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From: <rv...@us...> - 2009-06-18 09:38:55
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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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From: <yo...@us...> - 2010-02-02 20:54:54
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Revision: 481
http://treebase.svn.sourceforge.net/treebase/?rev=481&view=rev
Author: youjun
Date: 2010-02-02 20:54:48 +0000 (Tue, 02 Feb 2010)
Log Message:
-----------
fix sql, postgresql will not accept 1,0 for boolean type
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java 2010-01-25 20:27:40 UTC (rev 480)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java 2010-02-02 20:54:48 UTC (rev 481)
@@ -83,7 +83,7 @@
// DISCRETECHARSTATE_ID
ps.setDouble(1, e.getValue()); // Value
- ps.setShort(2, e.getGap()); // Gap
+ ps.setBoolean(2, e.getGap()); // Gap
ps.setLong(3, e.getMatrixColID()); // MATRIXCOLUMN_ID
// ps.setLong(4, 0); // ITEMDEFINITION_ID //Only by compound elements.
ps.setLong(4, e.getMatrixRowID()); // MATRIXROW_ID
@@ -125,8 +125,8 @@
*
* @return short mGap
*/
- public short getGap() {
- return mGap;
+ public boolean getGap() {
+ return (mGap!=0);
}
/**
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java 2010-01-25 20:27:40 UTC (rev 480)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java 2010-02-02 20:54:48 UTC (rev 481)
@@ -93,7 +93,7 @@
// Value: (continuous)
// ITEMDEFINITION_ID: (continuous)
- ps.setShort(1, e.getGap()); // Gap
+ ps.setBoolean(1, e.getGap()); // Gap
ps.setLong(2, e.getMatrixColID()); // MATRIXCOLUMN_ID
ps.setLong(3, e.getMatrixRowID()); // MATRIXROW_ID
@@ -138,8 +138,8 @@
*
* @return short mGap
*/
- public short getGap() {
- return mGap;
+ public boolean getGap() {
+ return (mGap!=0);
}
/**
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From: <vga...@us...> - 2010-02-11 16:35:36
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Revision: 491
http://treebase.svn.sourceforge.net/treebase/?rev=491&view=rev
Author: vgapeyev
Date: 2010-02-11 16:35:29 +0000 (Thu, 11 Feb 2010)
Log Message:
-----------
Modifying DB2-specific SQL to work under Pg
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
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 2010-02-11 06:51:56 UTC (rev 490)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2010-02-11 16:35:29 UTC (rev 491)
@@ -165,8 +165,10 @@
// insert new phylochar.
// Note: this is db2 specific code (faster), see EnvrionmentTest.testGetGeneratedKey()
// for generic jdbc code.
- String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?))";
-
+ //--String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?))";
+ //VG 2010-02-10 Replacing above DB2 sql with this PostreSQL:
+ String queryBuf = "INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?) returning phylochar_id";
+
PreparedStatement ps = pCon.prepareStatement(queryBuf);
for (MatrixColumnJDBC columnJDBC : columns) {
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 2010-02-11 06:51:56 UTC (rev 490)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2010-02-11 16:35:29 UTC (rev 491)
@@ -334,8 +334,10 @@
try {
// insert new discrete phylochar.
//Note: this is db2 specific code (faster), see EnvrionmentTest.testGetGeneratedKey() for generic jdbc code.
- String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) VALUES('D', default, 0, ?))";
-
+ //VG-- String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) VALUES('D', default, 0, ?))";
+ //VG 2010-02-10 Replacing above DB2 sql with this PostreSQL:
+ String queryBuf = "INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) VALUES('D', default, 0, ?) RETURNING phylochar_id";
+
PreparedStatement ps = pCon.prepareStatement(queryBuf);
// String stateStr = "INSERT INTO DISCRETECHARSTATE(DISCRETECHARSTATE_ID, VERSION,
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