Author: scooter
Date: 2011-09-24 11:33:24 -0700 (Sat, 24 Sep 2011)
New Revision: 26962
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
Log:
More clean up and updates
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2011-09-24 16:32:02 UTC (rev 26961)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2011-09-24 18:33:24 UTC (rev 26962)
@@ -66,12 +66,6 @@
private static int displayType = THREE_LETTER; // the current display
type
private boolean selected = false; // the selection state
- // Return the ChimeraResidue that matches this spec. If create is
true, and we don't have that
- // residue, create it.
- public static ChimeraResidue getResidueFromSpec(Chimera chimeraObject,
String spec, boolean create) {
- return null;
- }
-
/**
* Constructor to create a new ChimeraResidue
*
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-09-24 16:32:02 UTC (rev 26961)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-09-24 18:33:24 UTC (rev 26962)
@@ -78,6 +78,13 @@
return new Structure(name, node, type);
}
+ public static Structure getStructure(String name) {
+ if (structureMap.containsKey(name))
+ return structureMap.get(name);
+
+ return null;
+ }
+
/**
* Create a new Structure
*
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-09-24 16:32:02 UTC (rev 26961)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-09-24 18:33:24 UTC (rev 26962)
@@ -61,6 +61,7 @@
import cytoscape.data.Semantics;
import cytoscape.layout.LayoutProperties;
import cytoscape.layout.Tunable;
+import cytoscape.layout.TunableListener;
import cytoscape.view.CyNetworkView;
import giny.view.NodeView;
@@ -71,12 +72,14 @@
import structureViz.model.ChimeraChain;
import structureViz.model.ChimeraModel;
import structureViz.model.ChimeraResidue;
+import structureViz.model.ChimeraStructuralObject;
import structureViz.model.Structure;
+import structureViz.model.StructureUtils;
import structureViz.model.Structure.StructureType;
/**
*/
-public class CreateNetworkDialog extends JDialog implements ActionListener {
+public class CreateNetworkDialog extends JDialog implements
ActionListener,TunableListener {
// Instance variables
Chimera chimeraObject;
LayoutProperties properties;
@@ -84,6 +87,7 @@
boolean includeClashes = false;
boolean includeHBonds = false;
boolean includeConnectivity = false;
+ boolean includeConnectivityDistance = false;
int interactionBetween = 2; // Between selection & other models
static final int BETWEENMODELS = 0;
static final int BETWEENSELMODELS = 1;
@@ -152,8 +156,15 @@
Tunable.BOOLEAN, includeClashes));
properties.add(new Tunable("includeHBonds", "Include hydrogen
bonds (overlaps with contacts)",
Tunable.BOOLEAN, includeHBonds));
- properties.add(new Tunable("includeConnectivity", "Include
connectivity",
- Tunable.BOOLEAN,
includeConnectivity));
+ Tunable t = new Tunable("includeConnectivity", "Include
connectivity",
+ Tunable.BOOLEAN, includeConnectivity);
+ t.addTunableValueListener(this);
+ properties.add(t);
+ t = new Tunable("includeConnectivityDistance", "Calculate
connectivity distances (more time consuming)",
+ Tunable.BOOLEAN, includeConnectivityDistance);
+ if (!includeConnectivity)
+ t.setImmutable(true);
+ properties.add(t);
properties.add(new Tunable("interaction", "Include
interactions",
Tunable.LIST, new
Integer(interactionBetween),
(Object) interactionArray, (Object)
null, 0));
@@ -176,6 +187,10 @@
if ((t != null) && (t.valueChanged() || force))
includeConnectivity = ((Boolean)
t.getValue()).booleanValue();
+ t = properties.get("includeConnectivityDistance");
+ if ((t != null) && (t.valueChanged() || force))
+ includeConnectivityDistance = ((Boolean)
t.getValue()).booleanValue();
+
t = properties.get("interaction");
if ((t != null) && (t.valueChanged() || force))
interactionBetween = ((Integer)
t.getValue()).intValue();
@@ -193,7 +208,7 @@
if ("create".equals(e.getActionCommand())) {
updateTunables(true);
List<CyEdge> edgeList = null;
- List<CyNode> nodeList = new ArrayList<CyNode>();
+ Map<CyNode, CyNode> nodeMap = new HashMap<CyNode,
CyNode>();
String cutoff = "";
String type = "Clashes";
// Send the commands to Chimera and get the results
@@ -204,6 +219,11 @@
if (includeClashes || includeContacts) {
