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[Treebase-guts] SF.net SVN: treebase:[383] trunk/treebase-core/lib/mesquite
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From: <rv...@us...> - 2009-12-15 18:39:43
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Revision: 383
http://treebase.svn.sourceforge.net/treebase/?rev=383&view=rev
Author: rvos
Date: 2009-12-15 18:39:37 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/assoc/
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssocExtra.class
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssociates.class
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedLegend.class
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/WideTreeDrawing.class
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepCTreeWindow.class
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepContTreeWindow.class
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepTreeExtra.class
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationBlockTest.class
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationsBlock.class
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/ManageAssociations.class
trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/
trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/DistributionBlockTest.class
trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/ManageDistributionBlock.class
trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/
trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartCompatibilityTest.class
trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartitionFromAssociation.class
trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/
trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/StoredAssociations.class
trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt
trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/
trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/AssocEditor.class
trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/TaxonListAssoc.class
trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/
trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/aAssocIntro.class
trunk/treebase-core/lib/mesquite/assoc/explanation.txt
trunk/treebase-core/lib/mesquite/assoc/lib/
trunk/treebase-core/lib/mesquite/assoc/lib/AssociationHistory.class
trunk/treebase-core/lib/mesquite/assoc/lib/AssociationSource.class
trunk/treebase-core/lib/mesquite/assoc/lib/AssociationsManager.class
trunk/treebase-core/lib/mesquite/assoc/lib/ReconstructAssociation.class
trunk/treebase-core/lib/mesquite/assoc/lib/SimpleTaxaList.class
trunk/treebase-core/lib/mesquite/assoc/lib/TaxaAssociation.class
trunk/treebase-core/lib/mesquite/assoc/lib/TaxonWithTaxa.class
trunk/treebase-core/lib/mesquite/assoc/macros/
trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssocExtra.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssocExtra.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssociates.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssociates.class
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedLegend.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedLegend.class
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/WideTreeDrawing.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/WideTreeDrawing.class
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepCTreeWindow.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepCTreeWindow.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepContTreeWindow.class
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationBlockTest.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationBlockTest.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationsBlock.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationsBlock.class
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Added: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/ManageAssociations.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/ManageAssociations.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/DistributionBlockTest.class
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Added: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/ManageDistributionBlock.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/ManageDistributionBlock.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartCompatibilityTest.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartCompatibilityTest.class
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Added: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartitionFromAssociation.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartitionFromAssociation.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/StoredAssociations.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/StoredAssociations.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt 2009-12-15 18:39:37 UTC (rev 383)
@@ -0,0 +1,96 @@
+Format Specification for TaxaAssociation block of NEXUS file
+W. Maddison January 2003
+
+BEGIN TaxaAssociation;
+[TITLE <name of this association, a token>; [optional but recommended]]
+TAXA <name of first taxa block, a token> , <name of second taxa block, a token>;
+ASSOCIATES
+ <nt1> / <nt2> [<nt2> ...] ,
+ <nt1> / <nt2> [<nt2> ...] ,
+ .
+ .
+ .
+ <nt1> / <nt2> [<nt2> ...]
+
+;
+
+[ASSOCIATES ... ; may be repeated]
+
+END;
+
+
+where nt1 means name of a taxon in first block, nt2 means name of a taxon in first block (these would not, of course, all be the same). The two taxa blocks and their contained taxa must already be defined.
+
+Items may be repeated and there may be more than one ASSOCIATES command. Thus, the following 4 blocks are equivalent, indicating genes a1 and a2 are within species A, b1 and b2 within species B, and c1 and c2 within species C.
