Author: scooter
Date: 2012-07-05 17:29:19 -0700 (Thu, 05 Jul 2012)
New Revision: 29779
Added:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/commands/ExpandNodesCommand.java
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/ExpandNodesTask.java
Modified:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/actions/ExpandNodesAction.java
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/dialogs/AnnotateNetworkDialog.java
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/BridgeDBUtils.java
Log:
Added expand nodes functionality. Requires a new version of the metanode
plugin to work right.
Modified:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/actions/ExpandNodesAction.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/actions/ExpandNodesAction.java
2012-07-06 00:10:56 UTC (rev 29778)
+++
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/actions/ExpandNodesAction.java
2012-07-06 00:29:19 UTC (rev 29779)
@@ -40,7 +40,10 @@
import cytoscape.Cytoscape;
import cytoscape.CyNetwork;
import cytoscape.logger.CyLogger;
+import cytoscape.task.util.TaskManager;
+import bindingDB.tasks.ExpandNodesTask;
+
public class ExpandNodesAction extends AbstractAction {
private CyLogger logger = null;
@@ -51,5 +54,7 @@
public void actionPerformed (ActionEvent e)
{
+ ExpandNodesTask expand = new ExpandNodesTask(logger);
+ TaskManager.executeTask(expand,
expand.getDefaultTaskConfig());
}
}
Added:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/commands/ExpandNodesCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/commands/ExpandNodesCommand.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/commands/ExpandNodesCommand.java
2012-07-06 00:29:19 UTC (rev 29779)
@@ -0,0 +1,151 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2012 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package bindingDB.commands;
+
+import java.io.InputStream;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.logger.CyLogger;
+
+
+public class ExpandNodesCommand {
+ /**
+ * This command will create metanodes from each protein that has hits
and add nodes
+ * representing each hit.
+ */
+ static public CyCommandResult expandNodes(CyLogger logger, CyNode node)
{
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ CyCommandResult result = new CyCommandResult();
+
+ if (!nodeAttributes.hasAttribute(node.getIdentifier(),
AnnotateNetworkCommand.HIT_ATTR)) {
+ result.addMessage("Node "+node.getIdentifier()+"
doesn't have any hits");
+ return result;
+ }
+
+ Integer hitCount =
nodeAttributes.getIntegerAttribute(node.getIdentifier(),
+
AnnotateNetworkCommand.HIT_ATTR);
+
+ if (hitCount.intValue() == 0) {
+ result.addMessage("Node "+node.getIdentifier()+"
doesn't have any hits");
+ return result;
+ }
+
+ // Get all of our lists
+ List<String>monomerIDList = getStringList(nodeAttributes, node,
AnnotateNetworkCommand.ID_ATTR);
+ List<String>smilesList = getStringList(nodeAttributes, node,
AnnotateNetworkCommand.SMILES_ATTR);
+ List<String>typeList = getStringList(nodeAttributes, node,
AnnotateNetworkCommand.AFF_TYPE_ATTR);
+ List<String>affinityStrList = getStringList(nodeAttributes,
node, AnnotateNetworkCommand.AFFINITY_STR_ATTR);
+ List<Double>affinityList = getDoubleList(nodeAttributes, node,
AnnotateNetworkCommand.AFFINITY_ATTR);
+
+ // Create a list of new and edges
+ List<CyNode>nodeList = new ArrayList<CyNode>();
+
+ for (int index = 0; index < monomerIDList.size(); index++) {
+ String id = monomerIDList.get(index);
+ String smiles = smilesList.get(index);
+ String type = typeList.get(index);
+ String affinityStr = affinityStrList.get(index);
+ Double affinity = affinityList.get(index);
+ CyNode newNode = createNode(id, smiles);
+ CyEdge newEdge = createEdge(node, newNode, type,
affinityStr, affinity);
+ nodeList.add(newNode);
+ }
+
+ // Now, create the settings we want the metanode to use
+ String settings =
"hideMetanode=false;createMembershipEdges=false;dontExpandEmpty=true";
+ nodeAttributes.setAttribute(node.getIdentifier(),
"__metanodeSettings", settings);
+
+ // OK, now turn the node into a metanode
