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jalview.git
2018-01-12 kjvdheideJAL-2805 check actually works now commit | commitdiff | tree | snapshot
2018-01-12 kjvdheideMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2018-01-12 kjvdheideJAL-2798 Aptx is now saved to the project commit | commitdiff | tree | snapshot
2018-01-12 kjvdheideJAL-2805 removed unused Aptx instance creation code commit | commitdiff | tree | snapshot
2018-01-12 kjvdheideJAL-2805 added getter and setter for jalview associatio... commit | commitdiff | tree | snapshot
2018-01-12 kiramtJAL-2886 trivial unit test fix commit | commitdiff | tree | snapshot
2018-01-11 gmungocJAL-2754 renamed proguard.jar to include version number commit | commitdiff | tree | snapshot
2018-01-11 gmungocJAL-2754 5.3.3 update of proguard.jar commit | commitdiff | tree | snapshot
2018-01-11 gmungocJAL-2754 update to specify Java 1.8(+) commit | commitdiff | tree | snapshot
2018-01-11 kiramtMerge remote-tracking branch 'origin/task/JAL-2662... commit | commitdiff | tree | snapshot
2018-01-11 kiramtJAL-2662 Updated README task/JAL-2662 commit | commitdiff | tree | snapshot
2018-01-11 kjvdheideJAL-2884 old Newick trees are now loaded in as Aptx... commit | commitdiff | tree | snapshot
2018-01-11 kjvdheideJAL-2795 simplified instance creation from calculation commit | commitdiff | tree | snapshot
2018-01-11 kjvdheideJAL-2798 alignmentviewport's current external tree... commit | commitdiff | tree | snapshot
2018-01-10 kjvdheideJAL-1953 named various threads commit | commitdiff | tree | snapshot
2018-01-10 kjvdheideJAL-2795 calculated trees are now passed along as Newic... commit | commitdiff | tree | snapshot
2018-01-10 kjvdheideJAL-2795 disabled most tests for now commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 file identifying lines are turned to lowercase... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 correct nexus parser is now created commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 Creating jalview sequence now requires the... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added derive sequence when creating jalview... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 getNodeSequences returns a list now instead... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added check for null node sequences during... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 allow for non-xsd validating phyloxml parsing commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 check no longer errors if the sequence is... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added check for sequences already being presen... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 put the sequence setting in if statement ... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added Aptx factory method reading directly... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added nexus specific parser settings commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 broke off the phylogenetic file formats into... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 parser is now File based (instead of FileParse... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 Parse returns a TreeI array again commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 node sequence is now immediately filled in... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added forester --> jalview sequence converter commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-2805 added getter in trees for retrieving all node... commit | commitdiff | tree | snapshot
2018-01-09 kjvdheideJAL-1953 moved DataConversions to Forester package commit | commitdiff | tree | snapshot
2018-01-08 kjvdheideJAL-2844 changed threshold from double to float commit | commitdiff | tree | snapshot
2018-01-08 kjvdheideJAL-2844 start on moving tree partitioning code into... commit | commitdiff | tree | snapshot
2018-01-06 kjvdheideJAL-2877 added forester as jar once again commit | commitdiff | tree | snapshot
2018-01-06 kjvdheideJAL-281 first line also checked for PhyloXML identification commit | commitdiff | tree | snapshot
2018-01-06 kjvdheideJAL-2871 aptx Configuration now created through input... commit | commitdiff | tree | snapshot
2018-01-05 kjvdheideJAL-281 ForesterParser now extends from AlignFile commit | commitdiff | tree | snapshot
2018-01-04 kjvdheideJAL-1953 Moved config to resources folder commit | commitdiff | tree | snapshot
2018-01-04 kjvdheideJAL-281 ForesterParser factory methods added commit | commitdiff | tree | snapshot
2018-01-02 kjvdheideJAL-1953 start work on storing nodes in a map per tree... commit | commitdiff | tree | snapshot
2017-12-21 kjvdheideJAL-281 added file identify criteria for PhyloXML and... commit | commitdiff | tree | snapshot
2017-12-20 kjvdheideJAL-2874 made the actionlistener slightly clearer commit | commitdiff | tree | snapshot
2017-12-20 kjvdheideJAL-2838 JAL-2872 added sorting from the Aptx frame... commit | commitdiff | tree | snapshot
2017-12-20 kjvdheideJAL-281 moved utility methods to .io package commit | commitdiff | tree | snapshot
2017-12-20 kjvdheideJAL-281 split up TreeParser into separate format parsers commit | commitdiff | tree | snapshot
