JAL-2944: Allow structures to be opened in a specific structure view
Activity
CR-JAL-154 0
- Details
- Objectives
- General Comments 0
- Unresolved
- Resolved
- Number of files included: 156
-
jalview
0
-
Folder
.settings
0
- File org.eclipse.jdt.core.prefs 0 Remove
-
Folder
benchmarking
0
-
Folder
src/main/java/org/jalview
0
- File HiddenColsIteratorsBenchmark.java 0 Remove
- File HiddenColumnsBenchmark.java 0 Remove
- File SeqWidthBenchmark.java 0 Remove
- File README 0 Remove
-
Folder
src/main/java/org/jalview
0
-
Folder
examples/testdata
0
- File 4IM2_missing.pdb 0 Remove
- File 4IM2_missing_noid.pdb 0 Remove
- File 4IM2_nterm.pdb 0 Remove
-
Folder
help
0
-
Folder
html
0
-
Folder
features
0
- File splitView.html 0 Remove
- File releases.html 0 Remove
- File whatsNew.html 0 Remove
-
Folder
features
0
- File help.jhm 0 Remove
-
Folder
html
0
-
Folder
resources/images
0
- File idwidth.gif 0 Remove
-
Folder
src
0
-
Folder
MCview
0
- File PDBChain.java 0 Remove
-
Folder
jalview
0
-
Folder
analysis
0
- File AlignmentUtils.java 0 Remove
- File Dna.java 0 Remove
-
Folder
api/structures
0
- File JalviewStructureDisplayI.java 0 Remove
-
Folder
appletgui
0
- File AlignFrame.java 0 Remove
- File AlignmentPanel.java 0 Remove
- File AnnotationColumnChooser.java 0 Remove
- File AnnotationLabels.java 0 Remove
- File AnnotationPanel.java 0 Remove
- File FeatureSettings.java 0 Remove
- File IdCanvas.java 0 Remove
- File IdwidthAdjuster.java 0 Remove
- File OverviewCanvas.java 0 Remove
- File OverviewPanel.java 0 Remove
- File ScalePanel.java 0 Remove
- File SeqCanvas.java 0 Remove
- File SeqPanel.java 0 Remove
-
Folder
bin
0
- File Cache.java 0 Remove
- File JalviewLite.java 0 Remove
-
Folder
datamodel
0
- File Alignment.java 0 Remove
- File AlignmentAnnotation.java 0 Remove
- File AlignmentI.java 0 Remove
- File BoundedHiddenColsIterator.java 0 Remove
- File BoundedStartRegionIterator.java 0 Remove
- File CigarArray.java 0 Remove
- File DBRefSource.java 0 Remove
- File HiddenColsIterator.java 0 Remove
- File HiddenColumns.java 0 Remove
- File HiddenColumnsCursor.java 0 Remove
- File HiddenCursorPosition.java 0 Remove
- File RangeElementsIterator.java 0 Remove
- File RangeIterator.java 0 Remove
- File RegionsIterator.java 0 Remove
- File ReverseRegionsIterator.java 0 Remove
- File Sequence.java 0 Remove
- File SequenceGroup.java 0 Remove
- File SequenceI.java 0 Remove
- File StartRegionIterator.java 0 Remove
- File VisibleColsCollection.java 0 Remove
- File VisibleColsIterator.java 0 Remove
- File VisibleContigsIterator.java 0 Remove
-
Folder
ext
0
-
Folder
ensembl
0
- File EnsemblGenomes.java 0 Remove
- File EnsemblLookup.java 0 Remove
- File EnsemblRestClient.java 0 Remove
- File EnsemblSequenceFetcher.java 0 Remove
-
Folder
jmol
0
- File JalviewJmolBinding.java 0 Remove
- File JmolCommands.java 0 Remove
-
Folder
ensembl
0
-
Folder
fts/service/uniprot
0
- File UniProtFTSRestClient.java 0 Remove
-
Folder
