Author: rozagh
Date: 2012-06-13 16:12:27 -0700 (Wed, 13 Jun 2012)
New Revision: 29558
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
Log:
fixes #1109 the exception was thrown because of the changes made for bug #965 .
The data for virtual column does not needed to be cloned. Also, we need to copy
over the virtual columns as well in the cloned network.
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2012-06-13 23:09:13 UTC (rev 29557)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2012-06-13 23:12:27 UTC (rev 29558)
@@ -152,12 +152,13 @@
private void addColumns(CyTable parentTable, CyTable subTable) {
for (CyColumn col: parentTable.getColumns()){
- VirtualColumnInfo colInfo = col.getVirtualColumnInfo();
- if (colInfo.isVirtual())
- addVirtualColumn(col, subTable);
- else
- if (subTable.getColumn(col.getName()) == null)
+ if (subTable.getColumn(col.getName()) == null){
+ VirtualColumnInfo colInfo =
col.getVirtualColumnInfo();
+ if (colInfo.isVirtual())
+ addVirtualColumn(col, subTable);
+ else
copyColumn(col, subTable);
+ }
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2012-06-13 23:09:13 UTC (rev 29557)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2012-06-13 23:12:27 UTC (rev 29558)
@@ -45,6 +45,7 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.VirtualColumnInfo;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -112,10 +113,10 @@
final CyTable nodeTable = newNet.getDefaultNodeTable();
final CyTable edgeTable = newNet.getDefaultEdgeTable();
final CyTable networkTable = newNet.getDefaultNetworkTable();
- // copy default columns
- cloneColumns(origNet.getDefaultNodeTable(), nodeTable);
- cloneColumns(origNet.getDefaultEdgeTable(), edgeTable);
- cloneColumns(origNet.getDefaultNetworkTable(),
networkTable);
+ // copy default columns
+ addColumns(origNet.getDefaultNodeTable(), nodeTable);
+ addColumns(origNet.getDefaultEdgeTable(), edgeTable);
+ addColumns(origNet.getDefaultNetworkTable(), networkTable);
cloneNodes(origNet, newNet);
cloneEdges(origNet, newNet);
@@ -124,7 +125,7 @@
naming.getSuggestedNetworkTitle(origNet.getRow(origNet).get(CyNetwork.NAME,
String.class)));
return newNet;
}
-
+
private void cloneNodes(CyNetwork origNet, CyNetwork newNet) {
orig2NewNodeMap = new WeakHashMap<CyNode, CyNode>();
new2OrigNodeMap = new WeakHashMap<CyNode, CyNode>();
@@ -146,28 +147,43 @@
}
}
- private void cloneColumns(final CyTable from, final CyTable to) {
- for (final CyColumn fromColumn : from.getColumns()) {
- final CyColumn toColumn =
to.getColumn(fromColumn.getName());
-
- if (toColumn == null) {
- if
(List.class.isAssignableFrom(fromColumn.getType()))
-
to.createListColumn(fromColumn.getName(), fromColumn.getListElementType(),
false);
+ private void addColumns(CyTable parentTable, CyTable subTable) {
+ for (CyColumn col: parentTable.getColumns()){
+ if (subTable.getColumn(col.getName()) == null){
+ VirtualColumnInfo colInfo =
col.getVirtualColumnInfo();
+ if (colInfo.isVirtual())
+ addVirtualColumn(col, subTable);
else
- to.createColumn(fromColumn.getName(),
fromColumn.getType(), false);
- } else if (toColumn.getType() == fromColumn.getType()) {
- continue;
- } else {
- throw new IllegalArgumentException("column of
same name: " + fromColumn.getName()
- + "but types don't match
(orig): " + fromColumn.getType().getName() + " (new): "
- + toColumn.getType().getName());
+ copyColumn(col, subTable);
}
}
}
+ private void addVirtualColumn (CyColumn col, CyTable subTable){
+ VirtualColumnInfo colInfo = col.getVirtualColumnInfo();
+ CyColumn checkCol= subTable.getColumn(col.getName());
+ if(checkCol == null)
+ subTable.addVirtualColumn(col.getName(),
colInfo.getSourceColumn(), colInfo.getSourceTable(),
colInfo.getTargetJoinKey(), true);
+
+ else
+ if(!checkCol.getVirtualColumnInfo().isVirtual() ||
+
!checkCol.getVirtualColumnInfo().getSourceTable().equals(colInfo.getSourceTable())
||
+
!checkCol.getVirtualColumnInfo().getSourceColumn().equals(colInfo.getSourceColumn()))
+ subTable.addVirtualColumn(col.getName(),
colInfo.getSourceColumn(), colInfo.getSourceTable(),
colInfo.getTargetJoinKey(), true);
+ }
+
+ private void copyColumn(CyColumn col, CyTable subTable) {
+ if (List.class.isAssignableFrom(col.getType()))
+ subTable.createListColumn(col.getName(),
col.getListElementType(), false);
+ else
+ subTable.createColumn(col.getName(), col.getType(),
false);
+ }
+
private void cloneRow(final CyRow from, final CyRow to) {
- for (final CyColumn column : from.getTable().getColumns())
- to.set(column.getName(), from.getRaw(column.getName()));
+ for (final CyColumn column : from.getTable().getColumns()){
+ if (!column.getVirtualColumnInfo().isVirtual())
+ to.set(column.getName(),
from.getRaw(column.getName()));
+ }
}
}
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