String command = "findclash sel makePseudobonds
false log true namingStyle command "+cutoff ;
if (interactionBetween == BETWEENMODELS) {
+ // Get the first model
+ ChimeraModel model =
chimeraObject.getChimeraModels().get(0);
+ int modelNumber =
model.getModelNumber();
+ // Create the command
+ command = "findclash #"+modelNumber+"
makePseudobonds false log true namingStyle command test other "+cutoff;
} else if (interactionBetween ==
BETWEENSELMODELS)
command = command.concat(" test other");
else if (interactionBetween == BETWEENALL)
@@ -211,27 +231,31 @@
List<String>replyList =
chimeraObject.commandReply(command);
// printReply(replyList);
- edgeList = parseClashReplies(replyList,
nodeList, type);
+ edgeList = parseClashReplies(replyList,
nodeMap, type);
}
if (includeHBonds) {
+ // Get the first model
+ ChimeraModel model =
chimeraObject.getChimeraModels().get(0);
+ int modelNumber = model.getModelNumber();
String command =
- "findhbond selRestrict any intermodel
true makePseudobonds false log true namingStyle command";
+ "findhbond spec #"+modelNumber+"
intramodel false intermodel true makePseudobonds false log true namingStyle
command";
if (interactionBetween == BETWEENMODELS) {
+ command = "findhbond selRestrict any
intermodel true makePseudobonds false log true namingStyle command";
} else if (interactionBetween ==
BETWEENSELMODELS)
command = command.concat(" intramodel
false");
else if (interactionBetween == BETWEENALL)
command = command.concat(" intramodel
true");
List<String>replyList =
chimeraObject.commandReply(command);
if (edgeList == null)
- edgeList = parseHBondReplies(replyList,
nodeList);
+ edgeList = parseHBondReplies(replyList,
nodeMap);
else
-
edgeList.addAll(parseHBondReplies(replyList, nodeList));
+
edgeList.addAll(parseHBondReplies(replyList, nodeMap));
// printReply(replyList);
}
if (includeConnectivity) {
String command = "listphysicalchains";
List<String>replyList =
chimeraObject.commandReply(command);
-
edgeList.addAll(parseConnectivityReplies(replyList, nodeList));
+
edgeList.addAll(parseConnectivityReplies(replyList, new
ArrayList<CyNode>(nodeMap.keySet())));
}
int[] edges = new int[edgeList.size()];
@@ -259,7 +283,7 @@
// Activate structureViz for all of our nodes
CyAttributes nodeAttributes =
Cytoscape.getNodeAttributes();
- for (CyNode node: nodeList) {
+ for (CyNode node: nodeMap.keySet()) {
String residueSpec =
nodeAttributes.getStringAttribute(node.getIdentifier(), RESIDUE_ATTR);
String structure =
CyChimera.findStructures(residueSpec);
Structure s = Structure.getStructure(structure,
node, StructureType.PDB_MODEL);
@@ -271,6 +295,17 @@
}
}
+ public void tunableChanged(Tunable t) {
+ if (t.getName().equals("includeConnectivity")) {
+ Tunable icd =
properties.get("includeConnectivityDistance");
+ if (((Boolean)t.getValue()).booleanValue()) {
+ icd.setImmutable(false);
+ } else {
+ icd.setImmutable(true);
+ }
+ }
+ }
+
private void printReply(List<String> replyLog) {
for (String str: replyLog) System.out.println(str);
}
@@ -291,7 +326,7 @@
* and the clash lines look like:
* :2470.A@N :323.A@OD2 -0.394 3.454
*/
- private List<CyEdge> parseClashReplies(List<String> replyLog,
List<CyNode>nodes, String type) {
+ private List<CyEdge> parseClashReplies(List<String> replyLog,
Map<CyNode, CyNode>nodes, String type) {
// Scan for our header line
boolean foundHeader = false;
int index = 0;
@@ -353,7 +388,7 @@
* HOH 2541.A O GLU 2471.A OE1 no hydrogen 2.746 N/A
* HOH 2577.A O GLU 2471.A O no hydrogen 2.989 N/A
*/
- private List<CyEdge> parseHBondReplies(List<String> replyLog,
List<CyNode>nodes) {
+ private List<CyEdge> parseHBondReplies(List<String> replyLog,
Map<CyNode, CyNode>nodes) {
// Scan for our header line
boolean foundHeader = false;
int index = 0;
@@ -398,6 +433,7 @@
* same physical chain, we connect them with a "Connected" edge
*/
private List<CyEdge> parseConnectivityReplies(List<String> replyLog,
List<CyNode>nodes) {
+ List<CyEdge> edgeList = new ArrayList<CyEdge>();
List<ChimeraResidue[]> rangeList = new
ArrayList<ChimeraResidue[]>();
for (String line: replyLog) {
String[] tokens = line.split(" ");
@@ -408,41 +444,86 @@
ChimeraResidue[] range = new ChimeraResidue[2];
