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JAL-2795 neater error message
[jalview.git]
/
src
/
jalview
/
2017-10-30
kjvdheide
JAL-2795 added error catching for invalid identifier
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 changed getting index of identifier to Stream...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 rebuilt MatrixConverter to be purely static
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commitdiff
2017-10-30
kjvdheide
JAL-2795 finalized method arguments; commited forester...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed unneeded for loop (woops) and initiali...
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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...
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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...
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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...
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commitdiff
2017-10-27
kjvdheide
JAL-2795 start of Jalview's Matrix conversion
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commitdiff
2017-10-27
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-27
gmungoc
JAL-2526 updated javadoc
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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
Made FreeUpMemoryTest compatible with modified Calculat...
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commitdiff
2017-10-26
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-26
Jim Procter
JAL-2488 patch causes of NPE during testStoreAndRecover...
tree
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commitdiff
2017-10-26
kjvdheide
Added getters for scoremodel & scoreparams in TreeBuilder
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commitdiff
2017-10-26
Jim Procter
Merge branch 'feature/JAL-2488finalize' into develop
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commitdiff
2017-10-26
kjvdheide
TreeBuilder now stores the used ScoreModel and ScoreParams
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commitdiff
2017-10-26
kjvdheide
small name fixes in TreeBuilder
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commitdiff
2017-10-26
kjvdheide
Added TreeBuilder as parameter to the converter constructor
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commitdiff
2017-10-26
kjvdheide
Name changed of aptx treebuilder to treeconverter
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commitdiff
2017-10-26
kjvdheide
added getSeqData to TreeBuilder
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commitdiff
2017-10-26
Jim Procter
JAL-2793 cancelling font changed dialog didn't call...
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commitdiff
2017-10-26
kjvdheide
Added full names to the tree algorithm enum
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commitdiff
2017-10-26
kjvdheide
added abbreviations
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commitdiff
2017-10-26
kjvdheide
added enum for the different tree algorithms
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commitdiff
2017-10-26
kjvdheide
Couple more thread names
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commitdiff
2017-10-26
kjvdheide
named most Jalview threads
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commitdiff
2017-10-26
Jim Procter
Merge branch 'bug/JAL-2776toggleGroupColour' into develop
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commitdiff
2017-10-26
Jim Procter
Merge branch 'features/JAL-2685pairwiseSeqLimits' into...
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commitdiff
2017-10-26
kjvdheide
removed accidental added enters, commented out broken...
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commitdiff
2017-10-25
kjvdheide
finished up tests for trees made from jalview data
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2617mappedStopCodon' into develop
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2667mouseWheelWrapped' into develop
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2727closeAllFreeMemory' into...
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bugs/JAL-2779_osx_dialogsequencingbroke...
tree
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commitdiff
2017-10-25
Jim Procter
JAL-2779 remove empty block and if statement
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
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commitdiff
2017-10-25
Jim Procter
JAL-2790 provide a cancel button for JABAWS and AACon...
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commitdiff
2017-10-25
Jim Procter
JAL-2392 auto boxing rather than explicit Long as key
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commitdiff
2017-10-24
gmungoc
JAL-2495 highlight all mapped sequences from structure...
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commitdiff
2017-10-24
Jim Procter
Merge branch 'features/JAL-2608closeOverview' into...
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commitdiff
2017-10-24
kjvdheide
Tests for Aptx tree created from a Phylogeny object...
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commitdiff
2017-10-24
gmungoc
JAL-2788 corrected merge error in propertyChange
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commitdiff
2017-10-24
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2609attemptedmerge' into develop
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commitdiff
2017-10-23
Jim Procter
JAL-2609 remove unused AlignPanel.fastPaint flag and...
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2609attemptedmerge' into develop
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2739' into develop
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2682parseId' into develop
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commitdiff
2017-10-23
gmungoc
JAL-2776 repaint everything on toggle group colour
bug/JAL-2776toggleGroupColour
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2253' into develop
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commitdiff
2017-10-23
gmungoc
JAL-1854 keep fallthrough but with comment to suppress...
