Author: scooter
Date: 2012-10-10 15:33:48 -0700 (Wed, 10 Oct 2012)
New Revision: 30649
Added:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ValueUtils.java
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/ChemVizContextMenu.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/DepictionMenus.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateCompoundTableTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
Log:
Have many commands implemented -- moving forward!
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
2012-10-10 21:14:28 UTC (rev 30648)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -35,13 +35,17 @@
import java.lang.RuntimeException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Map;
+import java.util.Set;
// Cytoscape imports
+import cytoscape.CyEdge;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
import cytoscape.Cytoscape;
@@ -60,7 +64,10 @@
// chemViz imports
import chemViz.model.ChemInfoProperties;
import chemViz.model.Compound;
+import chemViz.model.Compound.AttriType;
import chemViz.model.Compound.DescriptorType;
+import chemViz.tasks.CreatePopupTask;
+import chemViz.tasks.CreateCompoundTableTask;
import chemViz.ui.ChemInfoSettingsDialog;
enum Command {
@@ -72,22 +79,25 @@
"nodelist"),
CLOSESTRUCTURES("close structures",
"Close the 2D structure grid",
- ""),
+ "dialog"),
CLOSETABLE("close table",
"Close the structure table",
- ""),
+ "dialog"),
GETDESC("get descriptors",
"Return chemical descriptors for nodes or edges",
"attribute|descriptors|edge|edgelist|network=current|node|nodelist|smiles"),
+ LISTDESC("list descriptors",
+ "Return the list of available chemical descriptors",
+ ""),
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"),
+ "node|nodelist|edge|edgelist|labelattribute"),
SHOWTABLE("show table",
"Show the structure table for a node/edge or group of
nodes/edges",
- "edge|edgelist|node|nodelist|descriptors|attributes"),
+ "edge|edgelist|node|nodelist|columnlist"),
SETPARAM("set parameter",
"Set chemViz parameters",
"fingerprinter=CDK|smilesAttributes|inchiAttributes|nodeSize=100|position=Centered|imageLabel");
@@ -113,21 +123,40 @@
* Inner class to handle CyCommands
*/
public class ChemVizCommandHandler extends AbstractCommandHandler {
- ChemInfoProperties props;
+ static final String ALL = "all";
static final String ATTRIBUTE = "attribute";
+ static final String COLUMNLIST = "columnlist";
static final String CURRENT = "current";
+ static final String DIALOG = "dialog";
static final String DESCRIPTORS = "descriptors";
static final String EDGE = "edge";
static final String EDGELIST = "edgelist";
+ static final String INCHI = "inchi";
+ static final String LABELATTRIBUTE = "labelattribute";
static final String NETWORK = "network";
static final String NODE = "node";
static final String NODELIST = "nodelist";
+ static final String SELECTED = "selected";
static final String SMILES = "smiles";
+ private ChemInfoProperties props;
+ private ChemInfoSettingsDialog dialog;
+
+ // Dialogs that we may want to dispose of...
+ static Map<Integer, CreatePopupTask> popupTasks = null;
+ static int popupTaskCount = 0;
+ static Map<Integer, CreateCompoundTableTask> tableTasks = null;
+ static int tableTaskCount = 0;
+
public ChemVizCommandHandler (ChemInfoSettingsDialog settingsDialog) {
super(CyCommandManager.reserveNamespace("chemViz"));
props = settingsDialog.getProperties();
+ dialog = settingsDialog;
+
+ for (Command command: Command.values()) {
+ addCommand(command.getCommand(),
command.getDescription(), command.getArgString());
+ }
}
public CyCommandResult execute(String command, Collection<Tunable>args)
@@ -146,21 +175,36 @@
}
// Pull out common args
- List<GraphObject> gObjList = getGraphObjectList(command, args);
+ List<GraphObject> gObjList =
ValueUtils.getGraphObjectList(command, args);
+ String objectType = "node";
