Author: scooter
Date: 2012-10-09 21:54:22 -0700 (Tue, 09 Oct 2012)
New Revision: 30642
Added:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ChemViz.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
Log:
Added first shot at CyCommands
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ChemViz.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ChemViz.java
2012-10-09 22:10:58 UTC (rev 30641)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ChemViz.java
2012-10-10 04:54:22 UTC (rev 30642)
@@ -52,6 +52,7 @@
import cytoscape.view.CytoscapeDesktop;
import ding.view.DGraphView;
+import chemViz.commands.ChemVizCommandHandler;
import chemViz.menus.ChemVizMenu;
import chemViz.menus.ChemVizContextMenu;
import chemViz.tasks.CreateNodeGraphicsTask;
@@ -117,6 +118,9 @@
logger.error("Unable to setup network listeners:
"+ccex.getMessage(), ccex);
return;
}
+
+ // Finally, register our commands
+ new ChemVizCommandHandler(settingsDialog);
}
/**
Added:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
2012-10-10 04:54:22 UTC (rev 30642)
@@ -0,0 +1,381 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 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 chemViz.commands;
+
+import java.lang.RuntimeException;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
+
+
+// Cytoscape imports
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.task.util.TaskManager;
+
+import giny.model.GraphObject;
+
+// chemViz imports
+import chemViz.model.ChemInfoProperties;
+import chemViz.model.Compound;
+import chemViz.model.Compound.DescriptorType;
+import chemViz.ui.ChemInfoSettingsDialog;
+
+enum Command {
+ ATTACH("attach",
+ "Attach 2D structures to nodes",
+ "nodelist|node|attribute|smiles"),
+ CALCULATE("calculate similarity",
+ "Create a similarity network for the current nodes",
+ "nodelist"),
+ CLOSESTRUCTURES("close structures",
+ "Close the 2D structure grid",
+ ""),
+ CLOSETABLE("close table",
+ "Close the structure table",
+ ""),
+ GETDESC("get descriptors",
+ "Return chemical descriptors for nodes or edges",
+
"attribute|descriptors|edge|edgelist|network=current|node|nodelist|smiles"),
+ REMOVE("remove",
+ "Remove 2D structures from nodes",
+ "nodelist|node"),
+ SHOWSTRUCTURES("show structures",
+ "Popup the 2D structures for a node/edge or group of
nodes/edges",
+ "node|nodelist|edge|edgelist"),
+ SHOWTABLE("show table",
+ "Show the structure table for a node/edge or group of
nodes/edges",
+ "edge|edgelist|node|nodelist|descriptors|attributes"),
+ SETPARAM("set parameter",
+ "Set chemViz parameters",
+
"fingerprinter=CDK|smilesAttributes|inchiAttributes|nodeSize=100|position=Centered|imageLabel");
+
+ private String command = null;
+ private String argList = null;
+ private String desc = null;
+
+ Command(String command, String description, String argList) {
+ this.command = command;
+ this.argList = argList;
+ this.desc = description;
+ }
+
+ public String getCommand() { return command; }
+ public String getArgString() { return argList; }
+ public String getDescription() { return desc; }
+ public boolean equals(String com) { return command.equals(com); }
+}
+
+
+/**
+ * Inner class to handle CyCommands
+ */
+public class ChemVizCommandHandler extends AbstractCommandHandler {
+ ChemInfoProperties props;
+ static final String ATTRIBUTE = "attribute";
+ static final String CURRENT = "current";
+ static final String DESCRIPTORS = "descriptors";
+ static final String EDGE = "edge";
+ static final String EDGELIST = "edgelist";
