jalview.git
2018-01-30 kjvdheideJAL-1953 added configuration font setters
2018-01-29 kjvdheideJAL-1953 some more comments, moved JalviewBinding
2018-01-28 kjvdheideJAL-1953 more javadoc comments
2018-01-26 kjvdheideJAL-1953 first pass of adding javadoc, some methods...
2018-01-26 kjvdheideJAL-2856 added refreshing of Aptx view when tree frame...
2018-01-26 kjvdheideJAL-2798 label name changed
2018-01-25 kjvdheideJAL-2844 allow clicks outside of the tree range again...
2018-01-25 kjvdheideJAL-2844 updated forester.jar for drawing partitioning...
2018-01-25 kjvdheideMerge branch 'develop' of https://source.jalview.org...
2018-01-25 kjvdheideJAL-2844 branch colour setter improved
2018-01-24 kjvdheideJAL-2866 remove forester's submodule folder
2018-01-24 kjvdheideJAL-2866 remove forester from .gitmodules
2018-01-24 kjvdheideJAL-2872 added setters for GUI sizes
2018-01-24 kjvdheideJAL-2798 added != null check for Aptx trees
2018-01-24 Jim ProcterJAL-2858 update release date and rejig what's new message
2018-01-23 Jim ProcterJAL-2858 fix what's new
2018-01-23 Jim ProcterJAL-2858 update latest release notes link in TOC
2018-01-23 Jim ProcterJAL-2859 release notes
2018-01-23 Jim ProcterJAL-2858 update release notes
2018-01-22 Jim ProcterJAL-2858 release notes for 2.10.3b1 (including revision...
2018-01-22 Jim ProcterJAL-2858 bump version number for 2.10.3b1
2018-01-22 kjvdheideRevert "JAL-2890 added CIPRES client .jar"
2018-01-22 kjvdheideRevert "JAL-2890 proper .jar this time and copied cipre...
2018-01-22 kjvdheideRevert "JAL-2890 added CIPRES' javadoc .jar to Jalview...
2018-01-19 kjvdheideJAL-2805 small redundant method call fix
2018-01-19 kjvdheideJAL-2890 added CIPRES' javadoc .jar to Jalview lib
2018-01-19 kjvdheideJAL-2890 proper .jar this time and copied cipres' examp...
2018-01-19 kjvdheideJAL-2890 added CIPRES client .jar
2018-01-18 gmungocJAL-2810 JAL-2886 i18n
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved...
2018-01-18 kjvdheideJAL-2805 disabled Nexus file identification(as its...
2018-01-17 kjvdheideJAL-1951 added comment to NexusFile clarifying Forester...
2018-01-17 kjvdheideJAL-2794 tree viewer frame now has its binding object...
2018-01-17 kjvdheideJAL-2798 now added to active views when associated...
2018-01-17 kjvdheideJAL-281 added initialising trees to FileLoader if filef...
2018-01-17 kjvdheideJAL-281 added isTreeFile() boolean
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri...
2018-01-16 kjvdheideJAL-2798 rough saving/loading a single Aptx view functi...
2018-01-16 kjvdheideJAL-2798 comments
2018-01-16 kjvdheideJAL-2798 tree frame is now added to active views when...
2018-01-16 kjvdheideJAL-2798 added methods for getting/adding external...
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren...
2018-01-16 kjvdheideJAL-2798 added method to tree for writing to jalview...
2018-01-12 kjvdheideJAL-2805 check actually works now
2018-01-12 kjvdheideMerge branch 'develop' of https://source.jalview.org...
2018-01-12 kjvdheideJAL-2798 Aptx is now saved to the project
2018-01-12 kjvdheideJAL-2805 removed unused Aptx instance creation code
2018-01-12 kjvdheideJAL-2805 added getter and setter for jalview associatio...
2018-01-12 kiramtJAL-2886 trivial unit test fix
2018-01-11 gmungocJAL-2754 renamed proguard.jar to include version number
2018-01-11 gmungocJAL-2754 5.3.3 update of proguard.jar
2018-01-11 gmungocJAL-2754 update to specify Java 1.8(+)
2018-01-11 kiramtMerge remote-tracking branch 'origin/task/JAL-2662...
