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Revert "JAL-2890 proper .jar this time and copied cipres' example class"
2018-01-22 kjvdheideRevert "JAL-2890 proper .jar this time and copied cipres...
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2018-01-22 kjvdheideRevert "JAL-2890 added CIPRES' javadoc .jar to Jalview...
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2018-01-19 kjvdheideJAL-2805 small redundant method call fix
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2018-01-19 kjvdheideJAL-2890 added CIPRES' javadoc .jar to Jalview lib
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2018-01-19 kjvdheideJAL-2890 proper .jar this time and copied cipres' example...
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2018-01-19 kjvdheideJAL-2890 added CIPRES client .jar
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2018-01-18 kjvdheideJAL-2805 disabled Nexus file identification(as its...
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2018-01-17 kjvdheideJAL-1951 added comment to NexusFile clarifying Forester...
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2018-01-17 kjvdheideJAL-2794 tree viewer frame now has its binding object...
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2018-01-17 kjvdheideJAL-2798 now added to active views when associated...
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2018-01-17 kjvdheideJAL-281 added initialising trees to FileLoader if fileformat...
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2018-01-17 kjvdheideJAL-281 added isTreeFile() boolean
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2018-01-16 kjvdheideJAL-2798 rough saving/loading a single Aptx view functionali...
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2018-01-16 kjvdheideJAL-2798 comments
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2018-01-16 kjvdheideJAL-2798 tree frame is now added to active views when...
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2018-01-16 kjvdheideJAL-2798 added methods for getting/adding external...
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2018-01-16 kjvdheideJAL-2798 added method to tree for writing to jalview...
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2018-01-12 kjvdheideJAL-2805 check actually works now
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2018-01-12 kjvdheideMerge branch 'develop' of https://source.jalview.org...
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2018-01-12 kjvdheideJAL-2798 Aptx is now saved to the project
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2018-01-12 kjvdheideJAL-2805 removed unused Aptx instance creation code
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2018-01-12 kjvdheideJAL-2805 added getter and setter for jalview association...
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2018-01-11 kjvdheideJAL-2884 old Newick trees are now loaded in as Aptx...
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2018-01-11 kjvdheideJAL-2795 simplified instance creation from calculation
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2018-01-11 kjvdheideJAL-2798 alignmentviewport's current external tree...
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2018-01-10 kjvdheideJAL-1953 named various threads
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2018-01-10 kjvdheideJAL-2795 calculated trees are now passed along as Newick...
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2018-01-10 kjvdheideJAL-2795 disabled most tests for now
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2018-01-09 kjvdheideJAL-2805 file identifying lines are turned to lowercase...
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2018-01-09 kjvdheideJAL-2805 correct nexus parser is now created
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2018-01-09 kjvdheideJAL-2805 Creating jalview sequence now requires the...
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2018-01-09 kjvdheideJAL-2805 added derive sequence when creating jalview...
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2018-01-09 kjvdheideJAL-2805 getNodeSequences returns a list now instead...
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2018-01-09 kjvdheideJAL-2805 added check for null node sequences during...
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2018-01-09 kjvdheideJAL-2805 allow for non-xsd validating phyloxml parsing
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2018-01-09 kjvdheideJAL-2805 check no longer errors if the sequence is...
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2018-01-09 kjvdheideJAL-2805 added check for sequences already being present...
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2018-01-09 kjvdheideJAL-2805 put the sequence setting in if statement ...
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2018-01-09 kjvdheideJAL-2805 added Aptx factory method reading directly...
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2018-01-09 kjvdheideJAL-2805 added nexus specific parser settings
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2018-01-09 kjvdheideJAL-2805 broke off the phylogenetic file formats into...
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2018-01-09 kjvdheideJAL-2805 parser is now File based (instead of FileParse...
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2018-01-09 kjvdheideJAL-2805 Parse returns a TreeI array again
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2018-01-09 kjvdheideJAL-2805 node sequence is now immediately filled in...
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2018-01-09 kjvdheideJAL-2805 added forester --> jalview sequence converter
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2018-01-09 kjvdheideJAL-2805 added getter in trees for retrieving all node...
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2018-01-09 kjvdheideJAL-1953 moved DataConversions to Forester package
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2018-01-08 kjvdheideJAL-2844 changed threshold from double to float
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2018-01-08 kjvdheideJAL-2844 start on moving tree partitioning code into...