+ static final String NETWORK = "network";
+ static final String NODE = "node";
+ static final String NODELIST = "nodelist";
+ static final String SMILES = "smiles";
+
+ public ChemVizCommandHandler (ChemInfoSettingsDialog settingsDialog) {
+ super(CyCommandManager.reserveNamespace("chemViz"));
+
+ props = settingsDialog.getProperties();
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args)
+ throws
CyCommandException, RuntimeException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args)
+ throws
CyCommandException, RuntimeException {
+ CyCommandResult result = new CyCommandResult();
+
+ List<String> legalArgs = getArguments(command);
+ for (String arg: args.keySet()) {
+ if (!legalArgs.contains(arg))
+ throw new RuntimeException("chemviz
"+command+": unknown argument: "+arg);
+ }
+
+ // Pull out common args
+ List<GraphObject> gObjList = getGraphObjectList(command, args);
+
+ String smiles = null;
+ if (args.containsKey(SMILES))
+ smiles = args.get(SMILES).toString();
+
+ String attribute = null;
+ if (args.containsKey(ATTRIBUTE))
+ attribute = args.get(ATTRIBUTE).toString();
+
+ // Main command cascade
+
+ // ATTACH("attach",
+ // "Attach 2D structures to nodes",
+ //
"nodelist|node|attribute|smiles"),
+ if (Command.ATTACH.equals(command)) {
+
+ // CALCULATE("calculate similarity",
+ // "Create a similarity network for the current
nodes",
+ // "nodelist"),
+ } else if (Command.CALCULATE.equals(command)) {
+
+ // CLOSESTRUCTURES("close structures",
+ // "Close the 2D structure grid",
+ // ""),
+ } else if (Command.CLOSESTRUCTURES.equals(command)) {
+
+ // CLOSETABLE("close table",
+ // "Close the structure table",
+ // ""),
+ } else if (Command.CLOSETABLE.equals(command)) {
+
+ // GETDESC("get descriptors",
+ // "Return chemical descriptors for a node",
+ // "descriptors|node|nodelist|smiles"),
+ } else if (Command.GETDESC.equals(command)) {
+ if (gObjList != null && smiles != null)
+ throw new RuntimeException("chemviz
"+command+": can't have both smiles string and nodes");
+
+ if (!args.containsKey(DESCRIPTORS))
+ throw new RuntimeException("chemviz
"+command+": descriptor list must be specified");
+ List<DescriptorType> descriptors =
getDescriptors(command, args.get(DESCRIPTORS).toString());
+
+ List<Compound> compoundList = getCompounds(gObjList,
smiles, attribute);
+ for (Compound compound: compoundList) {
+ for (DescriptorType type: descriptors) {
+
result.addResult(compound.toString()+":"+type.getShortName(),
compound.getDescriptor(type));
+ result.addMessage("Compound
"+compound.toString()+" "+type.toString()+" =
"+compound.getDescriptor(type).toString());
+ }
+ }
+
+ // REMOVE("remove",
+ // "Remove 2D structures from nodes",
+ // "nodelist|node"),
+ } else if (Command.REMOVE.equals(command)) {
+
+ // SHOWSTRUCTURES("show structures",
+ // "Popup the 2D structures for a node or
group of nodes",
+ // "node|nodelist"),
+ } else if (Command.SHOWSTRUCTURES.equals(command)) {
+
+ // SHOWTABLE("show table",
+ // "Show the structure table for a node or group
of nodes",
+ // "node|nodelist|descriptors|attributes"),
+ } else if (Command.SHOWTABLE.equals(command)) {
+ }
+
+ return result;
+ }
+
+ private void addCommand(String command, String description, String
argString) {
+ // Add the description first
+ addDescription(command, description);
+
+ if (argString == null) {
+ addArgument(command);
+ return;
+ }
+
+ // Split up the options
+ String[] options = argString.split("\\|");
+ for (int opt = 0; opt < options.length; opt++) {
+ String[] args = options[opt].split("=");