+ CyGroup group = CyGroupManager.createGroup(node, nodeList,
"metaNode", Cytoscape.getCurrentNetwork());
+
+ // Collapse the group
+ group.setState(2);
+ // ... and expand it
+ group.setState(1);
+
+ result.addMessage("Created "+nodeList.size()+" nodes and added
them to "+node.getIdentifier());
+
+ return result;
+ }
+
+ static CyNode createNode(String id, String smiles) {
+ CyNode newNode = Cytoscape.getCyNode(id, true);
+ CyAttributes nodeAttribute = Cytoscape.getNodeAttributes();
+ List<String>smList = new ArrayList<String>();
+ smList.add(smiles);
+ nodeAttribute.setListAttribute(id,
AnnotateNetworkCommand.SMILES_ATTR, smList);
+ Cytoscape.getCurrentNetwork().addNode(newNode);
+ return newNode;
+ }
+
+ static CyEdge createEdge(CyNode parent, CyNode child, String type,
String affStr, Double aff) {
+ CyEdge edge = Cytoscape.getCyEdge(parent, child,
Semantics.INTERACTION, type, true);
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ edgeAttributes.setAttribute(edge.getIdentifier(),
AnnotateNetworkCommand.AFFINITY_STR_ATTR, affStr);
+ edgeAttributes.setAttribute(edge.getIdentifier(),
AnnotateNetworkCommand.AFFINITY_ATTR, aff);
+ Cytoscape.getCurrentNetwork().addEdge(edge);
+ return edge;
+ }
+
+ static List<String> getStringList(CyAttributes attrs, CyNode node,
String attrName) {
+ if (!attrs.hasAttribute(node.getIdentifier(), attrName))
+ return new ArrayList<String>();
+
+ return
(List<String>)attrs.getListAttribute(node.getIdentifier(), attrName);
+ }
+
+ static List<Double> getDoubleList(CyAttributes attrs, CyNode node,
String attrName) {
+ if (!attrs.hasAttribute(node.getIdentifier(), attrName))
+ return new ArrayList<Double>();
+
+ return
(List<Double>)attrs.getListAttribute(node.getIdentifier(), attrName);
+ }
+
+}
Modified:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/dialogs/AnnotateNetworkDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/dialogs/AnnotateNetworkDialog.java
2012-07-06 00:10:56 UTC (rev 29778)
+++
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/dialogs/AnnotateNetworkDialog.java
2012-07-06 00:29:19 UTC (rev 29779)
@@ -51,6 +51,7 @@
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JSlider;
+import javax.swing.SwingWorker;
import javax.swing.border.Border;
import javax.swing.border.EtchedBorder;
@@ -82,16 +83,20 @@
JComboBox speciesList;
JSlider cutoffSlider;
JLabel speciesLabel;
- JFrame busyDialog = null;
+ // Default species list
+ static final String[] defaultSpecies = {"Human"};
+ // Default type list
+ static final String[] defaultTypes = {"Uniprot/TrEMBL"};
+
+ static final String[] loadingString = {"Loading..."};
+
public AnnotateNetworkDialog(CyLogger logger) {
super(Cytoscape.getDesktop(), "Annotate network");
this.logger = logger;
- showBusyDialog();
haveCyThesaurus = BridgeDBUtils.haveCyThesaurus();
initComponents();
- hideBusyDialog();
this.pack();
this.setSize(WIDTH, HEIGHT);
}
@@ -129,17 +134,18 @@
attrPanel.add(typeLabel);
typeLabel.setBounds(LEFT, y,
typeLabel.getPreferredSize().width, 25);
- typeList = new JComboBox(getTypeList("Human"));
- typeList.setSelectedItem("Uniprot/TrEMBL");
if (haveCyThesaurus) {
+ typeList = new JComboBox(getTypeList("Human"));
typeList.setToolTipText("If the attribute type
is not Uniprot/TrEMBL, it will be converted");
typeList.addActionListener(this);
} else {
+ typeList = new JComboBox(defaultTypes);
+ typeList.setSelectedItem("Uniprot/TrEMBL");
typeList.setToolTipText("CyThesaurus is
unavailable -- only Uniprot/TrEMBL is supported");
- typeList.setEnabled(false);
}
+ typeList.setEnabled(false);
attrPanel.add(typeList);
- typeList.setBounds(COLUMN1, y,
typeList.getPreferredSize().width, 25);
+ typeList.setBounds(COLUMN1, y, 150, 25);
}
// Show the species. This is only enabled if the Idenfier type
is not Uniprot/trembl
@@ -210,23 +216,18 @@
if
(typeList.getSelectedItem().equals("Uniprot/TrEMBL")) {
speciesList.setEnabled(false);
speciesLabel.setEnabled(false);
+ } else if (typeList.getSelectedItem().equals("Guess")) {
+ // TODO: At some point, we need to add the
guess type functionality....