+ if (gObjList != null && (gObjList.get(0) instanceof CyEdge))
+ objectType = "edge";
- String smiles = null;
- if (args.containsKey(SMILES))
- smiles = args.get(SMILES).toString();
+ String mstring = null;
+ AttriType mtype = AttriType.smiles;
+ if (args.containsKey(SMILES)) {
+ mstring = args.get(SMILES).toString();
+ } else if (args.containsKey(INCHI)) {
+ mstring = args.get(INCHI).toString();
+ mtype = AttriType.inchi;
+ }
- String attribute = null;
- if (args.containsKey(ATTRIBUTE))
- attribute = args.get(ATTRIBUTE).toString();
+ List<String> smilesAttrList = null;
+ List<String> inchiAttrList = null;
+ if (args.containsKey(ATTRIBUTE)) {
+ smilesAttrList.add(args.get(ATTRIBUTE).toString());
+ inchiAttrList.add(args.get(ATTRIBUTE).toString());
+ } else {
+ smilesAttrList =
dialog.getCompoundAttributes(objectType,AttriType.smiles);
+ inchiAttrList =
dialog.getCompoundAttributes(objectType,AttriType.inchi);
+ }
+
// Main command cascade
// ATTACH("attach",
// "Attach 2D structures to nodes",
- //
"nodelist|node|attribute|smiles"),
+ //
"nodelist|node|attribute|inchi|smiles"),
if (Command.ATTACH.equals(command)) {
// CALCULATE("calculate similarity",
@@ -169,29 +213,71 @@
} else if (Command.CALCULATE.equals(command)) {
// CLOSESTRUCTURES("close structures",
- // "Close the 2D structure grid",
- // ""),
+ // "Close the 2D structure grid(s)",
+ // "dialog"),
} else if (Command.CLOSESTRUCTURES.equals(command)) {
+ if (popupTasks != null && popupTasks.size() > 0) {
+ Set<Integer> dialogNumbers =
getDialogNumbers(popupTasks.keySet(), args);
+ for (Integer index: dialogNumbers) {
+ if (popupTasks.containsKey(index)) {
+ CreatePopupTask popup =
popupTasks.get(index);
+ popup.closePopup();
+ popupTasks.remove(index);
+ }
+ }
+ }
+
// CLOSETABLE("close table",
// "Close the structure table",
// ""),
} else if (Command.CLOSETABLE.equals(command)) {
+ if (tableTasks != null && tableTasks.size() > 0) {
+ Set<Integer> dialogNumbers =
getDialogNumbers(tableTasks.keySet(), args);
+ for (Integer index: dialogNumbers) {
+ if (tableTasks.containsKey(index)) {
+ CreateCompoundTableTask table =
tableTasks.get(index);
+ table.closePopup();
+ tableTasks.remove(index);
+ }
+ }
+ }
+
+ // LISTDESC("list descriptors",
+ // "Return the list of available chemical
descriptors",
+ // ""),
+ } else if (Command.LISTDESC.equals(command)) {
+ List<DescriptorType> descriptors =
ValueUtils.getDescriptors(command, "all");
+ List<String> descStrings = new ArrayList<String>();
+ result.addMessage("Available descriptors: ");
+ for (DescriptorType type: descriptors) {
+ String shortName = type.getShortName();
+ if (shortName.equals("image")) continue;
+
+ String name = type.toString();
+ result.addMessage(shortName+": "+name);
+ descStrings.add(shortName);
+ }
+ result.addResult("descriptors", descStrings);
+
// GETDESC("get descriptors",
// "Return chemical descriptors for a node",
- // "descriptors|node|nodelist|smiles"),
+ //
"edge|edgelist|descriptors|inchi|node|nodelist|inchi|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 (gObjList != null && mstring != null)
+ throw new RuntimeException("chemviz
"+command+": can't have both smiles/inchi string and nodes/edges");
+ if (gObjList == null && mstring == null)
+ throw new RuntimeException("chemviz
"+command+": must have one of smiles/inchi string or nodes/edges");
if (!args.containsKey(DESCRIPTORS))
throw new RuntimeException("chemviz
"+command+": descriptor list must be specified");
- List<DescriptorType> descriptors =
getDescriptors(command, args.get(DESCRIPTORS).toString());
+ List<DescriptorType> descriptors =
ValueUtils.getDescriptors(command, args.get(DESCRIPTORS).toString());
- List<Compound> compoundList = getCompounds(gObjList,
smiles, attribute);
+ List<Compound> compoundList =
ValueUtils.getCompounds(gObjList, mstring, mtype, smilesAttrList,
inchiAttrList);
for (Compound compound: compoundList) {
