Protein Family Alignment Annotation Tool svncode

changed	/trunk/pfaat/src/com/neogenesis/pfaat/pdb/PdbFrame.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/AlignmentSequenceAnnotList.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/FileUtil.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/FussyStringTokenizer.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/GetNameValueDialog.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/IterationListener.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchDialog.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchOptionsBase.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchOptionsParser.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchPanel.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/SearchOptionsBase.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/SelectNamesDialog.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/SequenceAnnotListBase.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/SymmetricEigenvalueDecomposition.java
removed	/trunk/pfaat/src/com/neogenesis/pfaat/util/Utils.java
changed	/trunk/pfaat/src/org/pfaat/commandline/msa/RenameSequences.java
changed	/trunk/pfaat/src/org/pfaat/commandline/tree/ParseTreebest.java
changed	/trunk/pfaat/src/org/pfaat/core/msa/Alignment.java
changed	/trunk/pfaat/src/org/pfaat/core/msa/Sequence.java
changed	/trunk/pfaat/src/org/pfaat/core/msa/io/AlignmentLoader.java
changed	/trunk/pfaat/src/org/pfaat/core/msa/io/PfaatLoader.java
changed	/trunk/pfaat/src/org/pfaat/core/msa/io/PfamLoader.java
changed	/trunk/pfaat/src/org/pfaat/core/tree/Node.java
changed	/trunk/pfaat/src/org/pfaat/core/tree/TreeSequenceAnnotationList.java
added	/trunk/pfaat/src/org/pfaat/gui/common/AlignmentSequenceAnnotList.java