} else {
speciesList.setEnabled(true);
speciesLabel.setEnabled(true);
}
return;
+
+ // Species changed?
} else if (e.getSource() == speciesList) {
- showBusyDialog();
// We changed the species -- update typelist
- String[] types =
getTypeList((String)speciesList.getSelectedItem());
- DefaultComboBoxModel model =
(DefaultComboBoxModel)typeList.getModel();
- typeList.removeActionListener(this);
- model.removeAllElements();
- for (String t: types) {
- model.addElement(t);
- }
- typeList.addActionListener(this);
- hideBusyDialog();
+
updateTypesList(getTypeList((String)speciesList.getSelectedItem()));
return;
}
@@ -276,16 +277,18 @@
return attrList.toArray(new String[1]);
}
- private String[] getTypeList(String species) {
- String[] defaultType = {"Uniprot/TrEMBL"};
+ private String[] getTypeList(final String species) {
if (!haveCyThesaurus) {
- return defaultType;
+ return defaultTypes;
}
- String[] types = BridgeDBUtils.getSupportedTypes(logger,
species);
- if (types == null)
- return defaultType;
- return types;
+ TypesLoader loader = new TypesLoader(species);
+ loader.execute();
+
+ if (typeList != null)
+ typeList.setEnabled(false);
+
+ return loadingString;
}
private String[] getSpeciesList() {
@@ -297,22 +300,46 @@
return species;
}
- private void showBusyDialog() {
- if (busyDialog == null)
- initBusyDialog();
- busyDialog.setVisible(true);
+ private void updateTypesList(String[] types) {
+ typeList.removeActionListener(this);
+ DefaultComboBoxModel model =
(DefaultComboBoxModel)typeList.getModel();
+ model.removeAllElements();
+
+ for (String t: types) {
+ model.addElement(t);
+ if (t.equals("Uniprot/TrEMBL")) {
+ typeList.setSelectedItem(t);
+ }
+ }
+ typeList.addActionListener(this);
}
- private void hideBusyDialog() {
- if (busyDialog != null)
- busyDialog.setVisible(false);
+
+ class TypesLoader extends SwingWorker<String[], Void> {
+ String species;
+
+ public TypesLoader(String species) {
+ this.species = species;
+ }
+
+ @Override
+ public String[] doInBackground() {
+ return BridgeDBUtils.getSupportedTypes(logger, species);
+ }
+
+ @Override
+ public void done() {
+ String[] types = defaultTypes;
+ boolean gotResult = true;
+ try {
+ types = get();
+ } catch (InterruptedException ignore) {
+ } catch (java.util.concurrent.ExecutionException e) {
+ logger.error("Unable to load types for species
"+species+": "+e.getMessage());
+ gotResult = false;
+ }
+
+ updateTypesList(types);
+ typeList.setEnabled(true);
+ }
}
- private void initBusyDialog() {
- busyDialog = new JFrame("Working...");
- JPanel contentPane = new JPanel(new BorderLayout());
- JLabel label = new JLabel("Contacting BridgeDB...");
- contentPane.add(label, BorderLayout.CENTER);
- busyDialog.setContentPane(contentPane);
- busyDialog.pack();
- }
-
}
Modified:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/BridgeDBUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/BridgeDBUtils.java
2012-07-06 00:10:56 UTC (rev 29778)
+++
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/BridgeDBUtils.java
2012-07-06 00:29:19 UTC (rev 29779)
@@ -53,10 +53,15 @@
static final String BASE_URL = "http://webservice.bridgedb.org/";;
static Map<String,String> resources = new HashMap<String,String>();
+ static Map<String,String[]> typeMap = new HashMap<String,String[]>();
static String selectedResource = null;
static boolean haveCyThesaurus = false;
+ static String[] speciesCache = null;
static public String[] getSpeciesList(CyLogger logger) {
+ if (speciesCache != null)
+ return speciesCache;
+
List<String> speciesList = new ArrayList<String>();
try {
URL speciesURL = new URL(SPECIES_URL);