for (DescriptorType type: descriptors) {
+ if
(type.getShortName().equals("image")) continue;
result.addResult(compound.toString()+":"+type.getShortName(),
compound.getDescriptor(type));
result.addMessage("Compound
"+compound.toString()+" "+type.toString()+" =
"+compound.getDescriptor(type).toString());
}
@@ -204,18 +290,61 @@
// SHOWSTRUCTURES("show structures",
// "Popup the 2D structures for a node or
group of nodes",
- // "node|nodelist"),
+ // "node|nodelist|edge|edgelist"),
} else if (Command.SHOWSTRUCTURES.equals(command)) {
-
+ if (gObjList == null)
+ throw new RuntimeException("chemviz
"+command+": node/edge or nodelist/edgelist required");
+
+ String labelAttribute = null;
+ if (args.containsKey(LABELATTRIBUTE))
+ labelAttribute =
args.get(LABELATTRIBUTE).toString();
+
+ CreatePopupTask loader = new CreatePopupTask(gObjList, dialog,
labelAttribute, dialog.getMaxCompounds());
+ TaskManager.executeTask(loader,
loader.getDefaultTaskConfig());
+
+ if (popupTasks == null) popupTasks = new
HashMap<Integer, CreatePopupTask>();
+ result.addMessage("Showing structures: dialog
#"+popupTaskCount);
+ popupTasks.put(popupTaskCount++, loader);
+
// SHOWTABLE("show table",
- // "Show the structure table for a node or group
of nodes",
- // "node|nodelist|descriptors|attributes"),
+ // "Show the structure table for a node/edge or
group of nodes/edges",
+ // "edge|edgelist|node|nodelist|columnlist"),
} else if (Command.SHOWTABLE.equals(command)) {
+ if (gObjList == null)
+ throw new RuntimeException("chemviz
"+command+": node/edge or nodelist/edgelist required");
+
+ List<String> columnList = null;
+ if (args.containsKey(COLUMNLIST)) {
+ String[] columnSpecs =
((String)args.get(COLUMNLIST)).split(",");
+ columnList = Arrays.asList(columnSpecs);
+ }
+ CreateCompoundTableTask loader = new
CreateCompoundTableTask(gObjList, dialog, dialog.getMaxCompounds(), columnList);
+ TaskManager.executeTask(loader,
loader.getDefaultTaskConfig());
+
+ if (tableTasks == null) tableTasks = new
HashMap<Integer, CreateCompoundTableTask>();
+ result.addMessage("Showing structure table: dialog
#"+tableTaskCount);
+ tableTasks.put(tableTaskCount++, loader);
}
return result;
}
+ private Set<Integer> getDialogNumbers(Set<Integer> dialogNumbers,
Map<String, Object> args) {
+ if (args.containsKey(DIALOG)) {
+ Set<Integer> dn = new HashSet<Integer>();
+
+ String dNumber = ((String)args.get(DIALOG)).trim();
+ if (!dNumber.equals(ALL)) {
+ String[] dList = dNumber.split(",");
+ for (String d: dList) {
+ dn.add(new Integer(d.trim()));
+ }
+ return dn;
+ }
+ }
+ return dialogNumbers;
+ }
+
private void addCommand(String command, String description, String
argString) {
// Add the description first
addDescription(command, description);
@@ -236,87 +365,6 @@
}
}
- 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);
@@ -334,48 +382,4 @@
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);
- }
- }
-
}
Added: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ValueUtils.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ValueUtils.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ValueUtils.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -0,0 +1,354 @@
+/* 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.CyEdge;
+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.data.Semantics;
+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.AttriType;
+import chemViz.model.Compound.DescriptorType;
+
+/**
+ * Inner class to handle CyCommands
+ */
+public class ValueUtils {
+ static final String ALL = "all";
+ 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 SELECTED = "selected";
+ static final String SMILES = "smiles";
+
+ static public 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'");
+
+ // Get the network
+ 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);
+ }
+
+ // OK, nodes or edges?