2018-01-11 kiramtJAL-2662 Updated README task/JAL-2662
2018-01-11 kjvdheideJAL-2884 old Newick trees are now loaded in as Aptx...
2018-01-11 kjvdheideJAL-2795 simplified instance creation from calculation
2018-01-11 kjvdheideJAL-2798 alignmentviewport's current external tree...
2018-01-10 kjvdheideJAL-1953 named various threads
2018-01-10 kjvdheideJAL-2795 calculated trees are now passed along as Newic...
2018-01-10 kjvdheideJAL-2795 disabled most tests for now
2018-01-09 kjvdheideJAL-2805 file identifying lines are turned to lowercase...
2018-01-09 kjvdheideJAL-2805 correct nexus parser is now created
2018-01-09 kjvdheideJAL-2805 Creating jalview sequence now requires the...
2018-01-09 kjvdheideJAL-2805 added derive sequence when creating jalview...
2018-01-09 kjvdheideJAL-2805 getNodeSequences returns a list now instead...
2018-01-09 kjvdheideJAL-2805 added check for null node sequences during...
2018-01-09 kjvdheideJAL-2805 allow for non-xsd validating phyloxml parsing
2018-01-09 kjvdheideJAL-2805 check no longer errors if the sequence is...
2018-01-09 kjvdheideJAL-2805 added check for sequences already being presen...
2018-01-09 kjvdheideJAL-2805 put the sequence setting in if statement ...
2018-01-09 kjvdheideJAL-2805 added Aptx factory method reading directly...
2018-01-09 kjvdheideJAL-2805 added nexus specific parser settings
2018-01-09 kjvdheideJAL-2805 broke off the phylogenetic file formats into...
2018-01-09 kjvdheideJAL-2805 parser is now File based (instead of FileParse...
2018-01-09 kjvdheideJAL-2805 Parse returns a TreeI array again
2018-01-09 kjvdheideJAL-2805 node sequence is now immediately filled in...
2018-01-09 kjvdheideJAL-2805 added forester --> jalview sequence converter
2018-01-09 kjvdheideJAL-2805 added getter in trees for retrieving all node...
2018-01-09 kjvdheideJAL-1953 moved DataConversions to Forester package
2018-01-08 kjvdheideJAL-2844 changed threshold from double to float
2018-01-08 kjvdheideJAL-2844 start on moving tree partitioning code into...
2018-01-06 kjvdheideJAL-2877 added forester as jar once again
2018-01-06 kjvdheideJAL-281 first line also checked for PhyloXML identification
2018-01-06 kjvdheideJAL-2871 aptx Configuration now created through input...
2018-01-05 kjvdheideJAL-281 ForesterParser now extends from AlignFile
2018-01-04 kjvdheideJAL-1953 Moved config to resources folder
2018-01-04 kjvdheideJAL-281 ForesterParser factory methods added
2018-01-02 kjvdheideJAL-1953 start work on storing nodes in a map per tree...
2017-12-21 kjvdheideJAL-281 added file identify criteria for PhyloXML and...
2017-12-20 kjvdheideJAL-2874 made the actionlistener slightly clearer
2017-12-20 kjvdheideJAL-2838 JAL-2872 added sorting from the Aptx frame...
2017-12-20 kjvdheideJAL-281 moved utility methods to .io package
2017-12-20 kjvdheideJAL-281 split up TreeParser into separate format parsers
2017-12-19 kjvdheideJAL-281 created Nexus and PhyloXML parser classes
2017-12-19 kjvdheideJAL-281 cleared out useless tree parser class
2017-12-19 kjvdheideJAL-281 added phyloxml and nexus to jalview fileformats
2017-12-18 kjvdheideJAL-1953 moved now-generic methods outside of Aptx...
2017-12-18 kjvdheideJAL-1953 -External from all interfaces names
2017-12-18 kjvdheideJAL-1953 attempt at changing Aptx's font to Jalview's
2017-12-18 kjvdheideJAL-2844 cladogram no longer vertically aligned (was...
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