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Updated to read and save .pfaat alignment file

pfaat_matt 2006-12-25

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Parent: [r804]

Child: [r806]

changed /trunk/pfaat/src/com/neogenesis/pfaat/io/AlignmentLoader.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/io/AllLoader.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/io/PfaatLoader.java
/trunk/pfaat/src/com/neogenesis/pfaat/io/AlignmentLoader.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/io/AllLoader.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/io/PfaatLoader.java Diff Switch to side-by-side view
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