+ if (args.containsKey(NODE) || args.containsKey(NODELIST))
+ return getNodeList(command, args, network);
+ else
+ return getEdgeList(command, args, network);
+ }
+
+ static public List<GraphObject> getNodeList(String command,
Map<String,Object> args, CyNetwork network) {
+ 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;
+ // Special case for "selected" nodes
+ if (nodes.equals(SELECTED)) {
+ objList.addAll(network.getSelectedNodes());
+ } else {
+ String[] nodeArray = nodes.split(",");
+ for (String str: nodeArray)
+ objList.add(getNode(command,
str.trim()));
+ }
+ }
+ return objList;
+ }
+
+ static public List<GraphObject> getEdgeList(String command,
Map<String,Object> args, CyNetwork network) {
+ List<GraphObject> objList = new ArrayList<GraphObject>();
+ 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;
+ // Special case for "selected" nodes
+ if (edges.equals(SELECTED)) {
+ objList.addAll(network.getSelectedEdges());
+ } else {
+ String[] edgeArray = edges.split(",");
+ for (String str: edgeArray)
+ objList.add(getEdge(command,
str.trim()));
+ }
+ }
+ return objList;
+ }
+
+ static public 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+"'");
+ }
+
+
+ static public GraphObject getEdge(String command, String edgeID) {
+ CyEdge edge = null;
+ String comp[] = edgeID.split("[()]");
+ CyNode source = Cytoscape.getCyNode(comp[0].trim(), false);
+ CyNode target = Cytoscape.getCyNode(comp[2].trim(), false);
+ if (source != null && target != null) {
+ edge = Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, comp[1].trim(), false);
+ }
+ if (edge == null)
+ throw new RuntimeException("chemviz "+command+": can't
find edge '"+edgeID+"'");
+ return edge;
+ }
+
+ static public 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>();
+
+ if (desc.trim().equals(ALL)) {
+ return fullList;
+ }
+
+ 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;
+ }
+
+ static public DescriptorType getDescriptor(List<DescriptorType>
fullList, String desc) {
+ for (DescriptorType type: fullList)
+ if (type.getShortName().equals(desc))
+ return type;
+ return null;
+ }
+
+ static public List<Compound> getCompounds(List<GraphObject> objList,
String mstring, AttriType type,
+ List<String> sList,
List<String> iList) {
+ List<Compound> compoundList = new ArrayList<Compound>();
+
+ // Handle special case of a bare smiles string
+ if (mstring != null) {
+ Compound c = new Compound(null, null, mstring, type,
false);
+ compoundList.add(c);
+ return compoundList;
+ }
+
+ for (GraphObject obj: objList) {
+ if (obj instanceof CyNode)
+ compoundList.addAll(getCompounds(obj,
Cytoscape.getNodeAttributes(), sList, iList, false));
+ else
+ compoundList.addAll(getCompounds(obj,
Cytoscape.getEdgeAttributes(), sList, iList, false));
+ }
+
+ return compoundList;
+ }
+
+ /**
+ * Returns all of the Compounds for a single graph object (Node or
Edge) based on the SMILES
+ * and InChI attributes.
+ *
+ * @param go the graph object we're looking at
+ * @param attributes the appropriate set of attributes (nodeAttributes
or edgeAttributes)
+ * @param sList the list of attributes that contain SMILES strings
+ * @param iList the list of attributes that contain InChI strings
+ * @param noStructures if 'true', the structures are fetched in the
background
+ * @return the list of compounds. If the compounds have not already
been created, they are created
+ * as a byproduct of this method.
+ */
+ public static List<Compound> getCompounds(GraphObject go, CyAttributes
attributes,
+ List<String> sList,
List<String> iList,
+ boolean noStructures) {
+ if ((sList == null || sList.size() == 0)
+ && (iList == null || iList.size() == 0))
+ return null;
+
+ List<Compound> cList = new ArrayList();
+
+ // Get the compound list from each attribute
+ for (String attr: sList) {
+ cList.addAll(getCompounds(go, attributes, attr,
AttriType.smiles, noStructures));
+ }
+
+ for (String attr: iList) {
+ cList.addAll(getCompounds(go, attributes, attr,
AttriType.inchi, noStructures));
+ }
+
+ return cList;
+ }
+
+ /**
+ * Returns all of the Compounds for a single graph object (Node or
Edge) based on the designated
+ * attribute of the specific type
+ *
+ * @param go the graph object we're looking at
+ * @param attributes the appropriate set of attributes (nodeAttributes
or edgeAttributes)
+ * @param attr the attribute that contains the compound descriptor
+ * @param type the type of the attribute (smiles or inchi)
+ * @param noStructures if 'true', the structures are fetched in the
background
+ * @return the list of compounds. If the compounds have not already
been created, they are created
+ * as a byproduct of this method.
