MCview

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JAL-3474 removed all .cvsignore files stored in the repo

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JAL-3210 MCview now mc_view

JAL-3210 delete old package post merge

Merge branch 'develop' into trialMerge

Conflicts:

.classpath

.project

.settings/org.eclipse.jdt.core.prefs

.settings/org.eclipse.jdt.groovy.core.prefs

.settings/org.eclipse.jdt.ui.prefs

build.xml

src/MCview/AppletPDBCanvas.java

src/MCview/Atom.java

src/MCview/PDBCanvas.java

src/jalview/appletgui/EmbmenuFrame.java

src/jalview/appletgui/OverviewPanel.java

src/jalview/appletgui/SeqPanel.java

src/jalview/bin/Jalview.java

src/jalview/ext/paradise/Annotate3D.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/FeatureTypeSettings.java

src/jalview/io/FileLoader.java

src/jalview/jbgui/GDesktop.java

src/jalview/util/ImageMaker.java

src/jalview/util/Platform.java

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JAL-3130 Lots of deprecation fixes. See utils/deprecation_auto_fixes.sh for commands used to fix the bulk of these (a couple of manual fixes at the end too).

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JAL-3130 Some automatically fixed deprecated calls. Mostly constructors converted to .valueOf() to use a final static version. See utils/deprecation_auto_fixes.sh

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JAL-3026 MCview -> mc_view

SwingJS requires standard package and class capitalization;

_ added to avoid PC capitalization issue

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JAL-2629 update spike branch to latest

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JAL-2952 set negative TempFactor values as AlignmentAnnotation.graphMin

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JAL-2944: Allow structures to be opened in a specific structure view
JAL-2944: Allow structures to be opened in a specific structure view
Updated with latest from mchmmer branch

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JAL-2781 mark aligned positions via StructureMapping’s Mapping object, and transfer residue positions via the Atom.resNum position rather than Residue.number

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JAL-1793 spike branch updated to latest

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Merge branch 'codereviews/JAL-1990_IProgressIndicator_jalview.structure' into patch/JAL-1990_JAL-2392_deadlockssm updated for 2.10.3. Still need to remove jalview.gui.IProgressBar imports from non-swing packages (appletgui, structures, etc)

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JAL-2738 copy to spikes/mungo

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JAL-2694 StructureSelectionManager.getMapping takes a list of Chain IDs per sequence to be bound to structure, and resolveChains adjusted accordingly. targetChains also dropped in StructureViewer constructor since resolveChains discovers extant chain mappings, and StructureSelectionManager infers any sequence/chain mappings that remain.

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Merge branch 'develop' into features/JAL-2446NCList

Conflicts:

src/MCview/PDBChain.java

src/jalview/analysis/AlignmentSorter.java

src/jalview/analysis/AlignmentUtils.java

src/jalview/analysis/Dna.java

src/jalview/appletgui/AlignFrame.java

src/jalview/appletgui/FeatureRenderer.java

src/jalview/appletgui/Finder.java

src/jalview/appletgui/SeqPanel.java

src/jalview/commands/EditCommand.java

src/jalview/datamodel/AlignedCodonFrame.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceFeature.java

src/jalview/datamodel/xdb/embl/EmblEntry.java

src/jalview/ext/ensembl/EnsemblGene.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AnnotationExporter.java

src/jalview/gui/CutAndPasteTransfer.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/Finder.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SeqCanvas.java

src/jalview/gui/SeqPanel.java

src/jalview/io/FeaturesFile.java

src/jalview/io/JSONFile.java

src/jalview/io/gff/InterProScanHelper.java

src/jalview/io/vamsas/Datasetsequence.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

src/jalview/util/RangeComparator.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

src/jalview/ws/jws2/AADisorderClient.java

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JAL-2418 source formatting

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JAL-2136 New Phyre2 branch + attempt to resynced with develop

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JAL-2446 merged to spike branch

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JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL
JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL
JAL-2557 removal of Sequence.sequenceFeatures

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JAL-2050 make SequenceFeature.score final, adjust constructor calls

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JAL-2505 use constructors to set (what will be) final fields in SequenceFeature

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Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url

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So this is a cut-down (and renamed) version of getPdbFiles()? Not clear how this fixes the problem. What about all the logic removed from the method - is it not needed, if not why not? (If it isn't...

So this is a cut-down (and renamed) version of getPdbFiles()?
Not clear how this fixes the problem.
What about all the logic removed from the method - is it not needed, if not why not?
(If it isn't needed saved method getPdbFilex should be deleted.)

Should not be in Functional group, as this cannot run without a network connection.

Should not be in Functional group, as this cannot run without a network connection.