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JAL-1951 added comment to NexusFile clarifying Forester's broken parser
[jalview.git] / src /
2018-01-17 kjvdheideJAL-1951 added comment to NexusFile clarifying Forester... tree | commitdiff
2018-01-17 kjvdheideJAL-2794 tree viewer frame now has its binding object... tree | commitdiff
2018-01-17 kjvdheideJAL-2798 now added to active views when associated... tree | commitdiff
2018-01-17 kjvdheideJAL-281 added initialising trees to FileLoader if filef... tree | commitdiff
2018-01-17 kjvdheideJAL-281 added isTreeFile() boolean tree | commitdiff
2018-01-16 kjvdheideJAL-2798 rough saving/loading a single Aptx view functi... tree | commitdiff
2018-01-16 kjvdheideJAL-2798 comments tree | commitdiff
2018-01-16 kjvdheideJAL-2798 tree frame is now added to active views when... tree | commitdiff
2018-01-16 kjvdheideJAL-2798 added methods for getting/adding external... tree | commitdiff
2018-01-16 kjvdheideJAL-2798 added method to tree for writing to jalview... tree | commitdiff
2018-01-12 kjvdheideJAL-2805 check actually works now tree | commitdiff
2018-01-12 kjvdheideJAL-2798 Aptx is now saved to the project tree | commitdiff
2018-01-12 kjvdheideJAL-2805 removed unused Aptx instance creation code tree | commitdiff
2018-01-12 kjvdheideJAL-2805 added getter and setter for jalview associatio... tree | commitdiff
2018-01-11 kjvdheideJAL-2884 old Newick trees are now loaded in as Aptx... tree | commitdiff
2018-01-11 kjvdheideJAL-2795 simplified instance creation from calculation tree | commitdiff
2018-01-11 kjvdheideJAL-2798 alignmentviewport's current external tree... tree | commitdiff
2018-01-10 kjvdheideJAL-1953 named various threads tree | commitdiff
2018-01-10 kjvdheideJAL-2795 calculated trees are now passed along as Newic... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 file identifying lines are turned to lowercase... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 correct nexus parser is now created tree | commitdiff
2018-01-09 kjvdheideJAL-2805 Creating jalview sequence now requires the... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added derive sequence when creating jalview... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 getNodeSequences returns a list now instead... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added check for null node sequences during... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 allow for non-xsd validating phyloxml parsing tree | commitdiff
2018-01-09 kjvdheideJAL-2805 check no longer errors if the sequence is... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added check for sequences already being presen... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 put the sequence setting in if statement ... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added Aptx factory method reading directly... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added nexus specific parser settings tree | commitdiff
2018-01-09 kjvdheideJAL-2805 broke off the phylogenetic file formats into... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 parser is now File based (instead of FileParse... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 Parse returns a TreeI array again tree | commitdiff
2018-01-09 kjvdheideJAL-2805 node sequence is now immediately filled in... tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added forester --> jalview sequence converter tree | commitdiff
2018-01-09 kjvdheideJAL-2805 added getter in trees for retrieving all node... tree | commitdiff
2018-01-09 kjvdheideJAL-1953 moved DataConversions to Forester package tree | commitdiff
2018-01-08 kjvdheideJAL-2844 changed threshold from double to float tree | commitdiff
2018-01-08 kjvdheideJAL-2844 start on moving tree partitioning code into... tree | commitdiff
2018-01-06 kjvdheideJAL-281 first line also checked for PhyloXML identification tree | commitdiff
2018-01-06 kjvdheideJAL-2871 aptx Configuration now created through input... tree | commitdiff
2018-01-05 kjvdheideJAL-281 ForesterParser now extends from AlignFile tree | commitdiff
2018-01-04 kjvdheideJAL-1953 Moved config to resources folder tree | commitdiff
2018-01-04 kjvdheideJAL-281 ForesterParser factory methods added tree | commitdiff
2018-01-02 kjvdheideJAL-1953 start work on storing nodes in a map per tree... tree | commitdiff
2017-12-21 kjvdheideJAL-281 added file identify criteria for PhyloXML and... tree | commitdiff
2017-12-20 kjvdheideJAL-2874 made the actionlistener slightly clearer tree | commitdiff
2017-12-20 kjvdheideJAL-2838 JAL-2872 added sorting from the Aptx frame... tree | commitdiff
