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JAL-2629 add simple jackhmmer functionality
[jalview.git]
/
src
/
jalview
/
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
tree
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commitdiff
2019-06-28
tva
JAL-2629 add ability to add background frequencies...
tree
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commitdiff
2019-06-28
tva
JAL-3336 add better method of determining where data...
tree
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commitdiff
2019-06-28
tva
JAL-3336 fix hmmsearch failing when parsing score table
tree
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commitdiff
2019-06-28
tva
JAL-2629 add file that should have been in previous...
tree
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commitdiff
2019-06-28
tva
JAL-2629 add HMM Match Score colour scheme
tree
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commitdiff
2019-06-10
tva
JAL-3297 pad gaps in alignment to ensure hmmalign runs
tree
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commitdiff
2019-06-07
tva
JAL-3291 issue fixed, passing tests added
tree
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commitdiff
2019-06-06
tva
JAL-3285 build Jalview XML file for current version
tree
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commitdiff
2019-06-06
tva
JAL-3285 fix incorrect file paths on HMMAlign/Search...
tree
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commitdiff
2019-06-06
tva
JAL-3285 add Cygwin environment path fix for Windows
tree
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commitdiff
2019-06-06
tva
JAL-3285 code changes to HMMER colour schemes not inclu...
tree
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commitdiff
2019-06-06
tva
JAL-3285 fix FileLoader failing to load HMMER file
tree
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commitdiff
2019-06-05
tva
JAL-3285 method call change tin Information to match...
tree
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commitdiff
2019-06-05
tva
JAL-3285 delete duplicate variables in AlignmentViewpor...
tree
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commitdiff
2019-06-05
tva
JAL-3285 method call change to HMMBuild not included...
tree
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commitdiff
2019-06-05
tva
JAL-3285 method call change in SeqPanel to match develop
tree
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commitdiff
2019-06-05
tva
JAL-3285 change method declaration in AAFrequency to...
tree
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commitdiff
2019-06-05
tva
JAL-3285 changed method call on AnnotationRenderer...
tree
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commitdiff
2019-06-05
tva
JAL-3285 code changes to Jalview2XML not included in...
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged code to AlignmentAnnotation
tree
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commitdiff
2019-06-05
tva
JAL-3285 method call name change to SeqPanel not includ...
tree
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commitdiff
2019-06-05
tva
JAL-3285 method call name change in OverviewPanel not...
tree
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commitdiff
2019-06-05
tva
JAL-3285 small method call name change to AnnotationLabels
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged code to SequenceGroup
tree
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commitdiff
2019-06-05
tva
JAL-3285 small method call name change missed in Consen...
tree
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commitdiff
2019-06-05
tva
JAL-3285 small code changes to ConsensusThread not...
tree
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commitdiff
2019-06-05
tva
JAL-3285 small code changes to AnnotationRenderer not...
tree
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commitdiff
2019-06-05
tva
JAL-3285 code changes to AnnotationLabels not included...
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged features to AlignViewportI
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged features to AlignViewport
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged features into AlignmentViewport
tree
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commitdiff
2019-06-05
tva
JAL-3285 add methods and small changes to StockholmFile...
tree
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commitdiff
2019-06-04
Jim Procter
Merge branch 'develop' into developtomchmmer
tree
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commitdiff
2019-05-31
Ben Soares
JAL-3247 Adjusted Uninstall Old Jalview.app to just...
tree
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commitdiff
2019-05-29
gmungoc
JAL-2738 error logging if no ##reference found
tree
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commitdiff
2019-05-29
gmungoc
JAL-2738 accept .csi, default to GRCh37:homo_sapiens...
tree
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commitdiff
2019-05-28
Ben Soares
JAL-1988 Some TEST code accidentally left in now remove...
tree
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commitdiff
2019-05-27
Ben Soares
JAL-3141 Added HashMap types for Java 1.8 compatibility
tree
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commitdiff
2019-05-27
Ben Soares
Merge branch 'task/JAL-3141_Customise_checkbox' into...
tree
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commitdiff
2019-05-27
Ben Soares
JAL-3141 Object array cast missing
tree
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commitdiff
2019-05-27
Ben Soares
Merge branch 'task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_...
tree
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commitdiff
2019-05-27
Ben Soares
JAL-3141 Generified the JvUtils.buildComboWithTooltips...
tree
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commitdiff
2019-05-25
Ben Soares
JAL-3141 One more error log fix
tree
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commitdiff
2019-05-25
Ben Soares
JAL-3141 Added tooltips on Schemes dropdown and Customi...
tree
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commitdiff
2019-05-24
Ben Soares
JAL-3141 Fixes recommended from gmc's test
tree
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commitdiff
2019-05-24
Ben Soares
JAL-3141 Fixed vertical size of the example filenames...
tree
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commitdiff
2019-05-24
Ben Soares
JAL-3141 Reworked a lot of BackupFiles to allow the...
tree
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commitdiff
2019-05-22
Ben Soares
Merge branch 'bug/JAL-3141_backupfiles_prefs_widget_dis...
tree
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commitdiff
2019-05-21
Ben Soares
JAL-3247 Launcher start improvements. RPM and DEB no...
tree
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commitdiff
2019-05-20
Ben Soares
JAL-3254 Improved memory setting (allows mem for OS...