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2018-01-06 kjvdheideJAL-2877 added forester as jar once again
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2018-01-06 kjvdheideJAL-281 first line also checked for PhyloXML identification
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2018-01-06 kjvdheideJAL-2871 aptx Configuration now created through input...
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2018-01-05 kjvdheideJAL-281 ForesterParser now extends from AlignFile
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2018-01-04 kjvdheideJAL-1953 Moved config to resources folder
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2018-01-04 kjvdheideJAL-281 ForesterParser factory methods added
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2018-01-02 kjvdheideJAL-1953 start work on storing nodes in a map per tree...
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2017-12-21 kjvdheideJAL-281 added file identify criteria for PhyloXML and...
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2017-12-20 kjvdheideJAL-2874 made the actionlistener slightly clearer
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2017-12-20 kjvdheideJAL-2838 JAL-2872 added sorting from the Aptx frame...
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2017-12-20 kjvdheideJAL-281 moved utility methods to .io package
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2017-12-20 kjvdheideJAL-281 split up TreeParser into separate format parsers
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2017-12-19 kjvdheideJAL-281 created Nexus and PhyloXML parser classes
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2017-12-19 kjvdheideJAL-281 cleared out useless tree parser class
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2017-12-19 kjvdheideJAL-281 added phyloxml and nexus to jalview fileformats
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2017-12-18 kjvdheideJAL-1953 moved now-generic methods outside of Aptx...
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2017-12-18 kjvdheideJAL-1953 -External from all interfaces names
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2017-12-18 kjvdheideJAL-1953 attempt at changing Aptx's font to Jalview's
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2017-12-18 kjvdheideJAL-2844 cladogram no longer vertically aligned (was...
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2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' of
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2017-12-18 kjvdheideJAL-2844 made null tree nodes return null wrappers...
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2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' into
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2017-12-18 kjvdheideJAL-1953 redundant tree interface instantiation removed
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2017-12-15 kjvdheideJAL-2852 EPS saving code ported from TreePanel to Aptx.
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2017-12-15 kjvdheideJAL-1953 added Y coordinate getter method
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2017-12-15 kjvdheideJAL-2852 merged the EPS button adding from main branch...
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2017-12-15 kjvdheideJAL-1953 node comparing now includes checking node...
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2017-12-15 kjvdheideJAL-1953 removed deprecated interfaces
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2017-12-15 kjvdheideJAL-2852 added EPS export button to File menu
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2017-12-14 kjvdheideJAL-1953 more progress on interfaces, jalview binding...
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2017-12-12 kjvdheideJAL-2874 filtering alignment now also works when just...
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2017-12-12 kjvdheideJAL-2874 added filtering when a subtree is selected
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2017-12-12 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' of https...
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2017-12-12 kjvdheideJAL-2877 disabled Jalview's own viewer for testing
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2017-12-11 kjvdheideJAL-2872 hide sort button in Aptx unless it's actually...
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2017-12-11 kjvdheideJAL-2877 disabled Jalview's default tree viewer when...
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2017-12-11 kjvdheideJAL-1953 fixed interface misnaming
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2017-12-11 kjvdheideJAL-1953 start on making everything interface based
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2017-12-08 kjvdheideJAL-1953 renaming of concrete implementation as well
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2017-12-08 kjvdheideJAL-2844 reallow clicks to the left of the root (groups...
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2017-12-07 kjvdheideJAL-2866 and .jar removed again
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2017-12-07 kjvdheideJAL-2866 forester .jar added to lib
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2017-12-07 kjvdheideJAL-2872 Redundant Aptx GUI menu items hidden, sorting...
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2017-12-06 kjvdheideJAL-2794 disabled branch colors on selection for now
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2017-12-06 kjvdheideJAL-2871 Added check whether configuration has been...
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2017-12-05 kjvdheideJAL-2838 Sorting from the alignment view menu now functional
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2017-12-05 kjvdheideJAL-2847 Rearranging and cleaning up of database query...
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2017-12-05 kjvdheideJAL-2794 associate leaves now iterates through ALL...
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2017-12-05 kjvdheideJAL-2847 various error popups for db querying now have...
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2017-12-05 kjvdheideJAL-2847 Strings for the various tree databases added
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2017-12-05 kjvdheideJAL-2847 if pfam id is detected in first sequence its...
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