Author: rodche
Date: 2012-06-12 07:57:22 -0700 (Tue, 12 Jun 2012)
New Revision: 29531
Removed:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTaskFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXTaskFactory.java
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
Log:
Removed unused code, edited comments.
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-06-12 01:28:07 UTC (rev 29530)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-06-12 14:57:22 UTC (rev 29531)
@@ -194,7 +194,7 @@
// default Quick Find Index
AttributeUtil.set(network, network, "quickfind.default_index",
CyNetwork.NAME, String.class);
- // (converted to L3, processed) RDF/XML data
+ // Serialize and Save the BioPAX L3 model as RDF+XML (OWL)
ByteArrayOutputStream baos = new ByteArrayOutputStream();
try {
convertToOWL(model, baos);
Deleted:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTaskFactory.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTaskFactory.java
2012-06-12 01:28:07 UTC (rev 29530)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTaskFactory.java
2012-06-12 14:57:22 UTC (rev 29531)
@@ -1,23 +0,0 @@
-package org.cytoscape.biopax.internal.action;
-
-import org.cytoscape.application.swing.CySwingApplication;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.task.AbstractNodeViewTaskFactory;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
-import org.cytoscape.work.TaskIterator;
-
-public class DisplayBioPaxXmlTaskFactory extends AbstractNodeViewTaskFactory {
-
- private CySwingApplication cySwingApplication;
-
- public DisplayBioPaxXmlTaskFactory(CySwingApplication
cySwingApplication) {
- this.cySwingApplication = cySwingApplication;
- }
-
- @Override
- public TaskIterator createTaskIterator(View<CyNode> nodeView,
CyNetworkView networkView) {
- return new TaskIterator(new DisplayBioPaxXmlTask(nodeView,
networkView, cySwingApplication));
- }
-
-}
Deleted:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXTaskFactory.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXTaskFactory.java
2012-06-12 01:28:07 UTC (rev 29530)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXTaskFactory.java
2012-06-12 14:57:22 UTC (rev 29531)
@@ -1,37 +0,0 @@
-package org.cytoscape.biopax.internal.action;
-
-import java.io.OutputStream;
-
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.write.CyNetworkViewWriterFactory;
-import org.cytoscape.io.write.CyWriter;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.view.model.CyNetworkView;
-
-public class ExportAsBioPAXTaskFactory implements CyNetworkViewWriterFactory {
-
- private final CyFileFilter filter;
- private OutputStream outputStream;
- private final String fileName;
-
- public ExportAsBioPAXTaskFactory(String fileName, CyFileFilter filter) {
- this.filter = filter;
- this.fileName = fileName;
- }
-
- @Override
- public CyWriter createWriter(OutputStream outputStream, CyNetwork
network) {
- return new ExportAsBioPAXTask(fileName, outputStream, network);
- }
-
- @Override
- public CyWriter createWriter(OutputStream outputStream, CyNetworkView
view) {
- return new ExportAsBioPAXTask(fileName, outputStream,
view.getModel());
- }
-
- @Override
- public CyFileFilter getFileFilter() {
- return filter;
- }
-
-}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
2012-06-12 01:28:07 UTC (rev 29530)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/AttributeUtil.java
2012-06-12 14:57:22 UTC (rev 29531)
@@ -1,7 +1,6 @@
package org.cytoscape.biopax.internal.util;
import java.util.List;
-import java.util.Map.Entry;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyRow;
@@ -12,37 +11,23 @@
public class AttributeUtil {
public static void set(CyNetwork network, CyIdentifiable entry, String
name, Object value, Class<?> type) {
- set(network, entry, null, name, value, type);
+ set(network, entry, CyNetwork.DEFAULT_ATTRS, name, value, type);
}
-
- public static void copyAttributes(CyNetwork network, CyIdentifiable
source, CyIdentifiable target) {
- CyRow sourceRow = network.getRow(source);
- for (Entry<String, Object> entry :
sourceRow.getAllValues().entrySet()) {
- String key = entry.getKey();
- Object value = entry.getValue();
- CyColumn column = sourceRow.getTable().getColumn(key);
- Class<?> type;
- if (value instanceof List) {
- type = column.getListElementType();
- } else {
- type = column.getType();
- }
- set(network, target, key, value, type);
- }
- }
-
public static void set(CyNetwork network, CyIdentifiable entry, String
tableName, String name, Object value, Class<?> type) {
- CyRow row = (tableName==null) ? network.getRow(entry) :
network.getRow(entry,tableName);
+ CyRow row = network.getRow(entry, tableName);
CyTable table = row.getTable();
CyColumn column = table.getColumn(name);
- if (column == null) {
- if (value instanceof List) {
- table.createListColumn(name, type, false);
- } else {
- table.createColumn(name, type, false);
+ if (value != null) {
+ if (column == null) {
+ if (value instanceof List) {
+ table.createListColumn(name, type,
false);
+ } else {
+ table.createColumn(name, type, false);
+ }
}
+ row.set(name, value);
}
- row.set(name, value);
}
+
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-06-12 01:28:07 UTC (rev 29530)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-06-12 14:57:22 UTC (rev 29531)
@@ -66,10 +66,6 @@
/**
* BioPax Utility Class - is a BioPAX Model Adapter
* that also defines additional constants.
- *
- * @author Ethan Cerami, Rex, Arman and Igor Rodchenkov
- *
- * @CyAPI.Final.Class
*/
public final class BioPaxUtil {
private static final Map<String,String> cellLocationMap;
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