+ */
+ public static List<Compound> getCompounds(GraphObject go, CyAttributes
attributes,
+ String attr, AttriType type,
+ boolean noStructures) {
+ byte atype = attributes.getType(attr);
+ List<Compound> cList = new ArrayList();
+
+ if (!attributes.hasAttribute(go.getIdentifier(), attr))
+ return cList;
+ if (atype == CyAttributes.TYPE_STRING) {
+ String cstring =
attributes.getStringAttribute(go.getIdentifier(), attr);
+ cList.addAll(getCompounds(go, attr, cstring, type,
noStructures));
+ } else if (atype == CyAttributes.TYPE_SIMPLE_LIST) {
+ List<String> stringList =
attributes.getListAttribute(go.getIdentifier(), attr);
+ for (String cstring: stringList) {
+ cList.addAll(getCompounds(go, attr, cstring,
type, noStructures));
+ }
+ }
+ return cList;
+ }
+
+ public static List<Compound> getCompounds(GraphObject go, String attr,
+ String compoundString,
AttriType type,
+ boolean noStructures) {
+ List<Compound> cList = new ArrayList();
+
+ String[] cstrings = null;
+
+ if (type == AttriType.smiles) {
+ cstrings = compoundString.split(",");
+ } else {
+ cstrings = new String[1];
+ cstrings[0] = compoundString;
+ }
+
+ for (int i = 0; i < cstrings.length; i++) {
+
+ Compound c = Compound.getCompound(go, attr,
cstrings[i], type);
+ if (c == null)
+ c = new Compound(go, attr, cstrings[i], type,
noStructures);
+
+ cList.add(c);
+ return cList;
+ }
+
+ return cList;
+ }
+
+ static public 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());
+ }
+ }
+ }
+ }
+
+ static public 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/menus/ChemVizContextMenu.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/ChemVizContextMenu.java
2012-10-10 21:14:28 UTC (rev 30648)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/ChemVizContextMenu.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -35,6 +35,7 @@
package chemViz.menus;
+import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
@@ -54,9 +55,9 @@
import cytoscape.CytoscapeInit;
import cytoscape.data.CyAttributes;
+import chemViz.commands.ValueUtils;
import chemViz.model.Compound;
import chemViz.model.Compound.AttriType;
-import chemViz.tasks.CreateCompoundsTask;
import chemViz.ui.ChemInfoSettingsDialog;
/**
@@ -151,12 +152,9 @@
type = "edge";
}
- // This little bit of strangeness is to avoid duplicating bunch
of code to handle
- // the creation of compounds that's already in
AbstractCompoundTask. Here, we
- // create a task, but just execute the run method directly
(synchronously)...
- CreateCompoundsTask t = new CreateCompoundsTask(go, attributes,
settingsDialog);
- t.run();
- List<Compound> cList = t.getCompoundList();
+ List<Compound> cList = ValueUtils.getCompounds(go, attributes,
+
settingsDialog.getCompoundAttributes(type,AttriType.smiles),
+
settingsDialog.getCompoundAttributes(type,AttriType.inchi), false);
Properties cytoProps = CytoscapeInit.getProperties();
if (cList == null || cList.size() == 0) {
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/DepictionMenus.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/DepictionMenus.java
2012-10-10 21:14:28 UTC (rev 30648)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/DepictionMenus.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -252,7 +252,7 @@
* @param dialog the settings dialog
*/
private void createPopup(Collection<GraphObject>selection,
ChemInfoSettingsDialog dialog) {
- CreatePopupTask loader = new CreatePopupTask(new ArrayList(selection),
dialog, dialog.getMaxCompounds());
+ CreatePopupTask loader = new CreatePopupTask(new ArrayList(selection),
dialog, null, dialog.getMaxCompounds());
TaskManager.executeTask(loader, loader.getDefaultTaskConfig());
}
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-10-10 21:14:28 UTC (rev 30648)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -262,6 +262,7 @@
private IFingerprinter fp;
private int lastImageWidth = -1;
private int lastImageHeight = -1;
+ private int index = 0;
private boolean lastImageFailed = false;
private DescriptorEngine descriptorEngine = null;
@@ -291,6 +292,7 @@
} else {
mapList = new ArrayList();
}
+ this.index = mapList.size();
mapList.add(this);
Compound.compoundMap.put(source, mapList);
createStructure();
@@ -419,6 +421,13 @@
return this.getSmiles().compareTo(o.getSmiles());
}
+ public String toString() {
+ if (source == null)
+ return maxString(moleculeString, 10);
+
+ return source.getIdentifier()+" ("+attribute+") ["+index+"]";
+ }
+
/**
* Handle requests for various compound descriptors. This is used
primarily by the CompoundTable, but
* could be used by other clients as well.