+
+=============================================
+BEGIN TaxaAssociation;
+TITLE species_Containing_Genes;
+TAXA species, genes;
+ASSOCIATES
+ A / a1 a2,
+ B / b1 b2,
+ C / c1 c2
+;
+END;
+
+=========
+BEGIN TaxaAssociation;
+TITLE species_Containing_Genes;
+TAXA species, genes;
+ASSOCIATES
+ A / a1,
+ A / a2
+;
+ASSOCIATES
+ B / b1 b2,
+ C / c1 c2
+;
+END;
+
+=========
+BEGIN TaxaAssociation;
+TITLE genes_In_Species;
+TAXA genes , species;
+ASSOCIATES
+ a1 / A ,
+ a2 / A ,
+ b1 / B ,
+ b2 / B ,
+ c1 / C ,
+ c2 / C
+;
+END;
+=========
+BEGIN TaxaAssociation;
+TITLE genes_In_Species;
+TAXA genes , species;
+ASSOCIATES
+ a1 a2 / A ,
+ b1 b2 / B ,
+ c1 c2 / C
+;
+END;
+=============================================
+
+
+Currently Mesquite reads and writes TaxaAssociation blocks in which a contained taxon is in more than one containing taxon (e.g. same haplotype in two populations) but its calculations cannot yet handle this situation.
+
+
+Questions:
+Do we allow a command which indicates the contained/containing polarity? e.g.
+ CONTAINED genes;
+One could imagine commands more for labelling, e.g.:
+ RELATIONSHIP host, parasite; [where order is that of blocks in TAXA command]
+
+Do we allow more than two taxa blocks to be associated simultaneously? e.g.
+
+BEGIN TaxaAssociation;
+TAXA genes , species, areas;
+ASSOCIATES
+ a1 a2 / A / Africa,
+ b1 b2 / B / Africa,
+ c1 c2 / C / South_America
+;
+END;
+
Added: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/AssocEditor.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/AssocEditor.class
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/TaxonListAssoc.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/TaxonListAssoc.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/aAssocIntro.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/aAssocIntro.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/assoc/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/assoc/explanation.txt 2009-12-15 18:39:37 UTC (rev 383)
@@ -0,0 +1,2 @@
+Taxa Associations Package
+Manages and does some basic calculations and graphics for associations between blocks of taxa (e.g., genes sequenced as one set of taxa; their containing species or populations as a second set of taxa). Required for many of the Coalescence calculations.
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationHistory.class
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationHistory.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationSource.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationSource.class
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Added: svn:mime-type
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Added: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationsManager.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationsManager.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/ReconstructAssociation.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/ReconstructAssociation.class
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/SimpleTaxaList.class
===================================================================
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Added: trunk/treebase-core/lib/mesquite/assoc/lib/TaxaAssociation.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/TaxaAssociation.class
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Added: svn:mime-type
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Added: trunk/treebase-core/lib/mesquite/assoc/lib/TaxonWithTaxa.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/TaxonWithTaxa.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro
===================================================================
--- trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro (rev 0)
+++ trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro 2009-12-15 18:39:37 UTC (rev 383)
@@ -0,0 +1,38 @@
+telling mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator 'Set up Associated Taxa block' 'Creates a block of taxa, creates an association between it and the previously existing block, and presents a way to build the associated block of taxa. Assumes the current file has a single block of taxa' 0;
+queryYesNo 'This macro assumes there is a single block of taxa available. It creates a second block and associates it with the first' 'Stop' 'Continue';
+Integer.answer *It;
+if *Integer.answer;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ String.existing *It;
+ newTaxa 1 'Associates';
+ tell It;
+ setTaxonName 0 'associate 1';
+ endTell;
+ endTell;
+
+ getEmployee #mesquite.assoc.ManageAssociations.ManageAssociations;
+ tell It;
+ makeAssociation 0 1;
+ endTell;
+
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ showTaxa 0 #mesquite.lists.TaxonList.TaxonList;
+ tell It;
+ getWindow;
+ tell It;
+ newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
+ newAssistant #mesquite.assoc.TaxonListAssoc.TaxonListAssoc;
+ tell It;
+ getEmployee #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+ alert 'In the List of Taxa window is now a column labelled Associates. Select rows and then touch on this column heading to get a menu in which you can indicate what taxa in the other block are associated with the selected taxa. You can also create new taxa in that other block using the drop down menu. In this way you can complete the specification of what are the associated taxa';
+endIf;
\ No newline at end of file
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