JAL-2714 HMMSearch cutoff by E-Value, Score or None
[jalview.git] / src / jalview / bin / Jalview.java
2018-05-09 gmungocJAL-2714 HMMSearch cutoff by E-Value, Score or None
2018-05-08 gmungocMerge branch 'develop' into features/mchmmer
2018-05-02 Jim ProcterJAL-2976 fallback to Vaqua for Macs that don’t work...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-09 TZVanaaltenJAL-2629 removed unnecessary exception throws from...
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect...
2016-12-16 gmungocJAL-2360 added UserColourScheme.toAppletParameter+test...
2016-12-16 gmungocJAL-2360 getColour() renamed to getColourScheme(),...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-14 tcofoegbuJAL-2322 Refactored unified architecture for data ...
2016-11-11 tcofoegbuJAL-2277 Refactored out duplicated method - printUnwrap...
2016-10-26 tcofoegbuJAL-2284 basic support for exporting BioJS MSA viewer... features/JAL-2284_export-biojsmsa-via-cli
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 gmungocJAL-1191 revert to using SequenceOntologyLite due to...
2016-10-05 gmungocJAL-1191 configure full SO for desktop, SOLite for...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-08 gmungocJAL-2168 document '-nonews' parameter
2016-08-05 gmungocJAL-2168 skip news feed if parameter "-nonews" is supplied
2016-07-11 gmungocfile format enum wip changes
2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-1812_JAL-2083_... features/JAL-1812_JAL-2083_groovyBinding
2016-05-04 gmungocMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into...
2016-05-02 gmungocJAL-1812 bind Groovy to Jalview rather than Desktop...
2016-04-28 gmungocJAL-2083 removed use of reflection for Groovy
2016-04-26 gmungocJAL-1981 catch any exception when setting QuaQua look...
2016-04-25 Jim ProcterJAL-2074 disable security manager at start up re: lopic...
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-10-05 gmungocJAL-1812 set/return currentAlFrame for Groovy in headle...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-07-13 tcofoegbuJAL-1788 added help documentation for biojson
2015-07-09 tcofoegbuJAL-1769 added test for commandline input operations
2015-07-08 gmungocJAL-1759 merge from develop
2015-07-06 tcofoegbuJAL-1769 fixed headless execution mode and created...
2015-07-02 tcofoegbuJAL-1443 data validation for empty content before loadi...
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and...
2015-05-21 tcofoegbuJAL-1740 implemented auto-update of BioJsMSA, introduce... features/JAL-1740_BioJsAutoUpdater
2015-03-26 gmungocJAL-1688 compiler warnings removed
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-02-05 Charles Ofoegbumerge commit
2015-02-04 Charles OfoegbuJAL-1643 Modified JalviewFileChooser to have a more...
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-12-08 Charles OfoegbuAdded annotation export configuration for Html export...
2014-12-05 Charles OfoegbuMerge branch 'features/JAL-1605_html-svg-export' into...
2014-12-05 Charles OfoegbuJAL-1605 added command line support for html export...
2014-12-05 gmungocJAL-1614 flag 'protein' removed
2014-12-05 gmungocJAL-1614 flag 'protein' removed
2014-11-28 Jim ProcterJAL-1611 revise log level to reduce verbosity
2014-11-19 gmungocJAL-1342 new command-line parameter -jabaws <URL>
2014-11-17 Charles Ofoegbucomand line support for svg generation
2014-11-17 Charles Ofoegbucomand line support for svg generation
2014-09-23 darolmarJAL-1355
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-06-13 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2
2013-06-13 Jim ProcterMerge branch 'JAL-1314_headlessFlag' into develop
2013-06-13 Jim ProcterJAL-1314 allow 'nogui' and 'headless' as synonyms for...
2012-12-07 jproctermenu for choosing between 'protein' and 'RNA' mode...
2012-11-15 jprocterMerge branch 'develop' into menard
2012-11-08 jproctertidy imports
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-04 jprocterJAL-1188 - set the user agent to Jalview Desktop/$...
2012-10-01 jprocterJAL-1183 showNews adds news discovery and display threa...
2012-10-01 jprocterJAL-1183 use dialog queue for usage statistics prompt
2012-08-24 jprocterMerge branch 'develop' into menard
2012-08-24 jprocterJAL-1087 skip processing any of the other command line...
2012-08-14 Anne Menardlast version stay many bugs ..
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2011-09-16 jprocterfix for JAL-895 - new exampleFile_2_7.jar and logic...
2011-08-17 jprocterJAL-898 - ensure we only remove a clargs progress bar...
2011-08-05 jprocterfetch groovy script from URL (JAL-899) and show progres...
2011-07-28 jprocterrefer to local default setting for proxy when connecting to
2011-04-08 jprocterallow groovy scripts to be run when in headless mode...
2011-04-07 jprocterallow groovy scripts to be run when in headless mode...
2011-04-07 jprocterallow groovy scripts to be run when in headless mode...
2011-01-07 jprocterrefactored dropFile allowing known information to be...
2010-11-14 jprocterrefactored to decouple dependencies due to FileParse...
2010-11-14 jprocterrefactored protocol check to jalview.io.FileParse
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-08-31 jprocternotes re JAL-629
2010-08-06 jprocterinteractive/batch mode test for groovy scripting (See...
2010-06-12 jprocterdocumented the -colour command line argument.
2010-06-09 jprocterOSX look and feel JAL-577
2010-05-14 jprocterstandard function for bootstrapping discovery threads
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