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[Treebase-guts] SF.net SVN: treebase:[386] trunk/treebase-core/lib/mesquite
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From: <rv...@us...> - 2009-12-15 18:44:10
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Revision: 386
http://treebase.svn.sourceforge.net/treebase/?rev=386&view=rev
Author: rvos
Date: 2009-12-15 18:44:03 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/categ/
trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/
trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/AmbiguityToPolym.class
trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/
trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/ConsensusSequenceStrip.class
trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/consensus.gif
trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/
trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/ConsensusStateForChar.class
trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/
trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/CategNexusCommandTest.class
trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.class
trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/
trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.class
trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/
trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/ManageProteinChars.class
trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/
trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/PolymToAmbiguity.class
trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/
trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/ResolveStateAmbiguity.class
trunk/treebase-core/lib/mesquite/categ/StateFrequency/
trunk/treebase-core/lib/mesquite/categ/StateFrequency/StateFrequency.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateAnnotation.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesEditor.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesTable.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesWindow.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/transpose.gif
trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/
trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/Ledge.class
trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/StateNamesStrip.class
trunk/treebase-core/lib/mesquite/categ/explanation.txt
trunk/treebase-core/lib/mesquite/categ/lib/
trunk/treebase-core/lib/mesquite/categ/lib/CategColorTable.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataAlterer.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataEditorInit.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataMatcher.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataSearcher.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataUtility.class
trunk/treebase-core/lib/mesquite/categ/lib/CategInternodeEvent.class
trunk/treebase-core/lib/mesquite/categ/lib/CategMatrixManager.class
trunk/treebase-core/lib/mesquite/categ/lib/CategStateForCharacter.class
trunk/treebase-core/lib/mesquite/categ/lib/CategTModel.class
trunk/treebase-core/lib/mesquite/categ/lib/CategTModelEditWindow.class
trunk/treebase-core/lib/mesquite/categ/lib/CategTModelTable.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalDistribution.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalState.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalStates.class
trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAColorTable.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataAlterer.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataAltererCon.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataSearcher.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataUtility.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAState.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalDistribution.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalStates.class
trunk/treebase-core/lib/mesquite/categ/lib/MDNAAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/MDNAEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/MDNAHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/MProteinAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/MProteinEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/MProteinHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/MesquiteSequence.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecDataEditorInit.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecularData.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecularDataAlterer.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecularState.class
trunk/treebase-core/lib/mesquite/categ/lib/OffersCategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/OffersDNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/OffersProteinData.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinCharacterHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinColorTable.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinData.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinState.class
trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/RNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/RNAState.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyCategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyDNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyMolecularData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresExactlyCategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresProteinData.class
Added: trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/AmbiguityToPolym.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/AmbiguityToPolym.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/ConsensusSequenceStrip.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/ConsensusSequenceStrip.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/consensus.gif
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/consensus.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/ConsensusStateForChar.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/ConsensusStateForChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/CategNexusCommandTest.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/CategNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/ManageProteinChars.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/ManageProteinChars.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/PolymToAmbiguity.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/PolymToAmbiguity.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/ResolveStateAmbiguity.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/ResolveStateAmbiguity.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateFrequency/StateFrequency.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateFrequency/StateFrequency.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateAnnotation.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateAnnotation.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesEditor.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesEditor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesTable.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesWindow.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesWindow.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/transpose.gif
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/transpose.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/Ledge.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/Ledge.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/StateNamesStrip.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/StateNamesStrip.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/categ/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/categ/explanation.txt 2009-12-15 18:44:03 UTC (rev 386)
@@ -0,0 +1,2 @@
+Categorical character package
+One of the core Mesquite packages. A package of fundamental modules and libraries for categorical character data. These define key elements of categorical data and manage categorical data matrices.
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategColorTable.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategColorTable.class
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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Added: trunk/treebase-core/lib/mesquite/categ/lib/CategMatrixManager.class
===================================================================
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Added: trunk/treebase-core/lib/mesquite/categ/lib/CategStateForCharacter.class
===================================================================
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Added: svn:mime-type
+ application/octet-stream
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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+ application/octet-stream
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===================================================================
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+ application/octet-stream
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MProteinHistory.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MesquiteSequence.class
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MesquiteSequence.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecDataEditorInit.class
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecDataEditorInit.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecularData.class
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecularData.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecularDataAlterer.class
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecularDataAlterer.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecularState.class
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecularState.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/OffersCategoricalData.class
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/OffersCategoricalData.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/OffersDNAData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/OffersDNAData.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/OffersProteinData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/OffersProteinData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinAdjustable.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinCharacterHistory.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinCharacterHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinColorTable.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinColorTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinEmbedded.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinState.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterAdjustable.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterHistory.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNAData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNAData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNAState.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNAState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyCategoricalData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyCategoricalData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyDNAData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyDNAData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyMolecularData.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyMolecularData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresExactlyCategoricalData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresExactlyCategoricalData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresProteinData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresProteinData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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