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JAL-2805 TreeParser now interface based
[jalview.git]
/
src
/
jalview
/
ext
/
2017-11-13
kjvdheide
JAL-2805 TreeParser now interface based
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 Added tree building interface
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 name change
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 deleted old Aptx class for loading just Newick...
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 more interface work
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commitdiff
2017-11-13
kjvdheide
JAL-2794 removed unused interface
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commitdiff
2017-11-13
kjvdheide
JAL-2805 undid accidental double (buggy) binding, more...
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 warning messages added if Forester detects...
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 First try at loading tree through Forester...
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 reorganized node select code, added subtree...
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 comments comments comments
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commitdiff
2017-11-10
kjvdheide
JAL-2794 most method parameters/class variables made...
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 comments, selected node now doesn't have to...
tree
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commitdiff
2017-11-09
kjvdheide
JAL-2794 PaintRefresher support, Aptx node selection...
tree
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commitdiff
2017-11-09
kjvdheide
JAL-2794 interface comment
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commitdiff
2017-11-09
kjvdheide
JAL-2794 Made HashMap with Nodes as keys and sequences...
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Aptx instances get their parent alignment...
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Cleaning up tree conversion, sequences are...
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2795 created static class for forester conversions
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Interface name change (oops)
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 made JalviewTreeViewerBinding an interface
tree
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commitdiff
2017-11-03
kjvdheide
JAL-2794 created tree viewer binding class
tree
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commitdiff
2017-11-03
kjvdheide
JAL-2795 bunch of cleanup and comments
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 added back test loop for Aptx tree naming...
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 Reverted code changes needed to cluster from...
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 Forester now NJ-clusters the DistanceMatrix...
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 moved matrix conversion to the ForesterMatrix...
tree
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commitdiff
2017-11-01
kjvdheide
JAL-2795 Sequence[] references now as SequenceI[] ...
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commitdiff
2017-11-01
kjvdheide
JAL-2795 removed sequences[] class variable, more comments
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commitdiff
2017-10-30
kjvdheide
JAL-2795 added error catching for invalid identifier
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commitdiff
2017-10-30
kjvdheide
JAL-2795 changed getting index of identifier to Stream...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 rebuilt MatrixConverter to be purely static
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 finalized method arguments; commited forester...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed unneeded for loop (woops) and initiali...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 implemented getting/setting identifiers
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commitdiff
2017-10-30
kjvdheide
JAL-2795 added comments links from ForesterMatrix to...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed now unneeded values variable in Forest...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 add get for all matrix values to MatrixI ...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 foresterMatrix now stores distance values...
tree
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commitdiff
2017-10-29
kjvdheide
JAL-2795 more matrix implementations
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commitdiff
2017-10-28
kjvdheide
JAL-2795 moved ForesterMatrix to ext.forester
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commitdiff
2017-10-28
kjvdheide
JAL-2795 Added get and set values to the converted...
tree
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commitdiff
2017-10-27
kjvdheide
JAL-2795 start of Jalview's Matrix conversion
tree
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commitdiff
2017-10-26
kjvdheide
Start of matrix converter
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commitdiff
2017-10-26
kjvdheide
Added proper title to aptx trees
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commitdiff
2017-10-26
kjvdheide
Added TreeBuilder as parameter to the converter constructor
tree
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commitdiff
2017-10-26
kjvdheide
Name changed of aptx treebuilder to treeconverter
tree
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commitdiff
2017-10-26
kjvdheide
named most Jalview threads
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commitdiff
2017-10-25
kjvdheide
finished up tests for trees made from jalview data
tree
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
tree
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commitdiff
2017-10-24
kjvdheide
Tests for Aptx tree created from a Phylogeny object...
tree
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commitdiff
2017-10-24
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2253' into develop
tree
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commitdiff
2017-10-23
gmungoc
JAL-1854 keep fallthrough but with comment to suppress...
tree
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commitdiff
2017-10-23
gmungoc
JAL-1854 remove fallthrough of switch case (Checkstyle...
tree
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commitdiff
2017-10-20
gmungoc
JAL-2253 pull up constant, additional unit test
bug/JAL-2253
tree
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commitdiff
2017-10-17
Jim Procter
JAL-2777 patch for whitespace chain
bugs/JAL-2777_whitespaceChain
tree
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commitdiff
2017-10-13
kjvdheide
basic tests for Aptx
tree
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commitdiff
2017-10-13
kjvdheide
ArchaeopteryxInit is now static
tree
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commitdiff
2017-10-13
kjvdheide
simplified aptx frame creation code
tree
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commitdiff
2017-10-13
kjvdheide
Slight Aptx colour change
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commitdiff
2017-10-12
kjvdheide
Custom aptx configuration added
tree
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commitdiff
2017-10-12
kjvdheide
moved Aptx creation from CalculationChooser to separate...
tree
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commitdiff
2017-10-12
kjvdheide
Created test class for Archaeopteryx tree viewing
tree
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commitdiff
2017-10-11
kjvdheide
forester as submodule with InternalFrame + start of...
tree
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commitdiff
2017-10-11
kjvdheide
just a comment
tree
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commitdiff
2017-10-11
kjvdheide
Added tree building (without distances yet)
tree
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commitdiff
2017-10-10
Jim Procter
Merge branch 'codereviews/JAL-1990_IProgressIndicator_j...
tree
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commitdiff
2017-10-10
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-10
kjvdheide
Start of programmatically creating Aptx trees
tree
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commitdiff
2017-10-09
kjvdheide
Start of creating tree nodes for Aptx
tree
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commitdiff
2017-10-09
kjvdheide
Fully separated tree GUI from calculation
tree
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commitdiff
2017-10-09
gmungoc
JAL-2523 basic sleep and retry (3 times) on 429 respons...
features/JAL-2523httpRetries
tree
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commitdiff
2017-10-09
gmungoc
JAL-2523 convenience method to get model organisms
tree
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commitdiff
2017-10-07
kjvdheide
Renaming
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commitdiff
2017-10-06
kjvdheide
Start of creating the objects Archaeopteryx needs
tree
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commitdiff
2017-10-05
kjvdheide
Blank interfaces added
tree
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commitdiff
2017-10-04
gmungoc
JAL-2523 start of refactoring...
tree
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commitdiff
2017-10-03
kjvdheide
Proper copyright dating added
tree
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commitdiff
2017-10-03
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-03
kjvdheide
Kept copyright test to just the new classes
tree
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commitdiff
2017-10-03
kjvdheide
Copyright test
tree
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commitdiff
2017-10-02
gmungoc
JAL-2525 lookup transcript features by Ontology
tree
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commitdiff
2017-09-29
kjvdheide
Begin separation of GUI and tree calculation logic
origin/spikes/koen
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commitdiff
2017-08-31
gmungoc
JAL-2105 REST versions updated to 6.1 (Ensembl) 6.0...
tree
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commitdiff
2017-08-31
gmungoc
JAL-2253 safer simpler resolution of identifiers using...
tree
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commitdiff
2017-08-25
gmungoc
JAL-2480 suppress debug timing output that got left in
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
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commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
tree
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commitdiff
2017-06-05
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2582 comment about IDs being lost if they resembl...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2582 recognise ENS…P peptide IDs and make two getPa...
tree
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commitdiff
2017-05-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
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commitdiff
2017-05-24
gmungoc
JAL-2529 add object_type=cdna to EnsemblCdna parameters
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commitdiff
2017-05-18
gmungoc
JAL-2490 retrieve visible features only
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