+ if (args.length == 1)
+ addArgument(command, args[0]);
+ else
+ addArgument(command, args[0], args[1]);
+ }
+ }
+
+ private List<GraphObject> getGraphObjectList(String command,
Map<String,Object> args) {
+ if (!args.containsKey(NODE) && !args.containsKey(NODELIST) &&
+ !args.containsKey(EDGE) && !args.containsKey(EDGE))
+ return null;
+
+ if (args.containsKey(NODE) && args.containsKey(NODELIST))
+ throw new RuntimeException("chemviz "+command+": can't
have both 'node' and 'nodeList'");
+
+ if (args.containsKey(EDGE) && args.containsKey(EDGELIST))
+ throw new RuntimeException("chemviz "+command+": can't
have both 'edge' and 'edgeList'");
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ if (args.containsKey(NETWORK)) {
+ String netName = args.get(NETWORK).toString();
+ if (!netName.equals(CURRENT) &&
Cytoscape.getNetwork(netName) != null)
+ network = Cytoscape.getNetwork(netName);
+ }
+
+ List<GraphObject> objList = new ArrayList<GraphObject>();
+ if (args.containsKey(NODE)) {
+ objList.add(getNode(command,
args.get(NODE).toString()));
+ } else if (args.containsKey(NODELIST)) {
+ String nodes = args.get(NODELIST).toString();
+ if (nodes == null || nodes.length() == 0) return null;
+ String[] nodeArray = nodes.split(",");
+ for (String str: nodeArray)
+ objList.add(getNode(command, str.trim()));
+ } else if (args.containsKey(EDGE)) {
+ objList.add(getEdge(command,
args.get(EDGE).toString()));
+ } else if (args.containsKey(EDGELIST)) {
+ String edges = args.get(EDGELIST).toString();
+ if (edges == null || edges.length() == 0) return null;
+ String[] edgeArray = edges.split(",");
+ for (String str: edgeArray)
+ objList.add(getEdge(command, str.trim()));
+ }
+ return objList;
+ }
+
+ private GraphObject getNode(String command, String nodeID) {
+ if (Cytoscape.getCyNode(nodeID, false) != null)
+ return (GraphObject)Cytoscape.getCyNode(nodeID, false);
+
+ if (Cytoscape.getCyNode(nodeID) != null)
+ return (GraphObject)Cytoscape.getCyNode(nodeID);
+
+ throw new RuntimeException("chemviz "+command+": can't find
node '"+nodeID+"'");
+ }
+
+ private GraphObject getEdge(String command, String edgeID) {
+ throw new RuntimeException("chemviz "+command+": edge support
isn't implemented yet");
+ }
+
+ private List<DescriptorType> getDescriptors(String command, String
desc) {
+ if (desc == null || desc.length() == 0)
+ throw new RuntimeException("chemviz "+command+":
descriptors list cannot be empty");
+
+ List<DescriptorType> fullList = Compound.getDescriptorList();
+ List<DescriptorType> resultList = new
ArrayList<DescriptorType>();
+
+ String[] descArray = desc.split(",");
+ for (String descriptor: descArray) {
+ if (getDescriptor(fullList,descriptor.trim()) == null)
+ throw new RuntimeException("chemviz
"+command+": descriptor '"+descriptor+"' isn't supported");
+
resultList.add(getDescriptor(fullList,descriptor.trim()));
+ }
+ return resultList;
+ }
+
+ private DescriptorType getDescriptor(List<DescriptorType> fullList,
String desc) {
+ for (DescriptorType type: fullList)
+ if (type.getShortName().equals(desc))
+ return type;
+ return null;
+ }
+
+ private List<Compound> getCompounds(List<GraphObject> objList, String
smiles, String attribute) {
+ return null;
+ }
+
+ private void addArguments(String command) {
+ if (props == null) {
+ addArgument(command);
+ return;
+ }
+
+ for (Tunable t: props.getTunables()) {
+ if (t.getType() == Tunable.BUTTON || t.getType() ==
Tunable.GROUP)
+ continue;
+
+ // Is there a default value for this prop?
