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| Deprecated Methods | |
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| org.virion.jam.layouts.CompassLayout.addLayoutComponent(String, Component)
replaced by addLayoutComponent(Component, Object). |
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| org.virion.jam.panels.OptionsPanel.addSeperator()
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| jebl.evolution.trees.RootedTree.conceptuallyUnrooted()
This should be removed. If this is a rooted tree then it is rooted. This can really only confuse things. Trees are unrooted, RootedTrees are rooted. This is not an implementation limitation. It may be that a RootedTree has an arbitrary root but it is still rooted. With a rooted tree, it is convenient to store branch information at the node (i.e., for the branch above the node) because there is no "branch" object. Andrew. |
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| Deprecated Constructors | |
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| jebl.evolution.io.FastaImporter(Reader, SequenceType)
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