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JAL-4090 bump version and set up release notes for 2.11.3

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patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
JAL-3253

sets setting for "unlikely argument type for collection" to warning; I

have set my workspace to error, but clearly it had not been like that,

because it found three errors. But now setting it to warning so that it

is not bothering me.

JAL-3225 This one file needed for project if git clean -dfx run

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JAL-3225 This one file needed for project if git clean -dfx run

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JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    ./org.eclipse.jdt.core.jalview.prefs
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JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    ./org.eclipse.jdt.core.jalview.prefs
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Java 11/Gradle 2.5 upgrade

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JAL-3559 temporary branch adding JS files complete

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    ./org.eclipse.wst.jsdt.ui.superType.container
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    ./org.eclipse.wst.jsdt.ui.superType.name
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Java 11 integration;

-- compiler complaining about javax.xml module

Failed to resolve resource /.build_properties:

@swingjs/j2s/jalview/bin/Cache.js:164:24

transpiler was 3.2.9-v1 now 3.2.4.07 for net.miginfocom.swing.MigLayout

TypeError: C$.UNIT_MAP.put$TK$TV is not a function

-- some runtime errors involving resources

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Revert "JAL-3210 default eclipse .project .classpath and .settings/org.eclipse.jdt.core.prefs so Eclipse as IDE can import without gradle"

This reverts commit aaa5f22a4544c3e72b5d29ef2f319e55af8e14f7.

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JAL-3210 default eclipse .project .classpath and .settings/org.eclipse.jdt.core.prefs so Eclipse as IDE can import without gradle

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JAL-3210 Automatic buildship/eclipse update to site when making changes to code

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    ./org.eclipse.jdt.core.jalview.prefs
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JAL-3210 Added jdt prefs from applet branch. Made IDE tasks more visible

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    ./org.eclipse.jdt.core.jalview.prefs
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JAL-3210 removed eclipse project, classpath and core settings files from branch. Now generate these (once only) with 'gradle eclipse'.

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JAL-3210 correcting gitignore for eclipse settings

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    ./org.eclipse.buildship.core.prefs
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    ./org.eclipse.jdt.core.jalview.prefs
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JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-3210 testing

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JAL-3210 test commit

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JAL-3210 updating. no test

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JAL-3210 ben testing

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    ./org.eclipse.jdt.core.prefs
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JAL-3210 ben testing

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JAL-3210 ben testing

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    ./org.eclipse.jdt.core.prefs
JAL-3210 ben testing

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JAL-3210 ben testing

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    ./org.eclipse.jdt.core.prefs
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JAL-3210 Merge branch 'develop' into trialMerge

Conflicts:

.classpath

.project

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

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

build.xml

resources/lang/Messages_es.properties

src/MCview/AppletPDBCanvas.java

src/MCview/Atom.java

src/MCview/PDBCanvas.java

src/jalview/analysis/AAFrequency.java

src/jalview/appletgui/EmbmenuFrame.java

src/jalview/appletgui/OverviewPanel.java

src/jalview/appletgui/SeqPanel.java

src/jalview/bin/Cache.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/DBRefEntry.java

src/jalview/datamodel/Sequence.java

src/jalview/ext/ensembl/EnsemblMap.java

src/jalview/ext/paradise/Annotate3D.java

src/jalview/fts/service/pdb/PDBFTSRestClient.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/FeatureTypeSettings.java

src/jalview/gui/WebserviceInfo.java

src/jalview/io/BackupFiles.java

src/jalview/io/FileLoader.java

src/jalview/jbgui/GDesktop.java

src/jalview/jbgui/GPreferences.java

src/jalview/project/Jalview2XML.java

src/jalview/util/ImageMaker.java

src/jalview/util/Platform.java

src/jalview/ws/SequenceFetcher.java

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    ./org.eclipse.jdt.core.prefs
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