[Treebase-guts] SF.net SVN: treebase:[58] trunk/treebase-core/src/main/java/org/cipres/ treebase/dao/jdbc

[<rv...@us...>]

Revision: 58
          http://treebase.svn.sourceforge.net/treebase/?rev=58&view=rev
Author:   rvos
Date:     2009-06-18 09:38:54 +0000 (Thu, 18 Jun 2009)

Log Message:
-----------
Added getters/setters for NeXML objects

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java	2009-06-18 09:34:25 UTC (rev 57)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java	2009-06-18 09:38:54 UTC (rev 58)
@@ -39,6 +39,7 @@
 import org.cipres.treebase.domain.matrix.ContinuousMatrix;
 import org.cipres.treebase.domain.matrix.ItemDefinition;
 import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
 
 /**
  * Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -83,6 +84,10 @@
 
 	private Map<String, Long> mItemDefNameToIDMap;
 
+	private org.nexml.model.ContinuousMatrix mNexmlCharacterData;
+
+	private NexmlMatrixConverter mNexmlMatrixConverter;
+
 	// Note: currently we support only one set of item definitions for the entire matrix.
 	// It is modeled in continuousMatrix.itemDefinitions.
 	// The matrixColumn.itemDefinitions are not supported at this time since Mesquite (and Nexus)
@@ -117,6 +122,15 @@
 
 	}
 
+	public ContinuousMatrixJDBC(ContinuousMatrix tbMatrix,
+			org.nexml.model.ContinuousMatrix xmlMatrix,
+			NexmlMatrixConverter nexmlMatrixConverter) {
+		this();
+		setCharacterMatrix(tbMatrix);
+		setNexmlCharacterData(xmlMatrix);
+		setNexmlMatrixConverter(nexmlMatrixConverter);
+	}
+
 	// /**
 	// * Return the ItemDefJDBCs field.
 	// *

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java	2009-06-18 09:34:25 UTC (rev 57)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java	2009-06-18 09:38:54 UTC (rev 58)
@@ -38,9 +38,11 @@
 import org.springframework.jdbc.UncategorizedSQLException;
 
 import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.matrix.ContinuousMatrix;
 import org.cipres.treebase.domain.matrix.DiscreteChar;
 import org.cipres.treebase.domain.matrix.DiscreteCharState;
 import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
 
 /**
  * Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -121,6 +123,15 @@
 			mRowSymbolBufs.add(new StringBuffer());
 		}
 	}
+	
+	public DiscreteMatrixJDBC(CharacterMatrix tbMatrix,
+			org.nexml.model.CategoricalMatrix xmlMatrix,
+			NexmlMatrixConverter nexmlMatrixConverter) {
+		this();
+		setCharacterMatrix(tbMatrix);
+		setNexmlCharacterData(xmlMatrix);
+		setNexmlMatrixConverter(nexmlMatrixConverter);
+	}	
 
 	/**
 	 * Return the RowSymbolBufs field.

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java	2009-06-18 09:34:25 UTC (rev 57)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java	2009-06-18 09:38:54 UTC (rev 58)
@@ -32,11 +32,13 @@
 import org.apache.log4j.Logger;
 import org.hibernate.Query;
 import org.hibernate.Session;
+import org.nexml.model.Matrix;
 import org.springframework.jdbc.UncategorizedSQLException;
 
 import org.cipres.treebase.domain.matrix.CharacterMatrix;
 import org.cipres.treebase.domain.matrix.ContinuousMatrix;
 import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
 
 /**
  * Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -86,6 +88,8 @@
 	private List<MatrixColumnJDBC> mMatrixColumnJDBCs;
 
 	private MesquiteMatrixConverter mMesqMatrixConverter;
+	private NexmlMatrixConverter mNexmlMatrixConverter;
+	private Matrix mNexmlCharacterData;
 
 	/**
 	 * Factory methods for creating a new MatrixJDBC instance based on the CharacterMatrix type.
@@ -287,6 +291,16 @@
 		mMesquiteCharacterData = pNewMesquiteCharacterData;
 	}
 
+	protected void setNexmlMatrixConverter(
+			NexmlMatrixConverter nexmlMatrixConverter) {
+		mNexmlMatrixConverter = nexmlMatrixConverter;				
+	}
+
+	protected void setNexmlCharacterData(
+			org.nexml.model.Matrix xmlMatrix) {
+		mNexmlCharacterData = xmlMatrix;		
+	}	
+	
 	/**
 	 * Return the discriminator value for the sub classes in MatrixElement class hierarchy.
 	 * 


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