@@ -76,6 +81,8 @@
String[] speciesArray = speciesList.toArray(new String[0]);
Arrays.sort(speciesArray);
+ speciesCache = speciesArray;
+
// System.out.println("Species:
"+Arrays.toString(speciesArray));
return speciesArray;
}
@@ -84,6 +91,10 @@
if (haveCyThesaurus) {
if (!resources.containsKey(species))
return null;
+
+ if (typeMap.containsKey(species))
+ return typeMap.get(species);
+
selectResource(resources.get(species));
try {
@@ -93,7 +104,6 @@
Set<String> idTypes = (Set<String>)
result.getResult();
String[] types = idTypes.toArray(new
String[0]);
Arrays.sort(types);
- // System.out.println("Types for
"+species+": "+Arrays.toString(types));
return types;
}
} catch (Exception e) {
@@ -132,9 +142,10 @@
Map<String,Object>args = new HashMap<String, Object>();
String connstring = "idmapper-bridgerest:"+BASE_URL+species;
args.put("connstring", connstring);
- args.put("classpath",
"org.bridgedb.webservice,bridgerest.BridgeRest");
+ args.put("classpath",
"org.bridgedb.webservice.bridgerest.BridgeRest");
try {
- CyCommandManager.execute("idmapping", "register
resource", args);
+ // System.out.println("Registering resource
"+connstring);
+ CyCommandResult result =
CyCommandManager.execute("idmapping", "register resource", args);
} catch (Exception e) {}
resources.put(species, connstring);
@@ -151,7 +162,8 @@
Map<String,Object>args = new HashMap<String, Object>();
args.put("connstring", connstring);
try {
- CyCommandManager.execute("idmapping", "deselect
resource", args);
+ // System.out.println("Deselecting resource
"+connstring);
+ CyCommandResult result =
CyCommandManager.execute("idmapping", "deselect resource", args);
} catch (Exception e) {}
}
@@ -162,7 +174,8 @@
Map<String,Object>args = new HashMap<String, Object>();
args.put("connstring", connstring);
try {
- CyCommandManager.execute("idmapping", "select
resource", args);
+ // System.out.println("Selecting resource "+connstring);
+ CyCommandResult result =
CyCommandManager.execute("idmapping", "select resource", args);
} catch (Exception e) {}
selectedResource = connstring;
Added:
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/ExpandNodesTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/ExpandNodesTask.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/bindingDb/src/main/java/bindingDB/tasks/ExpandNodesTask.java
2012-07-06 00:29:19 UTC (rev 29779)
@@ -0,0 +1,72 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2012 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package bindingDB.tasks;
+
+import java.util.List;
+import java.util.Set;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+import cytoscape.command.CyCommandResult;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import bindingDB.commands.ExpandNodesCommand;
+
+public class ExpandNodesTask extends AbstractTask {
+
+ public ExpandNodesTask(CyLogger logger) {
+ this.logger = logger;
+ }
+
+ public String getTitle() {
+ return "Expanding Nodes";
+ }
+
+ public void run() {
+ setStatus("Expanding hits");
+ double complete = 0.0;
+ Set<CyNode> selectedNodes =
(Set<CyNode>)Cytoscape.getCurrentNetwork().getSelectedNodes();
+ if (selectedNodes == null || selectedNodes.size() == 0)
+ selectedNodes =
(Set<CyNode>)Cytoscape.getCurrentNetwork().nodesList();
+ double stepSize = (100.0)/selectedNodes.size();
+ for (CyNode node: selectedNodes) {
+ CyCommandResult result =
ExpandNodesCommand.expandNodes(logger, node);
+ // logger.debug("Annotating "+node.getIdentifier());
+ complete += stepSize;
+ setPercentCompleted((int)complete);
+ if (canceled) break;
+ }
+ }
+}
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