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commitdiff
2017-10-23
gmungoc
JAL-1854 remove fallthrough of switch case (Checkstyle...
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commitdiff
2017-10-20
Jim Procter
JAL-2779 keep a reference to original Aqua manager...
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commitdiff
2017-10-20
Jim Procter
JAL-2779 remove OSX platform specific import (not neede...
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commitdiff
2017-10-20
gmungoc
JAL-2253 pull up constant, additional unit test
bug/JAL-2253
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commitdiff
2017-10-20
gmungoc
JAL-2609 fully erase scale above, tidy code change
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commitdiff
2017-10-19
gmungoc
JAL-2609 adjustments for test findings
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commitdiff
2017-10-19
kiramt
Merge branch 'develop' into bug/JAL-2609attemptedmerge
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commitdiff
2017-10-18
Jim Procter
JAL-2779 switch order for updating the current alignmen...
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commitdiff
2017-10-18
Jim Procter
JAL-2779 remove dead code
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commitdiff
2017-10-18
Jim Procter
JAL-2779 hook in our own AquaInternalFrameManager when...
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commitdiff
2017-10-18
Jim Procter
JAL-2779 JAL-1551 source formatting
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commitdiff
2017-10-18
Jim Procter
JAL-2779 patch so closing most recent frame doesn’t...
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commitdiff
2017-10-18
Jim Procter
JAL-2779 original version of AquaInternalFrame Manager
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commitdiff
2017-10-18
Jim Procter
Merge branch 'bugs/JAL-2777_whitespaceChain' into develop
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commitdiff
2017-10-18
Jim Procter
JAL-2777 remove duplicate code outside conditional...
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commitdiff
2017-10-17
Jim Procter
JAL-2773 renamed flags for clarity
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commitdiff
2017-10-17
Jim Procter
JAL-2777 patch for whitespace chain
bugs/JAL-2777_whitespaceChain
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commitdiff
2017-10-17
Jim Procter
JAL-2481 patch to fix findFeatureColour for end-of...
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commitdiff
2017-10-17
Jim Procter
JAL-2777 noticed exception raised on construction of...
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commitdiff
2017-10-13
kjvdheide
basic tests for Aptx
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commitdiff
2017-10-13
kjvdheide
ArchaeopteryxInit is now static
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commitdiff
2017-10-13
kjvdheide
simplified aptx frame creation code
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commitdiff
2017-10-13
kjvdheide
Slight Aptx colour change
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commitdiff
2017-10-12
Jim Procter
JAL-2773 add new flag to paintAlignment(updateOverview...
features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
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commitdiff
2017-10-12
kjvdheide
Custom aptx configuration added
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commitdiff
2017-10-12
kjvdheide
moved Aptx creation from CalculationChooser to separate...
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commitdiff
2017-10-12
kjvdheide
Created test class for Archaeopteryx tree viewing
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commitdiff
2017-10-11
kjvdheide
forester as submodule with InternalFrame + start of...
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commitdiff
2017-10-11
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-11
gmungoc
JAL-2772 check array bounds for sequence access
bug/JAL-2772pdbArrayBounds
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commitdiff
2017-10-11
kjvdheide
just a comment
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commitdiff
2017-10-11
gmungoc
JAL-2609 tidy label width code, some checkstyle warnings
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commitdiff
2017-10-11
gmungoc
Merge branch 'bug/JAL-2742' into develop
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commitdiff
2017-10-11
gmungoc
Merge branch 'bug/JAL-2757_uniprotftsbadquery' into...
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commitdiff
2017-10-11
gmungoc
JAL-2757 fix PDB also; suppress stack trace and compile...
bug/JAL-2757_uniprotftsbadquery
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commitdiff
2017-10-11
kjvdheide
Added tree building (without distances yet)
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commitdiff
2017-10-11
kiramt
JAL-2742 removed unused getViewAsCigars
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commitdiff
2017-10-11
kiramt
JAL-2609attemptedmerge tidy
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commitdiff
2017-10-10
kiramt
Merge remote-tracking branch 'origin/features/JAL-2609f...
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