+ if (t.getValue() != null)
+ addArgument(command, t.getName(),
t.getValue().toString());
+ else
+ addArgument(command, t.getName());
+ }
+ }
+
+ private void setTunables(ChemInfoProperties props,
Collection<Tunable>args) throws Exception {
+ // Set the Tunables
+ for (Tunable t: args) {
+ if (props.get(t.getName()) != null) {
+ Tunable target = props.get(t.getName());
+ Object value = t.getValue();
+ try {
+ if ((target.getType() == Tunable.LIST)
&&
+ (t.getType() == Tunable.STRING)) {
+ setListTunable(target,
value.toString());
+ } else {
+
target.setValue(value.toString());
+ }
+ target.updateValueListeners();
+ } catch (Exception e) {
+ throw new Exception("Unable to parse
value for "+
+ t.getName()+":
"+value.toString());
+ }
+ }
+ }
+ }
+
+ private void setListTunable(Tunable listTunable, String value) {
+ Object[] optionList = (Object [])listTunable.getLowerBound();
+ String[] inputList = value.split(",");
+ String v = "";
+ Integer first = null;
+ for (int i = 0; i < inputList.length; i++) {
+ for (int j = 0; j < optionList.length; j++) {
+ if
(optionList[j].toString().equals(inputList[i])) {
+ v = v+","+j;
+ if (first == null) first = new
Integer(j);
+ }
+ }
+ }
+ v = v.substring(1);
+ if (listTunable.checkFlag(Tunable.MULTISELECT)) {
+ listTunable.setValue(v);
+ } else {
+ listTunable.setValue(first);
+ }
+ }
+
+}
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-10-09 22:10:58 UTC (rev 30641)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-10-10 04:54:22 UTC (rev 30642)
@@ -133,34 +133,37 @@
public class Compound {
public enum AttriType { smiles, inchi };
public enum DescriptorType {
- IMAGE ("2D Image", Compound.class),
- ATTRIBUTE ("Attribute", String.class),
- IDENTIFIER ("Molecular String", String.class),
- WEIGHT ("Molecular Wt.", Double.class),
- ALOGP ("ALogP", Double.class),
- ALOGP2 ("ALogP2", Double.class),
- AMR ("Molar refractivity", Double.class),
- HBONDACCEPTOR ("HBond Acceptors", Integer.class),
- HBONDDONOR ("HBond Donors", Integer.class),
- LOBMAX ("Length over Breadth Max", Double.class),
- LOBMIN ("Length over Breadth Min", Double.class),
- RBONDS ("Rotatable Bonds Count", Integer.class),
- RULEOFFIVE ("Rule of Five Failures", Double.class),
- TPSA ("Topological Polar Surface Area", Double.class),
- WEINERPATH ("Wiener Path", Double.class),
- WEINERPOL ("Wiener Polarity", Double.class),
- MASS ("Exact Mass", Double.class);
+ IMAGE ("2D Image", "image", Compound.class),
+ ATTRIBUTE ("Attribute", "attribute", String.class),
+ IDENTIFIER ("Molecular String", "molstring", String.class),
+ WEIGHT ("Molecular Wt.", "weight", Double.class),
+ ALOGP ("ALogP", "alogp", Double.class),
+ ALOGP2 ("ALogP2", "alogp2", Double.class),
+ AMR ("Molar refractivity", "refractivity", Double.class),
+ HBONDACCEPTOR ("HBond Acceptors", "acceptors", Integer.class),
+ HBONDDONOR ("HBond Donors", "donors", Integer.class),
+ LOBMAX ("Length over Breadth Max", "lobmax", Double.class),
+ LOBMIN ("Length over Breadth Min", "lobmin", Double.class),
+ RBONDS ("Rotatable Bonds Count", "rotbonds", Integer.class),
+ RULEOFFIVE ("Rule of Five Failures", "roff", Double.class),
+ TPSA ("Topological Polar Surface Area", "polarsurface",
Double.class),
+ WEINERPATH ("Wiener Path", "wienerpath", Double.class),
+ WEINERPOL ("Wiener Polarity", "weinerpolarity", Double.class),
+ MASS ("Exact Mass", "mass", Double.class);
private String name;
private Class classType;
private int columnCount;
+ private String shortName;
- DescriptorType(String name, Class classType) {
+ DescriptorType(String name, String shortName, Class classType) {
this.name = name;
+ this.shortName = shortName;
this.classType = classType;
}
public String toString() { return this.name; }
+ public String getShortName() { return this.shortName; }
public Class getClassType() { return this.classType; }
}
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