jalview

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JAL-3840 don’t update the modal residue count for gaps

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    /src/jalview/datamodel/ResidueCount.java
JAL-3840 don’t update the modal residue count for gaps

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    /src/jalview/datamodel/ResidueCount.java
fixes JAL-3840

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    /src/jalview/datamodel/ResidueCount.java
fixes JAL-3840

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    /src/jalview/datamodel/ResidueCount.java
JAL-3840 failing test - show that addGaps overflows

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    /src/jalview/datamodel/ResidueCount.java
JAL-3840 failing test - show that addGaps overflows

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    /src/jalview/datamodel/ResidueCount.java
Merge branch 'develop' into improvement/JAL-3830_macOS_bundle_wrapper

JAL-3929_spike minor changes

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    /src/jalview/ws/dbsources/TDBeacons.java
JAL-3829_spike minor changes

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    /src/jalview/ws/dbsources/TDBeacons.java
Revert "Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration"

This reverts commit 95f4ae66fbaecbbdc1c3ab3c6c9c611a3a9a3e46, reversing

changes made to bc7c2cf5500c5a4124a69ef8e7b1374d8997558f.

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    /src/jalview/ws/api/JPredServiceI.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
JAL-3248 Moved old README to doc/old_README and put pointers in new README for deskopt application building and JalviewJS building

JAL-3248 Archived old README. Added new README to point user to doc/building.md

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    /doc/old_ant_build_README
JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3833 Allow setHiDPI and setHiDPIScale to work more usefully in real life

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

JAL-3830 Improved jalview.bat to find either pwsh.exe or powershell.exe, and give better messages to the user

JAL-3832 Gui working, with 3DBeacons parameters

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    /resources/fts/tdbeacons_data_columns.txt
JAL-3832 Gui working, with 3DBeacons parameters

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    /resources/fts/tdbeacons_data_columns.txt
Merge branch 'arnaud/develop' into arnaud/JAL-3929_spike, to insert the previous changes

Merge branch 'arnaud/develop' into arnaud/JAL-3929_spike, to insert the previous changes

JAL-3929 forgot to add in the dummy 3d-beacons db proxy

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    /src/jalview/ws/dbsources/TDBeacons.java
JAL-3829 forgot to add in the dummy 3d-beacons db proxy

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    /src/jalview/ws/dbsources/TDBeacons.java
JAL-3832 dummy 3d-beacons database client and code to create the TDBeaconsFTSPanel via the sequence fetcher dropdown menu

JAL-3829 more testing wit tdbeacons data columns and FTSclient

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    /resources/fts/tdbeacons_data_columns.txt
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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 attempt to fix my changes to follow the Jira issue

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    /resources/fts/tdbeacons_data_columns.txt
JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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    /utils/getdown/bin/jalview.bat
JAL-3830 Follow all SymbolicLinks in Windows powershell wrapper