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JAL-2798 added != null check for Aptx trees
[jalview.git]
/
src
/
jalview
/
ext
/
2018-01-22
kjvdheide
Revert "JAL-2890 proper .jar this time and copied cipre...
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commitdiff
2018-01-19
kjvdheide
JAL-2805 small redundant method call fix
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commitdiff
2018-01-19
kjvdheide
JAL-2890 proper .jar this time and copied cipres' examp...
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commitdiff
2018-01-17
kjvdheide
JAL-1951 added comment to NexusFile clarifying Forester...
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commitdiff
2018-01-17
kjvdheide
JAL-2794 tree viewer frame now has its binding object...
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commitdiff
2018-01-17
kjvdheide
JAL-2798 now added to active views when associated...
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commitdiff
2018-01-16
kjvdheide
JAL-2798 tree frame is now added to active views when...
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commitdiff
2018-01-16
kjvdheide
JAL-2798 added method to tree for writing to jalview...
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commitdiff
2018-01-12
kjvdheide
JAL-2805 check actually works now
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commitdiff
2018-01-12
kjvdheide
JAL-2805 removed unused Aptx instance creation code
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commitdiff
2018-01-12
kjvdheide
JAL-2805 added getter and setter for jalview associatio...
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commitdiff
2018-01-11
kjvdheide
JAL-2795 simplified instance creation from calculation
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commitdiff
2018-01-11
kjvdheide
JAL-2798 alignmentviewport's current external tree...
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commitdiff
2018-01-10
kjvdheide
JAL-1953 named various threads
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commitdiff
2018-01-10
kjvdheide
JAL-2795 calculated trees are now passed along as Newic...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 correct nexus parser is now created
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commitdiff
2018-01-09
kjvdheide
JAL-2805 Creating jalview sequence now requires the...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added derive sequence when creating jalview...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 getNodeSequences returns a list now instead...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added check for null node sequences during...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 allow for non-xsd validating phyloxml parsing
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commitdiff
2018-01-09
kjvdheide
JAL-2805 check no longer errors if the sequence is...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added check for sequences already being presen...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 put the sequence setting in if statement ...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added Aptx factory method reading directly...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added nexus specific parser settings
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commitdiff
2018-01-09
kjvdheide
JAL-2805 broke off the phylogenetic file formats into...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 parser is now File based (instead of FileParse...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 Parse returns a TreeI array again
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commitdiff
2018-01-09
kjvdheide
JAL-2805 node sequence is now immediately filled in...
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added forester --> jalview sequence converter
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commitdiff
2018-01-09
kjvdheide
JAL-2805 added getter in trees for retrieving all node...
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commitdiff
2018-01-09
kjvdheide
JAL-1953 moved DataConversions to Forester package
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commitdiff
2018-01-08
kjvdheide
JAL-2844 changed threshold from double to float
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2018-01-08
kjvdheide
JAL-2844 start on moving tree partitioning code into...
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commitdiff
2018-01-06
kjvdheide
JAL-2871 aptx Configuration now created through input...
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commitdiff
2018-01-05
kjvdheide
JAL-281 ForesterParser now extends from AlignFile
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commitdiff
2018-01-04
kjvdheide
JAL-1953 Moved config to resources folder
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commitdiff
2018-01-04
kjvdheide
JAL-281 ForesterParser factory methods added
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commitdiff
2018-01-02
kjvdheide
JAL-1953 start work on storing nodes in a map per tree...
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commitdiff
2017-12-20
kjvdheide
JAL-2874 made the actionlistener slightly clearer
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commitdiff
2017-12-20
kjvdheide
JAL-2838 JAL-2872 added sorting from the Aptx frame...
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commitdiff
2017-12-20
kjvdheide
JAL-281 moved utility methods to .io package
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commitdiff
2017-12-20
kjvdheide
JAL-281 split up TreeParser into separate format parsers
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commitdiff
2017-12-19
kjvdheide
JAL-281 created Nexus and PhyloXML parser classes
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commitdiff
2017-12-19
kjvdheide
JAL-281 cleared out useless tree parser class
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commitdiff
2017-12-18
kjvdheide
JAL-1953 moved now-generic methods outside of Aptx...
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commitdiff
2017-12-18
kjvdheide
JAL-1953 -External from all interfaces names
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commitdiff
2017-12-18
kjvdheide
JAL-1953 attempt at changing Aptx's font to Jalview's
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commitdiff
2017-12-18
kjvdheide
JAL-2844 made null tree nodes return null wrappers...
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commitdiff
2017-12-18
kjvdheide
Merge branch 'kjvdh/features/PhylogenyViewer' into
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commitdiff
2017-12-18
kjvdheide
JAL-1953 redundant tree interface instantiation removed
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commitdiff
2017-12-15
kjvdheide
JAL-2852 EPS saving code ported from TreePanel to Aptx.
