Author: kono
Date: 2010-02-18 12:54:01 -0800 (Thu, 18 Feb 2010)
New Revision: 19366
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
Log:
Fixed minor bugs and added new Tunable to send list of selected nodes only.
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java
2010-02-18 19:07:25 UTC (rev 19365)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java
2010-02-18 20:54:01 UTC (rev 19366)
@@ -112,7 +112,7 @@
// props.add(new Tunable("max_interactions",
"Maximum number of records", Tunable.INTEGER,
// new Integer(1000)));
- //props.add(new Tunable("search_depth", "Search depth",
Tunable.INTEGER, new Integer(0)));
+ props.add(new Tunable("selected_only", "Map selected nodes
only", Tunable.BOOLEAN, new Boolean(false)));
props.add(new Tunable("import_all", "Import all available
entries", Tunable.BOOLEAN,
new Boolean(false)));
@@ -181,7 +181,7 @@
private List<String> mapping(BufferedReader reader, String key, String
keyAttrName) throws IOException, CyWebServiceException {
String line = reader.readLine();
- //System.out.println("Table Header: " + line);
+ System.out.println("Table Header: " + line);
final String[] columnNames = line.split("\\t");
if (columnNames[0].contains("Query ERROR"))
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
2010-02-18 19:07:25 UTC (rev 19365)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
2010-02-18 20:54:01 UTC (rev 19366)
@@ -204,12 +204,12 @@
String dbID;
for (int i = 0; i < locSize; i++) {
+
attrList = locations.item(i).getAttributes();
attrLen = attrList.getLength();
// First, get the key value
dbID = attrList.getNamedItem("name").getNodeValue();
-
Map<String, String> entry = new HashMap<String,
String>();
for (int j = 0; j < attrLen; j++) {
@@ -239,10 +239,8 @@
try {
getRegistry();
} catch (ParserConfigurationException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
} catch (SAXException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
}
@@ -401,7 +399,7 @@
*/
public BufferedReader sendQuery(String xmlQuery) throws IOException {
- System.out.println("=======Query = " + xmlQuery);
+ System.out.println("Generated Query:\n\n" + xmlQuery);
URL url = new URL(baseURL);
URLConnection uc = URLUtil.getURLConnection(url);
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
2010-02-18 19:07:25 UTC (rev 19365)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
2010-02-18 20:54:01 UTC (rev 19366)
@@ -61,6 +61,7 @@
import cytoscape.data.webservice.CyWebServiceEvent;
import cytoscape.data.webservice.WebServiceClientManager;
import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.layout.Tunable;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
@@ -342,9 +343,6 @@
// This is not the best way, but cannot provide universal
solution.
if (dbName.contains("REACTOME")) {
attrs[0] = new
Attribute(stub.toAttributeName("REACTOME", filterName));
- } else if (dbName.contains("UNIPROT")) {
- //System.out.println("UNIPROT found");
- attrs[0] = new
Attribute(stub.toAttributeName("UNIPROT", filterName));
} else if (dbName.contains("VARIATION")) {
// String newName = filterName.replace("_id",
"_stable_id");
// newName = newName.replace("_ensembl", "");
@@ -386,11 +384,24 @@
// Execute Task in New Thread; pop open JTask Dialog Box.
TaskManager.executeTask(task, jTaskConfig);
- firePropertyChange(CLOSE_EVENT, null, null);
+ //firePropertyChange(CLOSE_EVENT, null, null);
}
private static String getIDFilterString(String keyAttrName) {
- final List<Node> nodes = Cytoscape.getRootGraph().nodesList();
+
+ final Tunable tunable =
WebServiceClientManager.getClient("biomart").getProps().get("selected_only");
+ tunable.updateValue();
+ final Object value = tunable.getValue();
+
+ final List<Node> nodes;
+ if (value != null && Boolean.parseBoolean(value.toString())) {
+ // Selected nodes only
+ nodes = new
ArrayList<Node>(Cytoscape.getCurrentNetwork().getSelectedNodes());
+ } else {
+ // Send all nodes in current network
+ nodes = Cytoscape.getCurrentNetwork().nodesList();
+ }
+
final StringBuilder builder = new StringBuilder();
// If attribute name is ID, then use node id as the key.
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
2010-02-18 19:07:25 UTC (rev 19365)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
2010-02-18 20:54:01 UTC (rev 19366)
@@ -35,6 +35,8 @@
package edu.ucsd.bioeng.idekerlab.biomartclient.ui;
import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridLayout;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
@@ -53,7 +55,6 @@
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
-import cytoscape.util.SwingWorker;
/**
@@ -67,7 +68,6 @@
private static BiomartMainDialog mainDialog = null;
protected static Object pcsO = new Object();
protected static PropertyChangeSupport pcs = new
SwingPropertyChangeSupport(pcsO);
- private JPanel filterPanel;
/**
* DOCUMENT ME!
@@ -111,54 +111,32 @@
final JTabbedPane tabs = new JTabbedPane();
final List<Tunable> tunables =
WebServiceClientManager.getClient("biomart").getProps()
.getTunables();
+
+ final JPanel tunablePanel = new JPanel();
+ tunablePanel.setBackground(Color.white);
final JPanel tPanel = new JPanel();
+ final Dimension panelSize = new Dimension(220, 250);
+ tPanel.setMinimumSize(panelSize);
+ tPanel.setMaximumSize(panelSize);
+ tPanel.setSize(panelSize);
+
tPanel.setBackground(Color.white);
- tPanel.setLayout(new java.awt.GridBagLayout());
+ tPanel.setLayout(new GridLayout(0,1));
- java.awt.GridBagConstraints gridBagConstraints;
-
for (Tunable t : tunables) {
- JPanel propPanel = t.getPanel();
-
+ final JPanel propPanel = t.getPanel();
propPanel.setBackground(Color.white);
-
- if (t.getDescription().equalsIgnoreCase("Import all
available entries")){
- gridBagConstraints = new
java.awt.GridBagConstraints();
- gridBagConstraints.anchor =
java.awt.GridBagConstraints.WEST;
- gridBagConstraints.insets = new java.awt.Insets(10, 10,
10, 10);
- tPanel.add(propPanel, gridBagConstraints);
- }
- if (t.getDescription().equalsIgnoreCase("Show all
available filters")){
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 1;
- gridBagConstraints.anchor =
java.awt.GridBagConstraints.WEST;
- gridBagConstraints.insets = new java.awt.Insets(10, 10,
10, 10);
- tPanel.add(propPanel, gridBagConstraints);
- }
- if (t.getDescription().equalsIgnoreCase("Biomart Base
URL")){
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 2;
- gridBagConstraints.anchor =
java.awt.GridBagConstraints.WEST;
- gridBagConstraints.weightx = 1.0;
- gridBagConstraints.insets = new java.awt.Insets(10, 10,
10, 10);
- tPanel.add(propPanel, gridBagConstraints);
- }
+ tPanel.add(propPanel);
}
- // Add a label for place holder
- javax.swing.JLabel jLabel4 = new javax.swing.JLabel("");
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 3;
- gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
- gridBagConstraints.weightx = 1.0;
- tPanel.add(jLabel4, gridBagConstraints);
-
+ tunablePanel.add(tPanel);
+
panel = new BiomartAttrMappingPanel(monitor);
panel.addPropertyChangeListener(this);
tabs.addTab("Query", panel);
- tabs.addTab("Property", tPanel);
+ tabs.addTab("Options", tunablePanel);
add(tabs);
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