2017-12-20 kjvdheideJAL-281 moved utility methods to .io package tree | commitdiff
2017-12-20 kjvdheideJAL-281 split up TreeParser into separate format parsers tree | commitdiff
2017-12-19 kjvdheideJAL-281 created Nexus and PhyloXML parser classes tree | commitdiff
2017-12-19 kjvdheideJAL-281 cleared out useless tree parser class tree | commitdiff
2017-12-19 kjvdheideJAL-281 added phyloxml and nexus to jalview fileformats tree | commitdiff
2017-12-18 kjvdheideJAL-1953 moved now-generic methods outside of Aptx... tree | commitdiff
2017-12-18 kjvdheideJAL-1953 -External from all interfaces names tree | commitdiff
2017-12-18 kjvdheideJAL-1953 attempt at changing Aptx's font to Jalview's tree | commitdiff
2017-12-18 kjvdheideJAL-2844 made null tree nodes return null wrappers... tree | commitdiff
2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' into tree | commitdiff
2017-12-18 kjvdheideJAL-1953 redundant tree interface instantiation removed tree | commitdiff
2017-12-15 kjvdheideJAL-2852 EPS saving code ported from TreePanel to Aptx. tree | commitdiff
2017-12-15 kjvdheideJAL-1953 added Y coordinate getter method tree | commitdiff
2017-12-15 kjvdheideJAL-2852 merged the EPS button adding from main branch... tree | commitdiff
2017-12-15 kjvdheideJAL-1953 node comparing now includes checking node... tree | commitdiff
2017-12-15 kjvdheideJAL-1953 removed deprecated interfaces tree | commitdiff
2017-12-15 kjvdheideJAL-2852 added EPS export button to File menu tree | commitdiff
2017-12-14 kjvdheideJAL-1953 more progress on interfaces, jalview binding... tree | commitdiff
2017-12-12 kjvdheideJAL-2874 filtering alignment now also works when just... tree | commitdiff
2017-12-12 kjvdheideJAL-2874 added filtering when a subtree is selected tree | commitdiff
2017-12-12 kjvdheideJAL-2877 disabled Jalview's own viewer for testing spikes/thomas tree | commitdiff
2017-12-11 kjvdheideJAL-2872 hide sort button in Aptx unless it's actually... tree | commitdiff
2017-12-11 kjvdheideJAL-2877 disabled Jalview's default tree viewer when... tree | commitdiff
2017-12-11 kjvdheideJAL-1953 fixed interface misnaming tree | commitdiff
2017-12-11 kjvdheideJAL-1953 start on making everything interface based tree | commitdiff
2017-12-08 kjvdheideJAL-1953 renaming of concrete implementation as well tree | commitdiff
2017-12-08 kjvdheideJAL-2844 reallow clicks to the left of the root (groups... tree | commitdiff
2017-12-07 kjvdheideJAL-2872 Redundant Aptx GUI menu items hidden, sorting... tree | commitdiff
2017-12-06 kjvdheideJAL-2794 disabled branch colors on selection for now tree | commitdiff
2017-12-06 kjvdheideJAL-2871 Added check whether configuration has been... tree | commitdiff
2017-12-05 kjvdheideJAL-2838 Sorting from the alignment view menu now funct... tree | commitdiff
2017-12-05 kjvdheideJAL-2847 Rearranging and cleaning up of database query... tree | commitdiff
2017-12-05 kjvdheideJAL-2794 associate leaves now iterates through ALL... tree | commitdiff
2017-12-05 kjvdheideJAL-2847 various error popups for db querying now have... tree | commitdiff
2017-12-05 kjvdheideJAL-2847 Strings for the various tree databases added tree | commitdiff
2017-12-05 kjvdheideJAL-2847 if pfam id is detected in first sequence its... tree | commitdiff
2017-12-05 kjvdheideJAL-2847 added pfam to DBRef source name lookup tree | commitdiff
2017-12-05 kjvdheideJAL-2805 JAL-2847 JAL-281 added file path to Aptx frame... tree | commitdiff
2017-12-05 kjvdheideJAL-2838 tree viewer interface expanded to include... tree | commitdiff
2017-12-05 kjvdheideMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-12-05 kjvdheideJAL-2838 filled in actionPerformed of the tree sort... tree | commitdiff
2017-12-05 kjvdheideJAL-2838 Aptx frames now appear in the alignment sortin... tree | commitdiff
2017-12-03 kjvdheideJAL-2847 start of cleaning up db loading code tree | commitdiff
2017-12-03 kjvdheideJAL-2844 rearranging code tree | commitdiff
2017-11-30 Jim ProcterJAL-2849 JAL-2863 file format preferences TODO
 tree | commitdiff
2017-11-30 Jim ProcterJAL-2849 fix tree | commitdiff
2017-11-29 kjvdheideJAL-2844 check added for clicks left of root node tree | commitdiff
2017-11-29 kjvdheideJAL-2844 entirely X coord based partitioning tree | commitdiff
2017-11-29 kjvdheideJAL-2844 somewhat better repainting tree | commitdiff
2017-11-29 kjvdheideJAL-2844 temporary kludge to draw a line tree | commitdiff
2017-11-29 kjvdheideJAL-2844 added grouping to alignment panel based on... tree | commitdiff
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