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commitdiff
2017-12-15
kjvdheide
JAL-1953 added Y coordinate getter method
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commitdiff
2017-12-15
kjvdheide
JAL-2852 merged the EPS button adding from main branch...
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commitdiff
2017-12-15
kjvdheide
JAL-1953 node comparing now includes checking node...
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commitdiff
2017-12-15
kjvdheide
JAL-1953 removed deprecated interfaces
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commitdiff
2017-12-15
kjvdheide
JAL-2852 added EPS export button to File menu
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commitdiff
2017-12-14
kjvdheide
JAL-1953 more progress on interfaces, jalview binding...
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commitdiff
2017-12-12
kjvdheide
JAL-2874 filtering alignment now also works when just...
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commitdiff
2017-12-12
kjvdheide
JAL-2874 added filtering when a subtree is selected
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commitdiff
2017-12-12
kjvdheide
JAL-2877 disabled Jalview's own viewer for testing
spikes/thomas
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commitdiff
2017-12-11
kjvdheide
JAL-2872 hide sort button in Aptx unless it's actually...
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commitdiff
2017-12-11
kjvdheide
JAL-2877 disabled Jalview's default tree viewer when...
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commitdiff
2017-12-11
kjvdheide
JAL-1953 fixed interface misnaming
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commitdiff
2017-12-11
kjvdheide
JAL-1953 start on making everything interface based
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commitdiff
2017-12-08
kjvdheide
JAL-1953 renaming of concrete implementation as well
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commitdiff
2017-12-08
kjvdheide
JAL-2844 reallow clicks to the left of the root (groups...
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commitdiff
2017-12-07
kjvdheide
JAL-2872 Redundant Aptx GUI menu items hidden, sorting...
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commitdiff
2017-12-06
kjvdheide
JAL-2794 disabled branch colors on selection for now
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commitdiff
2017-12-06
kjvdheide
JAL-2871 Added check whether configuration has been...
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commitdiff
2017-12-05
kjvdheide
JAL-2838 Sorting from the alignment view menu now funct...
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commitdiff
2017-12-05
kjvdheide
JAL-2847 Rearranging and cleaning up of database query...
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commitdiff
2017-12-05
kjvdheide
JAL-2794 associate leaves now iterates through ALL...
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commitdiff
2017-12-05
kjvdheide
JAL-2847 various error popups for db querying now have...
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commitdiff
2017-12-05
kjvdheide
JAL-2847 if pfam id is detected in first sequence its...
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commitdiff
2017-12-05
kjvdheide
JAL-2805 JAL-2847 JAL-281 added file path to Aptx frame...
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commitdiff
2017-12-05
kjvdheide
JAL-2838 tree viewer interface expanded to include...
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commitdiff
2017-12-05
kjvdheide
JAL-2838 filled in actionPerformed of the tree sort...
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commitdiff
2017-12-05
kjvdheide
JAL-2838 Aptx frames now appear in the alignment sortin...
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commitdiff
2017-12-03
kjvdheide
JAL-2847 start of cleaning up db loading code
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commitdiff
2017-12-03
kjvdheide
JAL-2844 rearranging code
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commitdiff
2017-11-29
kjvdheide
JAL-2844 check added for clicks left of root node
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commitdiff
2017-11-29
kjvdheide
JAL-2844 entirely X coord based partitioning
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commitdiff
2017-11-29
kjvdheide
JAL-2844 somewhat better repainting
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commitdiff
2017-11-29
kjvdheide
JAL-2844 temporary kludge to draw a line
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commitdiff
2017-11-29
kjvdheide
JAL-2844 added grouping to alignment panel based on...
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commitdiff
2017-11-29
kjvdheide
JAL-2844 start on colouring back onto the alignment
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commitdiff
2017-11-29
kjvdheide
JAL-2844 added colouring to partition selection
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commitdiff
2017-11-28
kjvdheide
JAL-2844 added offset to x coord to make it equal 0...
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commitdiff
2017-11-28
kjvdheide
JAL-2844 first go at partitioning, based on actual...
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commitdiff
2017-11-27
kjvdheide
JAL-2844 added selection threshold (non-adjusted calcul...
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commitdiff
2017-11-27
kjvdheide
JAL-2799 re-enabled change listener for Aptx's tabs...
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commitdiff
2017-11-27
kjvdheide
JAL-2844 line drawing at mouse click added on top of...
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commitdiff
2017-11-26
kjvdheide
JAL-2847 first rough attempt at loading in via database ID
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commitdiff
2017-11-24
kjvdheide
JAL-2799 rearranged AptxInit code
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commitdiff
2017-11-24
kjvdheide
JAL-2799 ALL trees are now loaded in as separate Aptx...
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commitdiff
2017-11-24
kjvdheide
JAL-2794 binding now exclusively supports single tab...
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commitdiff
2017-11-24
kjvdheide
Merge branch 'kjvdh/features/PhylogenyViewer' of https...
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commitdiff
2017-11-24
kjvdheide
JAL-2838 start on sorting
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