// Get the residues from the reside spec
- range[0] =
ChimeraResidue.getResidueFromSpec(chimeraObject, start, false);
- range[1] =
ChimeraResidue.getResidueFromSpec(chimeraObject, end, false);
+ range[0] = StructureUtils.getResidue(start,
chimeraObject);
+ range[1] = StructureUtils.getResidue(end,
chimeraObject);
rangeList.add(range);
}
+ // If we don't have any nodes, get all of the residues in the
connectivity
+ // list and create them as nodes
+
+ // For each node pair, figure out if the pair is connected
+ for (int i = 0; i < nodes.size(); i++) {
+ CyNode node1 = nodes.get(i);
+ // System.out.println("Getting the range for the first
node..."+node1);
+ ChimeraResidue[] range = getRange(rangeList, node1);
+ if (range == null) continue;
+ for (int j = i+1; j < nodes.size(); j++) {
+ CyNode node2 = nodes.get(j);
+ // System.out.println("Seeing if node2
"+node2+" is in the range...");
+ if (inRange(range, node2)) {
+ // System.out.println("....it is");
+ // These two nodes are connected
+ CyEdge edge =
Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, "connected", true);
+
edgeList.add(createConnectivityEdge(node1, node2));
+ }
+ }
+ }
+
// Now, make the edges based on whether any pair of nodes are
in the same range
- return null;
+ return edgeList;
}
- private CyEdge createEdge(List<CyNode>nodes, String sourceAlias, String
targetAlias, String type) {
+ private CyEdge createEdge(Map<CyNode, CyNode>nodes, String sourceAlias,
String targetAlias, String type) {
// Create our two nodes. Note that makeResidueNode also adds
three attributes:
// 1) FunctionalResidues
// 2) Seed
// 3) SideChainOnly
CyNode source = makeResidueNode(sourceAlias);
CyNode target = makeResidueNode(targetAlias);
- nodes.add(source);
- nodes.add(target);
+ nodes.put(source, source);
+ nodes.put(target, target);
// Create our edge
return Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, type, true);
}
+ private CyEdge createConnectivityEdge(CyNode node1, CyNode node2) {
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2,
Semantics.INTERACTION, "connected", true);
+
+ // Get the residue for node1 and node2 and ask Chimera to
calculate the distance
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String residueAttr =
nodeAttributes.getStringAttribute(node1.getIdentifier(), RESIDUE_ATTR);
+ ChimeraStructuralObject cso1 =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
+ residueAttr =
nodeAttributes.getStringAttribute(node2.getIdentifier(), RESIDUE_ATTR);
+ ChimeraStructuralObject cso2 =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
+ if (cso1 instanceof ChimeraResidue && cso2 instanceof
ChimeraResidue) {
+ String spec1 = cso1.toSpec()+"@CA";
+ String spec2 = cso2.toSpec()+"@CA";
+ System.out.println("Getting distance between "+spec1+"
and "+spec2);
+
+ List<String>replyList =
chimeraObject.commandReply("distance "+spec1+" "+spec2);
+ int offset = replyList.get(0).indexOf(':');
+ Double distance =
Double.valueOf(replyList.get(0).substring(offset+1));
+ CyAttributes edgeAttributes =
Cytoscape.getEdgeAttributes();
+ edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distance);
+ chimeraObject.chimeraSend("~distance "+spec1+" "+spec2);
+ }
+ return edge;
+ }
+
private CyNode makeResidueNode(String alias) {
// alias is a atomSpec of the form [#model]:residueNumber@atom
// We want to convert that to a node identifier of [pdbid#]ABC
nnn
// and add FunctionalResidues and BackboneOnly attributes
boolean singleModel = false;
- ChimeraModel model = getModel(alias);
+ ChimeraModel model = StructureUtils.getModel(alias,
chimeraObject);
if (model == null) {
model = chimeraObject.getChimeraModels().get(0);
singleModel = true;
}
- ChimeraResidue residue = getResidue(alias, model);
- boolean backbone = isBackbone(alias);
+ ChimeraResidue residue = StructureUtils.getResidue(alias,
model, chimeraObject);
+ boolean backbone = StructureUtils.isBackbone(alias,
chimeraObject);
int displayType = ChimeraResidue.getDisplayType();
ChimeraResidue.setDisplayType(ChimeraResidue.THREE_LETTER);
@@ -469,43 +550,6 @@
return node;
}
- private ChimeraModel getModel(String alias) {
- String[] split = alias.split(":");
- // No model specified....
