Protein Family Alignment Annotation Tool svncode

Brought to you by: carlsonjf, dcaffrey, eshuang, simonxi

Commit [r1936] Maximize Restore History

1) Deleted most classes in src/forester/datastructures and src/forester/tools/ as they were used for speciation-duplication inference and are not needed. 2) Move PostDuplicationBranchLengths.java and printAllSpecies.java to src/org/pfaat/commandline/tree/ .

Authored by: dcaffrey 2023-07-26

Browse code at this revision

Parent: [r1935]

Child: [r1937]

removed	/trunk/pfaat/src/forester/datastructures/BasketDataStructure.java
removed	/trunk/pfaat/src/forester/tools/DistanceCalculator.java
removed	/trunk/pfaat/src/forester/tools/DoRIO.java
removed	/trunk/pfaat/src/forester/tools/Int.java
removed	/trunk/pfaat/src/forester/tools/NameAndValues.java
removed	/trunk/pfaat/src/forester/tools/OE.java
removed	/trunk/pfaat/src/forester/tools/PostDuplicationBranchLengths.java
removed	/trunk/pfaat/src/forester/tools/RIO.java
removed	/trunk/pfaat/src/forester/tools/SDI.java
removed	/trunk/pfaat/src/forester/tools/SDIdirectory.java
removed	/trunk/pfaat/src/forester/tools/SDIse.java
removed	/trunk/pfaat/src/forester/tools/SDIunrooted.java
removed	/trunk/pfaat/src/forester/tools/printAllSpecies.java
removed	/trunk/pfaat/src/forester/tools/printSameOrder.java
removed	/trunk/pfaat/src/forester/tools/testNHX.java
removed	/trunk/pfaat/src/forester/tools/transfersBranchLenghts.java
added	/trunk/pfaat/src/org/pfaat/commandline/tree/PostDuplicationBranchLengths.java
added	/trunk/pfaat/src/org/pfaat/commandline/tree/printAllSpecies.java
changed	/trunk/pfaat/src/org/pfaat/gui/tree/ATVjframe.java