jalview

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

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

JAL-3830 delete channel.props and channel.propsv when uninstalling

JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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    /utils/getdown/bin/jalview.ps1
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    /utils/getdown/bin/jalview.sh
JAL-3830 Allow paths to start with '~'. Make path check more succinct.

JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

JAL-3830 add the windows bash script to getdown files and install4j installers

JAL-3830 bash script that works in both cygwin and WSL (Windows Subsystem for Linux)

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    /utils/getdown/jalviewc-windows
JAL-3830 Delete wrapper scripts and getdown *v files when uninstalling

JAL-3830 powershell wrapper tested on linux, macos and windows including spaces in paths. This is the way.

JAL-3830 minor fix in powershell wrapper

JAL-3830 powershell follows symlinks as they do exist in NTFS, and of course in linux

JAL-3830 Powershell wrapper now works cross-platform. Who needs bash?!

JAL-3830 Make wrapper scripts executable

JAL-3830 powershell wrapper tested and fixed

JAL-3830 improved bash scripts. Added powershell script. Needs testing

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    /utils/getdown/jalviewc.ps1
JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

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    /utils/getdown/jalviewc
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    /utils/getdown/jalviewc-macos
JAL-3830 Improved for .app dir name with spaces, e.g. Jalview Local. Tested on mac to be working.

JAL-3830 install4j adds script to Jalview.app/Contents/MacOS/jalview but we need install4j9 to make it executable

JAL-3830 first draft of wrapper script to go in macOS Jalview.app/Contents/MacOS/jalview

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    /utils/install4j/macos_jalview
Merge branch 'task/JAL-3796_notarization' into develop

Merge branch 'develop' into task/JAL-3796_notarization

JAL-3796 minimal steps for notarization and the entitlements.txt file needed for the codesign tool

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    /utils/osx_signing/README
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    /utils/osx_signing/entitlements.txt
JAL-3618 Enable appBundleIsTraversable in JFileChooser on macOS

JAL-3594 Allow a channel to use a different preferences file than .jalview_properties, with initial read from .jalview_properties

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    /src/jalview/util/ChannelProperties.java
This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method