pfaat gitcode changes

new version for TreeLoader.java and associated subclasses

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

new version for TreeLoader.java and associated subclasses
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Created TreeLoader.java and its subclasses NhxLoader.java, NhLoader.java etc to provide a scaleable and reusable framework for file extensions. Importantly, the file extensions determine how a file...

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

Created TreeLoader.java and its subclasses NhxLoader.java, NhLoader.java etc to provide a scaleable and reusable framework for file extensions. Importantly, the file extensions determine how a file is read and saved in a consistent manner. The code is now used by the gui and all relevant command line tools. All references to the code in the gui were tested and seem to work as expected. The mrbayes format was not tested but all other formats were tested. About 5 of the commandline tools that rely on the new code were tested /run sucessfully and therefore unlikely to cause issues for the other commandline tools. The creation of these classes means that gui/msa/analysis/action/NHTreeLoader.java is deleted and several methods from pfaat/core/tree/TreeHelper.java are commented out. Likewise, the inner classes NHXFilter, ConsensusFilter, NexusFilter,and NHFilter are deleted from TreeFrame and all references to instances of these objects are commented out / deleted.
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reformat a tree based on the file extensions

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

reformat a tree based on the file extensions
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Add javadppc and comments

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

Add javadppc and comments
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TreeFrame now calls TreeFrame.exit() when it is a stand alone application

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

TreeFrame now calls TreeFrame.exit() when it is a stand alone application
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TreeFrame now calls TreeFrame.exit() when it is a stand alone application

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

TreeFrame now calls TreeFrame.exit() when it is a stand alone application
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TreeFrame now calls TreeFrame.exit() when it is a stand alone application

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

TreeFrame now calls TreeFrame.exit() when it is a stand alone application
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Treeviewer.java now prepends the current working directory to a treefile when the user doesn't include ./ in the file name. This fixes isse where Treeviewer.java could open a file name file.nh from...

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

Treeviewer.java now prepends the current working directory to a treefile when the user doesn't include ./ in the file name. This fixes isse where Treeviewer.java could open a file name file.nh fromthe cwd
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Add comment to document the fact that ToolTipManager manages all tooltips and changes made to the sharedInstance will be applied to every tooltip in your application. This is a problem as ttm.setDi...

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

Add comment to document the fact that ToolTipManager manages all tooltips and changes made to the sharedInstance will be applied to every tooltip in your application. This is a problem as ttm.setDismissDelay(30000) in AlignmentPanel.java means the Dismiss Delay is too short for SequenceAnnotation1Panel.java etc
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Added the --verbose option so that we only report sequences in the cDNA file that are missing in the protein MSA when --verbose is specified

Daniel Caffrey — Mon, 22 Dec 2025 18:18:50 -0000

Added the --verbose option so that we only report sequences in the cDNA file that are missing in the protein MSA when --verbose is specified
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