gui
0
- File AlignFrame.java 0 Remove
- File AlignViewport.java 0 Remove
- File AlignmentPanel.java 0 Remove
- File AnnotationColumnChooser.java 0 Remove
- File AnnotationLabels.java 0 Remove
- File AnnotationPanel.java 0 Remove
- File AppJmol.java 0 Remove
- File AquaInternalFrameManager.java 0 Remove
- File ChimeraViewFrame.java 0 Remove
- File Desktop.java 0 Remove
- File FeatureSettings.java 0 Remove
- File IdCanvas.java 0 Remove
- File IdPanel.java 0 Remove
- File IdwidthAdjuster.java 0 Remove
- File Jalview2XML.java 0 Remove
- File OverviewCanvas.java 0 Remove
- File OverviewPanel.java 0 Remove
- File PopupMenu.java 0 Remove
- File Preferences.java 0 Remove
- File RotatableCanvas.java 0 Remove
- File ScalePanel.java 0 Remove
- File SeqCanvas.java 0 Remove
- File SeqPanel.java 0 Remove
- File StructureChooser.java 0 Remove
- File StructureViewer.java 0 Remove
- File StructureViewerBase.java 0 Remove
- File VamsasApplication.java 0 Remove
-
Folder
io
0
- File AnnotationFile.java 0 Remove
- File FormatAdapter.java 0 Remove
-
Folder
jbgui
0
- File GStructureChooser.java 0 Remove
-
Folder
renderer
0
- File AnnotationRenderer.java 0 Remove
- File OverviewRenderer.java 0 Remove
- File ScaleRenderer.java 0 Remove
-
Folder
structure
0
- File StructureMapping.java 0 Remove
- File StructureSelectionManager.java 0 Remove
-
Folder
util
0
- File MappingUtils.java 0 Remove
-
Folder
viewmodel
0
- File AlignmentViewport.java 0 Remove
- File OverviewDimensions.java 0 Remove
- File OverviewDimensionsHideHidden.java 0 Remove
- File OverviewDimensionsShowHidden.java 0 Remove
- File ViewportRanges.java 0 Remove
-
Folder
ws
0
-
Folder
dbsources
0
- File Pfam.java 0 Remove
- File PfamFull.java 0 Remove
- File PfamSeed.java 0 Remove
- File Rfam.java 0 Remove
- File RfamFull.java 0 Remove
- File RfamSeed.java 0 Remove
- File Uniprot.java 0 Remove
- File Xfam.java 0 Remove
-
Folder
jws1
0
- File JPredThread.java 0 Remove
-
Folder
sifts
0
- File SiftsClient.java 0 Remove
- File DBRefFetcher.java 0 Remove
-
Folder
dbsources
0
-
Folder
analysis
0
-
Folder
MCview
0
-
Folder
test/jalview
0
-
Folder
analysis
0
- File AlignmentUtilsTests.java 0 Remove
- File CrossRefTest.java 0 Remove
- File DnaTest.java 0 Remove
-
Folder
datamodel
0
- File AlignmentAnnotationTests.java 0 Remove
- File AlignmentTest.java 0 Remove
- File BoundedStartRegionIteratorTest.java 0 Remove
- File CigarArrayTest.java 0 Remove
- File ColumnSelectionTest.java 0 Remove
- File HiddenColumnsCursorTest.java 0 Remove
- File HiddenColumnsTest.java 0 Remove
- File RangeElementsIteratorTest.java 0 Remove
- File SequenceTest.java 0 Remove
- File StartRegionIteratorTest.java 0 Remove
- File VisibleColsIteratorTest.java 0 Remove
- File VisibleContigsIteratorTest.java 0 Remove
-
Folder
ext
0
-
Folder
ensembl
0
- File EnsemblGeneTest.java 0 Remove
-
Folder
jmol
0
- File JmolCommandsTest.java 0 Remove
- File JmolViewerTest.java 0 Remove
-
Folder
ensembl
0