tree
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commitdiff
2019-05-06
gmungoc
JAL-3239 release note
tree
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commitdiff
2019-05-06
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3239monosp...
tree
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commitdiff
2019-05-06
gmungoc
JAL-3244 delete obsolete method
tree
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commitdiff
2019-05-02
gmungoc
JAL-3239 draw EPS or SVG one character at a time (even...
bug/JAL-3239monospacedEps
tree
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commitdiff
2019-05-02
gmungoc
JAL-3244 renamed Platform method for clarity
bug/JAL-3244jmolWindows
tree
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commitdiff
2019-05-01
gmungoc
JAL-3244 ignore file path separator when comparing...
tree
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commitdiff
2019-04-30
gmungoc
JAL-3241 simplified enum constructors for classloadabil...
tree
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commitdiff
2019-04-29
gmungoc
JAL-2738 JAL-2743 update unit test to match new VCF...
tree
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commitdiff
2019-04-26
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2019-04-26
gmungoc
JAL-2743 class Javadoc
tree
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commitdiff
2019-04-26
gmungoc
JAL-2738 JAL-2743 properties to map VCF header to speci...
tree
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commitdiff
2019-04-26
Ben Soares
JAL-3233 Added isAMac check for -Xdock:icon addition...
tree
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commitdiff
2019-04-26
gmungoc
JAL-3010 borderless 'x' for "delete this filter condition"
tree
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commitdiff
2019-04-26
gmungoc
JAL-2808 better tooltip 'delete this condition'
tree
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commitdiff
2019-04-25
Ben Soares
JAL-3224 JAL-3225 Some fixes in install4j template...
tree
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commitdiff
2019-04-25
Ben Soares
JAL-3224 JAL-3225 Added lines to check for updates...
tree
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commitdiff
2019-04-24
Jim Procter
Merge branch 'task/JAL-3225_Integration_Gradle_building...
tree
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commitdiff
2019-04-23
Jim Procter
Merge branch 'develop' into bug/JAL-3224_getdown_change...
tree
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commitdiff
2019-04-20
gmungoc
JAL-2791 tailored message if find fails on selection...
tree
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commitdiff
2019-04-18
gmungoc
JAL-3193 dbSource always "ENSEMBL"
tree
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commitdiff
2019-04-16
gmungoc
Merge branch 'bug/JAL-3218scalePanelPopups' into develop
tree
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commitdiff
2019-04-15
Ben Soares
JAL-3130 Helper classes to take Class Exceptions when...
tree
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commitdiff
2019-04-15
gmungoc
JAL-3193 no separatge EnsemblGenomes source in Sequence...
tree
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commitdiff
2019-04-11
Jim Procter
Merge branch 'develop' into task/JAL-3130_Java_11_inves...
tree
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commitdiff
2019-04-10
gmungoc
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
tree
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commitdiff
2019-04-10
gmungoc
JAL-3018 REST version updated to 10.0
tree
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commitdiff
2019-04-05
Ben Soares
JAL-3130 This commit concentrates on the Mac OS X DMG...
tree
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commitdiff
2019-04-04
Ben Soares
JAL-3130 trying to be Java 1.8 source compatible -...
tree
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commitdiff
2019-04-03
gmungoc
JAL-3021 show Sequence Details with cursor at top
tree
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commitdiff
2019-04-02
gmungoc
JAL-3218 allow both Hide and Reveal in scale panel...
bug/JAL-3218scalePanelPopups
tree
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commitdiff
2019-04-01
Ben Soares
JAL-3130 JAL-3007 Added gradle build for Java 11 and...
tree
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commitdiff
2019-03-28
gmungoc
Merge branch 'feature/JAL-3181linkOrdering' into develop
tree
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commitdiff
2019-03-27
gmungoc
JAL-2620 improved error reporting on failure to load...
tree
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commitdiff
2019-03-25
gmungoc
JAL-2717 adjusted code so default correctly returned...
tree
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commitdiff
2019-03-23
gmungoc
JAL-1889 explicit recalc of geometry for scale left...
bug/JAL-1889serverTestSuite
tree
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commitdiff
2019-03-23
gmungoc
JAL-1889 remove debug logging, add updateLayout()
tree
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commitdiff
2019-03-22
gmungoc
JAL-1889 more debug logging
tree
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commitdiff
2019-03-21
gmungoc
JAL-1889 better debug logging
tree
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commitdiff
2019-03-21
gmungoc
JAL-1889 temporary debug in findColumn()
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3141 Disabled the 'Include Backup Files' checkbox...
tree
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commitdiff
2019-03-20
gmungoc
JAL-3093 fine tuning of SeqPanel tooltip
tree
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commitdiff
2019-03-20
gmungoc
JAL-3212 unit test and fix for Scale Panel bug
tree
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commitdiff
2019-03-19
Ben Soares
JAL-3141 Removed 'Save Project' File Menu item
tree
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commitdiff
2019-03-19
Ben Soares
JAL-3141 patch for Backups preferences enable/disable...
tree
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commitdiff
2019-03-19
Ben Soares
JAL-3130 remove some comments on quit. fix modules...
tree
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commitdiff
2019-03-19
Ben Soares
JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben...
tree
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commitdiff
2019-03-15
gmungoc
JAL-2964 missed branch for restore link tree to all...
tree
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commitdiff
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