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Commit [r1740]  Maximize  Restore  History

1. Several method names related to sequence annotations were renamed as previously referred to as Properties and sometimes tags. Similar renames will appear in the next commit for other files. 2. There may be other things that I forgot about. They probably relate to renaming field and method names to improve readbility of code.

dcaffrey 2023-04-28

Browse code at this revision

Parent: [r1739]

Child: [r1741]

changed /trunk/pfaat/src/com/neogenesis/pfaat/Alignment.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/AlignmentPanel.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/analysis/ConservationScores/ConservationScores.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/FindSequenceAction.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/Sequence.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/residueAnnotation/ResidueSearchOptions.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentMultiSearchOptions.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentSearchDialog.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentSearchOptions.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentSearchPanel.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchOptionsBase.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchOptionsParser.java
changed /trunk/pfaat/src/forester/tree/Tree.java
changed /trunk/pfaat/src/forester/tree/TreePropertyList.java
changed /trunk/pfaat/src/forester/tree/TreeSearchOptions.java
/trunk/pfaat/src/com/neogenesis/pfaat/Alignment.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/AlignmentPanel.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/analysis/ConservationScores/ConservationScores.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/FindSequenceAction.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/Sequence.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/residueAnnotation/ResidueSearchOptions.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentMultiSearchOptions.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentSearchDialog.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentSearchOptions.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/sequence/sequenceAnnotation/AlignmentSearchPanel.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchOptionsBase.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/util/MultiSearchOptionsParser.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/tree/Tree.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/tree/TreePropertyList.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/tree/TreeSearchOptions.java Diff Switch to side-by-side view
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