-
Folder
gui
0
- File AlignFrameTest.java 0 Remove
- File AnnotationColumnChooserTest.java 0 Remove
- File PopupMenuTest.java 0 Remove
- File SeqCanvasTest.java 0 Remove
-
Folder
io
0
- File AnnotatedPDBFileInputTest.java 0 Remove
- File CrossRef2xmlTests.java 0 Remove
- File JSONFileTest.java 0 Remove
- File Jalview2xmlBase.java 0 Remove
- File Jalview2xmlTests.java 0 Remove
-
Folder
renderer
0
- File OverviewRendererTest.java 0 Remove
-
Folder
structure
0
- File StructureSelectionManagerTest.java 0 Remove
-
Folder
util
0
- File MappingUtilsTest.java 0 Remove
-
Folder
ws
0
-
Folder
dbsources
0
- File PfamFullTest.java 0 Remove
- File PfamSeedTest.java 0 Remove
- File RfamFullTest.java 0 Remove
- File RfamSeedTest.java 0 Remove
- File XfamFetcherTest.java 0 Remove
-
Folder
sifts
0
- File SiftsClientTest.java 0 Remove
- File PDBSequenceFetcherTest.java 0 Remove
-
Folder
dbsources
0
-
Folder
analysis
0
-
Folder
utils
0
- File proguard.jar 0 Remove
- File proguard_5.3.3.jar 0 Remove
- File .ant-targets-build.xml 0 Remove
- File .classpath 0 Remove
- File RELEASE 0 Remove
- File build.xml 0 Remove
-
Folder
.settings
0
-
Filter
- Only show me content:
- Unfiltered files: dynamically added content
- Filtered files: dynamically added content
- Clear filters
Keyboard shortcuts
Summarize the review outcomes (optional)
#permalink
Details
Warning: no files are visible, they have all been filtered.
Participant | Role | Time Spent | Comments | Latest Comment |
---|---|---|---|---|
Author | ||||
Reviewer - 2% reviewed | 1m | |||
Total | 1m | 0 |
-
Linked Issue:
JAL-2944
-
#permalink
Objectives
On selecting a structure to view, Jalview prompts the user about adding the structure to an existing view (each in turn), before opening it in a new view. The sequential prompt is a modal dialog, and cumbersome when many structure views are available - it would be better if the user could select the destination prior to initiating retrieval/display.
Selecting the destination for structures would also make it easier to add several structures to an existing view, because in 2.10.3 and earlier, when several structures are selected, Jalview always opens a new view.
Branches in review
Repository | Branch to review | Branched from |
---|
/.settings/org.eclipse.jdt.core.prefs
Changed
0
(0)
/benchmarking/.../jalview/HiddenColsIteratorsBenchmark.java
Added
0
(0)
/benchmarking/.../jalview/HiddenColumnsBenchmark.java
Changed
0
(0)
/benchmarking/.../jalview/SeqWidthBenchmark.java
Added
0
(0)
/benchmarking/README
Changed
0
(0)
/examples/testdata/4IM2_missing.pdb
Added
0
(0)
/examples/testdata/4IM2_missing_noid.pdb
Added
0
(0)
/examples/testdata/4IM2_nterm.pdb
Added
0
(0)
/help/html/features/splitView.html
Changed
0
(0)
/help/html/releases.html
Changed
0
(0)
/help/html/whatsNew.html
Changed
0
(0)
/help/help.jhm
Changed
0
(0)
/resources/images/idwidth.gif
Deleted
0
(0)
/src/MCview/PDBChain.java
Changed
0
(0)