@@ -784,4 +793,9 @@
return bufferedImage;
}
+ private String maxString(String str, int max) {
+ if (str.length() <= max) return str;
+
+ return str.substring(0,max-3)+"...";
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateCompoundTableTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateCompoundTableTask.java
2012-10-10 21:14:28 UTC (rev 30648)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateCompoundTableTask.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -59,6 +59,8 @@
public class CreateCompoundTableTask extends AbstractCompoundTask {
Collection<GraphObject> selection;
ChemInfoSettingsDialog settingsDialog;
+ CompoundTable compoundTable = null;
+ List<String> columnList = null;
/**
* Creates the task.
@@ -74,6 +76,16 @@
this.compoundCount = 0;
}
+ public CreateCompoundTableTask(Collection<GraphObject> selection,
ChemInfoSettingsDialog dialog,
+ int maxCompounds, List<String>
columnList) {
+ this.selection = selection;
+ this.settingsDialog = dialog;
+ this.canceled = false;
+ this.maxCompounds = maxCompounds;
+ this.compoundCount = 0;
+ this.columnList = columnList;
+ }
+
public String getTitle() {
return "Creating Table";
}
@@ -101,8 +113,15 @@
settingsDialog.getCompoundAttributes(type,AttriType.smiles),
settingsDialog.getCompoundAttributes(type,AttriType.inchi));
if (cList.size() > 0 && !canceled) {
- CompoundTable cTable = new CompoundTable(cList);
+ compoundTable = new CompoundTable(cList, columnList);
}
}
+ public void closePopup() {
+ if (compoundTable != null) {
+ compoundTable.dispose();
+ compoundTable = null;
+ }
+ }
+
}
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
2012-10-10 21:14:28 UTC (rev 30648)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -62,6 +62,7 @@
List<GraphObject> objectList;
ChemInfoSettingsDialog dialog;
String labelAttribute;
+ CompoundPopup compoundPopup = null;
/**
* Creates the task.
@@ -83,6 +84,7 @@
this.maxCompounds = maxCompounds;
this.compoundCount = 0;
this.labelAttribute = dialog.getLabelAttribute();
+ this.compoundPopup = null;
}
/**
@@ -91,13 +93,18 @@
* @param objects the graph objects that we're creating the popup for
* @param dialog the settings dialog, which we use to pull the
attribute names that contain the compound descriptors
*/
- public CreatePopupTask(List<GraphObject>selection, ChemInfoSettingsDialog
dialog, int maxCompounds) {
+ public CreatePopupTask(List<GraphObject>selection, ChemInfoSettingsDialog
dialog, String labelAttribute, int maxCompounds) {
this.objectList = selection;
this.dialog = dialog;
this.canceled = false;
this.maxCompounds = maxCompounds;
this.compoundCount = 0;
- this.labelAttribute = dialog.getLabelAttribute();
+ if (labelAttribute == null)
+ this.labelAttribute = dialog.getLabelAttribute();
+ else
+ this.labelAttribute = labelAttribute;
+
+ this.compoundPopup = null;
}
public String getTitle() {
@@ -126,13 +133,20 @@
dialog.getCompoundAttributes(type,AttriType.inchi));
if (cList.size() > 0 && !canceled) {
if (objectList.size() == 1) {
- CompoundPopup popup = new CompoundPopup(cList,
objectList, null);
+ compoundPopup = new CompoundPopup(cList,
objectList, null);
} else {
if (labelAttribute.equals("ID"))
- new CompoundPopup(cList, objectList,
type+".ID");
+ compoundPopup = new
CompoundPopup(cList, objectList, type+".ID");
else
- new CompoundPopup(cList, objectList,
labelAttribute);
+ compoundPopup = new
CompoundPopup(cList, objectList, labelAttribute);
}
}
}
+
+ public void closePopup() {
+ if (compoundPopup != null) {
+ compoundPopup.dispose();
+ compoundPopup = null;
+ }
+ }
}
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
2012-10-10 21:14:28 UTC (rev 30648)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
2012-10-10 22:33:48 UTC (rev 30649)
@@ -83,6 +83,7 @@
