Commit [r143] Maximize Restore History

Initial commit of CassetteOptimizer and associated classes

monkeymanstan 2013-08-23

added /trunk/Source/edu/utah/ames/bioinfo/Cartridge.java
added /trunk/Source/edu/utah/ames/bioinfo/CassetteOptimizer.java
added /trunk/Source/edu/utah/ames/bioinfo/CodonUtils.java
added /trunk/Source/edu/utah/ames/bioinfo/FileFind2.java
changed /trunk/Source/edu/utah/ames/bioinfo/Autoaligner.java
/trunk/Source/edu/utah/ames/bioinfo/Cartridge.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/CassetteOptimizer.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/CodonUtils.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/FileFind2.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Autoaligner.java Diff Switch to side-by-side view
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