/src/jalview/analysis/AlignmentUtils.java
Changed
0
(0)
/src/jalview/analysis/Dna.java
Changed
0
(0)
/src/.../structures/JalviewStructureDisplayI.java
Changed
0
(0)
/src/jalview/appletgui/AlignFrame.java
Changed
0
(0)
/src/jalview/appletgui/AlignmentPanel.java
Changed
0
(0)
/src/.../appletgui/AnnotationColumnChooser.java
Changed
0
(0)
/src/.../appletgui/AnnotationLabels.java
Changed
0
(0)
/src/.../appletgui/AnnotationPanel.java
Changed
0
(0)
/src/.../appletgui/FeatureSettings.java
Changed
0
(0)
/src/jalview/appletgui/IdCanvas.java
Changed
0
(0)
/src/.../appletgui/IdwidthAdjuster.java
Changed
0
(0)
/src/jalview/appletgui/OverviewCanvas.java
Changed
0
(0)
/src/jalview/appletgui/OverviewPanel.java
Changed
0
(0)
/src/jalview/appletgui/ScalePanel.java
Changed
0
(0)
/src/jalview/appletgui/SeqCanvas.java
Changed
0
(0)
/src/jalview/appletgui/SeqPanel.java
Changed
0
(0)
/src/jalview/bin/Cache.java
Changed
0
(0)
/src/jalview/bin/JalviewLite.java
Changed
0
(0)
/src/jalview/datamodel/Alignment.java
Changed
0
(0)
/src/.../datamodel/AlignmentAnnotation.java
Changed
0
(0)
/src/jalview/datamodel/AlignmentI.java
Changed
0
(0)
/src/.../datamodel/BoundedHiddenColsIterator.java
Deleted
0
(0)
/src/.../datamodel/BoundedStartRegionIterator.java
Deleted
0
(0)
/src/jalview/datamodel/CigarArray.java
Changed
0
(0)
/src/jalview/datamodel/DBRefSource.java
Changed
0
(0)
/src/.../datamodel/HiddenColsIterator.java
Deleted
0
(0)
/src/jalview/datamodel/HiddenColumns.java
Changed
0
(0)
/src/.../datamodel/HiddenColumnsCursor.java
Added
0
(0)
/src/.../datamodel/HiddenCursorPosition.java
Added
0
(0)
/src/.../datamodel/RangeElementsIterator.java
Added
0
(0)
/src/jalview/datamodel/RangeIterator.java
Added
0
(0)
/src/.../datamodel/RegionsIterator.java
Deleted
0
(0)
/src/.../datamodel/ReverseRegionsIterator.java
Deleted
0
(0)
/src/jalview/datamodel/Sequence.java
Changed
0
(0)
/src/jalview/datamodel/SequenceGroup.java
Changed
0
(0)
/src/jalview/datamodel/SequenceI.java
Changed
0
(0)
/src/.../datamodel/StartRegionIterator.java
Added
0
(0)
/src/.../datamodel/VisibleColsCollection.java
Changed
0
(0)
/src/.../datamodel/VisibleColsIterator.java
Deleted
0
(0)
/src/.../datamodel/VisibleContigsIterator.java
Added
0
(0)
/src/jalview/.../ensembl/EnsemblGenomes.java
Changed
0
(0)
/src/jalview/.../ensembl/EnsemblLookup.java
Changed
0
(0)
/src/.../ensembl/EnsemblRestClient.java
Changed
0
(0)
/src/.../ensembl/EnsemblSequenceFetcher.java
Changed
0
(0)
/src/jalview/.../jmol/JalviewJmolBinding.java
Changed
0
(0)
/src/jalview/ext/jmol/JmolCommands.java
Changed
0
(0)
/src/.../uniprot/UniProtFTSRestClient.java
Changed
0
(0)
/src/jalview/gui/AlignFrame.java
Changed
0
(0)
/src/jalview/gui/AlignViewport.java
Changed
0
(0)
/src/jalview/gui/AlignmentPanel.java
Changed
0
(0)
/src/.../gui/AnnotationColumnChooser.java
Changed
0
(0)
/src/jalview/gui/AnnotationLabels.java
Changed
0
(0)
/src/jalview/gui/AnnotationPanel.java
Changed
0
(0)
/src/jalview/gui/AppJmol.java
Changed
0
(0)