import javax.swing.event.ChangeEvent;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
+import javax.swing.filechooser.FileNameExtensionFilter;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.DefaultTableCellRenderer;
import javax.swing.table.JTableHeader;
@@ -104,6 +105,7 @@
import cytoscape.logger.CyLogger;
import cytoscape.view.CyNetworkView;
+import chemViz.commands.ValueUtils;
import chemViz.model.ChemInfoTableModel;
import chemViz.model.Compound;
import chemViz.model.Compound.DescriptorType;
@@ -136,7 +138,7 @@
private List<CompoundColumn> columns;
private List<Compound> compoundList;
- public CompoundTable (List<Compound> compoundList) {
+ public CompoundTable (List<Compound> compoundList, List<String>
columnList) {
super(Cytoscape.getDesktop());
network = Cytoscape.getCurrentNetwork();
networkView = Cytoscape.getCurrentNetworkView();
@@ -145,9 +147,48 @@
setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
this.rowMap = new HashMap();
- // See if we have any table attributes stored
- columns =
TableAttributeHandler.getAttributes(Cytoscape.getCurrentNetwork());
+ GraphObject obj = compoundList.get(0).getSource();
+ String objType = "node.";
+ CyAttributes attributes = Cytoscape.getNodeAttributes();
+ if (obj instanceof CyEdge) {
+ objType = "edge.";
+ attributes = Cytoscape.getEdgeAttributes();
+ }
+
+ if (columnList != null && columnList.size() > 0) {
+ columns = new ArrayList<CompoundColumn>();
+ for (String s: columnList) {
+ String[] tokens = s.trim().split("[:;]");
+ if (tokens.length != 3 && tokens.length != 2)
+ throw new RuntimeException("Illegal
column specification: "+s);
+ if (tokens[0].equalsIgnoreCase("descriptor") ||
tokens[0].equalsIgnoreCase("desc")) {
+ DescriptorType type =
ValueUtils.getDescriptor(Compound.getDescriptorList(),tokens[1]);
+ int columnWidth = -1;
+ if (tokens.length == 3) columnWidth =
Integer.parseInt(tokens[2]);
+ columns.add(new CompoundColumn(type,
columnWidth));
+ } else if
(tokens[0].equalsIgnoreCase("attribute") || tokens[0].equalsIgnoreCase("attr"))
{
+ String attribute = tokens[1];
+ byte type = CyAttributes.TYPE_STRING;
+ if (!attribute.equals("ID")) {
+ type =
attributes.getType(attribute);
+ if (type ==
CyAttributes.TYPE_UNDEFINED)
+ continue;
+ }
+ int columnWidth = -1;
+ if (tokens.length == 3) columnWidth =
Integer.parseInt(tokens[2]);
+
+ if (attribute.equals("ID"))
+ columns.add(new
CompoundColumn("ID", "", CyAttributes.TYPE_STRING, columnWidth));
+ else
+ columns.add(new
CompoundColumn(attribute, objType, type, columnWidth));
+ }
+ }
+ } else {
+ // See if we have any table attributes stored
+ columns =
TableAttributeHandler.getAttributes(Cytoscape.getCurrentNetwork());
+ }
+
// Create the table
initTable();
@@ -312,6 +353,9 @@
} else if (e.getActionCommand().equals("export")) {
// Get the file name
JFileChooser chooser = new JFileChooser();
+ FileNameExtensionFilter filter = new
FileNameExtensionFilter(
+ "Text file formats", "txt", "tsv");
+ chooser.setFileFilter(filter);
chooser.setDialogTitle("Export Table to File");
int returnVal = chooser.showSaveDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
@@ -339,10 +383,16 @@
int row = sorter.modelIndex(viewRow);
Compound cmpd = compoundList.get(row);
for (int viewCol = 0; viewCol < columns.size();
viewCol++) {
- if (viewCol > 0)
- writer.write("\t");
int col =
table.convertColumnIndexToModel(viewCol);
- columns.get(col).output(writer, cmpd);
+ CompoundColumn c = columns.get(col);
+
+ // warning -- if the image column is the first
column, then we'll get a
+ // leading tab
+ if (c.getColumnType() != ColumnType.DESCRIPTOR
|| c.getDescriptor() != DescriptorType.IMAGE) {
+ if (viewCol > 0)
+ writer.write("\t");
+ c.output(writer, cmpd);
+ }
}
writer.write("\n");
}
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