2017-12-19 kjvdheideJAL-281 created Nexus and PhyloXML parser classes commit | commitdiff | tree | snapshot
2017-12-19 kjvdheideJAL-281 cleared out useless tree parser class commit | commitdiff | tree | snapshot
2017-12-19 kjvdheideJAL-281 added phyloxml and nexus to jalview fileformats commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideJAL-1953 moved now-generic methods outside of Aptx... commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideJAL-1953 -External from all interfaces names commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideJAL-1953 attempt at changing Aptx's font to Jalview's commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideJAL-2844 cladogram no longer vertically aligned (was... commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' of commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideJAL-2844 made null tree nodes return null wrappers... commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' into commit | commitdiff | tree | snapshot
2017-12-18 kjvdheideJAL-1953 redundant tree interface instantiation removed commit | commitdiff | tree | snapshot
2017-12-15 kjvdheideJAL-2852 EPS saving code ported from TreePanel to Aptx. commit | commitdiff | tree | snapshot
2017-12-15 kjvdheideJAL-1953 added Y coordinate getter method commit | commitdiff | tree | snapshot
2017-12-15 kjvdheideJAL-2852 merged the EPS button adding from main branch... commit | commitdiff | tree | snapshot
2017-12-15 kjvdheideJAL-1953 node comparing now includes checking node... commit | commitdiff | tree | snapshot
2017-12-15 kjvdheideJAL-1953 removed deprecated interfaces commit | commitdiff | tree | snapshot
2017-12-15 kjvdheideJAL-2852 added EPS export button to File menu commit | commitdiff | tree | snapshot
2017-12-14 kjvdheideJAL-1953 more progress on interfaces, jalview binding... commit | commitdiff | tree | snapshot
2017-12-12 kjvdheideJAL-2874 filtering alignment now also works when just... commit | commitdiff | tree | snapshot
2017-12-12 kjvdheideJAL-2874 added filtering when a subtree is selected commit | commitdiff | tree | snapshot
2017-12-12 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' of https... commit | commitdiff | tree | snapshot
2017-12-12 kjvdheideJAL-2877 disabled Jalview's own viewer for testing spikes/thomas commit | commitdiff | tree | snapshot
2017-12-11 kjvdheideJAL-2872 hide sort button in Aptx unless it's actually... commit | commitdiff | tree | snapshot
2017-12-11 kjvdheideJAL-2877 disabled Jalview's default tree viewer when... commit | commitdiff | tree | snapshot
2017-12-11 kjvdheideJAL-1953 fixed interface misnaming commit | commitdiff | tree | snapshot
2017-12-11 kjvdheideJAL-1953 start on making everything interface based commit | commitdiff | tree | snapshot
2017-12-08 kjvdheideJAL-1953 renaming of concrete implementation as well commit | commitdiff | tree | snapshot
2017-12-08 kjvdheideJAL-2844 reallow clicks to the left of the root (groups... commit | commitdiff | tree | snapshot
2017-12-07 kjvdheideJAL-2866 and .jar removed again commit | commitdiff | tree | snapshot
2017-12-07 kjvdheideJAL-2866 forester .jar added to lib commit | commitdiff | tree | snapshot
2017-12-07 kjvdheideJAL-2872 Redundant Aptx GUI menu items hidden, sorting... commit | commitdiff | tree | snapshot
2017-12-06 kjvdheideJAL-2794 disabled branch colors on selection for now commit | commitdiff | tree | snapshot
2017-12-06 kjvdheideJAL-2871 Added check whether configuration has been... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2838 Sorting from the alignment view menu now funct... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2847 Rearranging and cleaning up of database query... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2794 associate leaves now iterates through ALL... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2847 various error popups for db querying now have... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2847 Strings for the various tree databases added commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2847 if pfam id is detected in first sequence its... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2847 added pfam to DBRef source name lookup commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2805 JAL-2847 JAL-281 added file path to Aptx frame... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2838 tree viewer interface expanded to include... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideMerge remote-tracking branch 'origin/develop' into... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2838 filled in actionPerformed of the tree sort... commit | commitdiff | tree | snapshot
2017-12-05 kjvdheideJAL-2838 Aptx frames now appear in the alignment sortin... commit | commitdiff | tree | snapshot
2017-12-03 kjvdheideJAL-2847 start of cleaning up db loading code commit | commitdiff | tree | snapshot
2017-12-03 kjvdheideJAL-2844 rearranging code commit | commitdiff | tree | snapshot
2017-11-30 Jim ProcterJAL-2849 release notes commit | commitdiff | tree | snapshot
2017-11-30 Jim ProcterMerge branch 'bug/JAL-2849' into develop commit | commitdiff | tree | snapshot
2017-11-30 Jim ProcterJAL-2849 JAL-2863 file format preferences TODO
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