13:28 +0000 (14:13 +0100)]
JAL-1551 formatting
Jim Procter [Fri, 18 Aug 2017 13:08:03 +0000 (14:08 +0100)]
JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.
TZVanaalten [Thu, 17 Aug 2017 13:53:47 +0000 (14:53 +0100)]
JAL-2599 move fillSymbol method to HMFile
Jim Procter [Thu, 17 Aug 2017 12:07:53 +0000 (13:07 +0100)]
JAL-2418 ahem - correct year for what's new
Jim Procter [Thu, 17 Aug 2017 11:37:50 +0000 (12:37 +0100)]
JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9
Jim Procter [Thu, 17 Aug 2017 10:41:33 +0000 (11:41 +0100)]
JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed
TZVanaalten [Thu, 17 Aug 2017 09:18:53 +0000 (10:18 +0100)]
JAL-2599 some slight renaming of variables and methods
TZVanaalten [Thu, 17 Aug 2017 09:11:02 +0000 (10:11 +0100)]
JAL-2629 add documentation to previous work
Jim Procter [Wed, 16 Aug 2017 22:24:25 +0000 (23:24 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 22:24:13 +0000 (23:24 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 22:23:59 +0000 (23:23 +0100)]
JAL-2418 formatting
Jim Procter [Wed, 16 Aug 2017 22:23:53 +0000 (23:23 +0100)]
JAL-2418 occupancy row in What’s New
Jim Procter [Wed, 16 Aug 2017 21:37:37 +0000 (22:37 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 21:30:21 +0000 (22:30 +0100)]
JAL-2418 add GPL to main sources
Jim Procter [Wed, 16 Aug 2017 21:22:11 +0000 (22:22 +0100)]
JAL-2418 source formatting
Jim Procter [Wed, 16 Aug 2017 20:52:55 +0000 (21:52 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 20:52:36 +0000 (21:52 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 20:52:07 +0000 (21:52 +0100)]
JAL-2418 mirror fonts option doc tweak
Jim Procter [Wed, 16 Aug 2017 19:17:43 +0000 (20:17 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 19:17:03 +0000 (20:17 +0100)]
JAL-2418 whats new for 2.10.2
Jim Procter [Wed, 16 Aug 2017 19:16:52 +0000 (20:16 +0100)]
JAL-2418 reclassify some issues to features/bugs resolved
Jim Procter [Wed, 16 Aug 2017 18:23:33 +0000 (19:23 +0100)]
JAL-2418 typos in release notes
Jim Procter [Wed, 16 Aug 2017 18:16:08 +0000 (19:16 +0100)]
JAL-2418 check groovy script one-liners for restoring legacy score model behaviour
TZVanaalten [Wed, 16 Aug 2017 15:11:54 +0000 (16:11 +0100)]
JAL-2599 HMM annotation now shows consensus characters at each column
TZVanaalten [Wed, 16 Aug 2017 14:50:28 +0000 (15:50 +0100)]
JAL-2599 fix background frequency storage and correct colour scheme
TZVanaalten [Wed, 16 Aug 2017 10:07:48 +0000 (11:07 +0100)]
JAL-2629 fix for hmmbuild not loading a HMM onto the current frame
TZVanaalten [Wed, 16 Aug 2017 09:56:57 +0000 (10:56 +0100)]
JAL-2629 add hmmbuild validation check which also gets the HMMER version
TZVanaalten [Tue, 15 Aug 2017 16:30:47 +0000 (17:30 +0100)]
JAL-2629 prevent hmmbuild from running if there are no sequences
Jim Procter [Tue, 15 Aug 2017 16:15:25 +0000 (17:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 16:14:32 +0000 (17:14 +0100)]
JAL-2116 fix typo in build.xml for j2se element
TZVanaalten [Tue, 15 Aug 2017 16:10:10 +0000 (17:10 +0100)]
JAL-2629 configure file chooser to select either a folder or a file
TZVanaalten [Tue, 15 Aug 2017 16:05:15 +0000 (17:05 +0100)]
JAL-2629 add checks for executing hmmer commands as .exe
Jim Procter [Tue, 15 Aug 2017 15:55:22 +0000 (16:55 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 15:55:06 +0000 (16:55 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
tzvanaalten [Tue, 15 Aug 2017 15:18:58 +0000 (16:18 +0100)]
JAL-2629 fix file loading issues on Mac
Jim Procter [Tue, 15 Aug 2017 14:02:19 +0000 (15:02 +0100)]
JAL-2418 bump release to Thursday
Jim Procter [Tue, 15 Aug 2017 13:54:20 +0000 (14:54 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
TZVanaalten [Tue, 15 Aug 2017 11:48:09 +0000 (12:48 +0100)]
JAL-2629 add HMMER version check
TZVanaalten [Tue, 15 Aug 2017 11:21:15 +0000 (12:21 +0100)]
JAL-2629 selected HMM name now shown in HMMER menu
TZVanaalten [Tue, 15 Aug 2017 11:14:13 +0000 (12:14 +0100)]
JAL-2629 exported HMMs are now named correctly
TZVanaalten [Tue, 15 Aug 2017 09:55:35 +0000 (10:55 +0100)]
JAL-2629 fix uniquified sequence names appearing when running hmmbuild
TZVanaalten [Tue, 15 Aug 2017 09:45:55 +0000 (10:45 +0100)]
JAL-2599 fix HMMER scheme not colouring inserts and made red darker
TZVanaalten [Tue, 15 Aug 2017 09:40:32 +0000 (10:40 +0100)]
JAL-2629 the HMMER tab is now disabled when HMMER is not installed
Jim Procter [Mon, 14 Aug 2017 16:25:16 +0000 (17:25 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 16:23:46 +0000 (17:23 +0100)]
JAL-2418 release notes for JAL-2663
Jim Procter [Mon, 14 Aug 2017 16:21:45 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2335_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 16:21:16 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 16:20:28 +0000 (17:20 +0100)]
JAL-2116 add 1.8 1.7 compatible launch string
TZVanaalten [Mon, 14 Aug 2017 14:51:48 +0000 (15:51 +0100)]
JAL-2629 remove annotation when exporting for hmmbuild
TZVanaalten [Mon, 14 Aug 2017 14:49:33 +0000 (15:49 +0100)]
JAL-2629 remove gap padding, and now has option to remove annotations
TZVanaalten [Mon, 14 Aug 2017 14:16:46 +0000 (15:16 +0100)]
JAL-2629 add insert sequence at method on alignment
TZVanaalten [Mon, 14 Aug 2017 14:13:06 +0000 (15:13 +0100)]
JAL-2629 fix expected length error for hmmbuild by uniquifying sequences
TZVanaalten [Mon, 14 Aug 2017 13:58:19 +0000 (14:58 +0100)]
JAL-2629 add padding for .sto annotations to fix issues with hmmbuild
git://source.jalview.org / jalview.git / log