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Commit [r1915]  Maximize  Restore  History

Now use org.pfaat.gui.msa.analysis.action.SimilarityMatrixEncoder instead of src/org/pfaat/gui/msa/analysis/seqspace/action/SeqSpaceEncoder.java

dcaffrey 2023-07-25

changed /trunk/pfaat/src/com/neogenesis/pfaat/comparison/Comparison.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/EmpiricAl.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/GetMutualInformationForShortReads.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/GetRepresentedResidues.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/GetResidueCounts.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/GetResidueCountsQuickly.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/ModifiedShannon.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/PamForSelect.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/SubfamilySummary.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/VneFamily.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/VneScore.java
changed /trunk/pfaat/src/org/pfaat/commandline/msa/VneSpecificityScore.java
changed /trunk/pfaat/src/org/pfaat/commandline/structure/GetCavity.java
changed /trunk/pfaat/src/org/pfaat/commandline/structure/GetChainLengths.java
changed /trunk/pfaat/src/org/pfaat/commandline/structure/GetChains.java
changed /trunk/pfaat/src/org/pfaat/commandline/structure/GetPatches.java
changed /trunk/pfaat/src/org/pfaat/core/msa/ConsensusSequence.java
changed /trunk/pfaat/src/org/pfaat/core/msa/Sequence.java
changed /trunk/pfaat/src/org/pfaat/gui/msa/analysis/action/ConservationScores.java
changed /trunk/pfaat/src/org/pfaat/gui/msa/analysis/action/NJTreeCalculator.java
changed /trunk/pfaat/src/org/pfaat/gui/msa/colorscheme/Blosum62ColorScheme.java
changed /trunk/pfaat/src/org/pfaat/gui/unused/PairwiseAlignmentFrame.java
/trunk/pfaat/src/com/neogenesis/pfaat/comparison/Comparison.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/EmpiricAl.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/GetMutualInformationForShortReads.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/GetRepresentedResidues.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/GetResidueCounts.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/GetResidueCountsQuickly.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/ModifiedShannon.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/PamForSelect.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/SubfamilySummary.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/VneFamily.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/VneScore.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/msa/VneSpecificityScore.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/structure/GetCavity.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/structure/GetChainLengths.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/structure/GetChains.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/commandline/structure/GetPatches.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/core/msa/ConsensusSequence.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/core/msa/Sequence.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/gui/msa/analysis/action/ConservationScores.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/gui/msa/analysis/action/NJTreeCalculator.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/gui/msa/colorscheme/Blosum62ColorScheme.java Diff Switch to side-by-side view
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/trunk/pfaat/src/org/pfaat/gui/unused/PairwiseAlignmentFrame.java Diff Switch to side-by-side view
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