- if (split[0].length() == 0) return null;
-
- int model = 0;
- int submodel = 0;
- String[] subSplit = split[0].substring(1).split(".");
- model = Integer.parseInt(subSplit[0]);
- if (subSplit.length > 1)
- submodel = Integer.parseInt(subSplit[1]);
-
- return chimeraObject.getChimeraModel(model, submodel);
- }
-
- private ChimeraResidue getResidue(String alias, ChimeraModel model) {
- String[] split = alias.split(":|@");
-
- // Split into residue and chain
- String[] residueChain = split[1].split("\\.");
-
- if (residueChain.length == 1)
- return model.getResidue(residueChain[0]); // No chain...
-
- ChimeraChain chain = model.getChain(residueChain[1]);
- return chain.getResidue(residueChain[0]);
- }
-
- private boolean isBackbone(String alias) {
- String[] split = alias.split("@");
- String atom = split[1];
- if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
|| atom.equals("H") ||
- atom.equals("O"))
- return true;
- return false;
- }
-
private void updateMap(Map<CyEdge, Double>map, CyEdge edge, String
value, int comparison) {
// Save the minimum distance between atoms
Double v = Double.valueOf(value);
@@ -518,5 +562,64 @@
map.put(edge, v);
}
}
+
+ private ChimeraResidue[] getRange(List<ChimeraResidue[]> rangeList,
CyNode node) {
+ for (ChimeraResidue[] range: rangeList) {
+ if (inRange(range, node)) return range;
+ }
+ return null;
+ }
+
+ private boolean inRange(ChimeraResidue[] range, CyNode node) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String residueAttr =
nodeAttributes.getStringAttribute(node.getIdentifier(), RESIDUE_ATTR);
+ ChimeraStructuralObject cso =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
+ // Models can't be in a range...
+ if (cso == null || cso instanceof ChimeraModel) return false;
+
+ // A chain might be in a range -- check this
+ if (cso instanceof ChimeraChain) {
+ String chainID = ((ChimeraChain)cso).getChainId();
+ return inChainRange(range, chainID);
+ }
+
+ // OK, we have a residue, but we need to be careful to make
+ // sure that the chains match
+ ChimeraResidue residue = (ChimeraResidue)cso;
+ if (inChainRange(range, residue.getChainId())) {
+ return true;
+ }
+
+ int startIndex = Integer.parseInt(range[0].getIndex());
+ int endIndex = Integer.parseInt(range[1].getIndex());
+ int residueIndex = Integer.parseInt(residue.getIndex());
+
+ if (endIndex < startIndex) {
+ if (endIndex <= residueIndex && residueIndex <=
startIndex) return true;
+ } else {
+ if (startIndex <= residueIndex && residueIndex <=
endIndex) return true;
+ }
+
+ return false;
+
+ }
+
+ private boolean inChainRange(ChimeraResidue[] range, String chainID) {
+ String start = range[0].getChainId();
+ String end = range[1].getChainId();
+
+ if (start == null || end == null) return false;
+
+ if (start.equals(end)) return false;
+
+ if (start.compareTo(end) > 0) {
+ end = range[0].getChainId();
+ start = range[1].getChainId();
+ }
+
+ if (start.compareTo(chainID) <= 0 && chainID.compareTo(end) <=
0) return true;
+
+ return false;
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-09-24 16:32:02 UTC (rev 26961)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-09-24 18:33:24 UTC (rev 26962)
@@ -101,6 +101,7 @@
private boolean isCollapsing = false;
private TreePath collapsingPath = null;
private boolean isExpanding = false;
+ private List<JMenuItem> selectionDependentMenus = null;
// Dialog components
private JLabel titleLabel;
@@ -151,6 +152,9 @@
pack();
}
+ private void updateMenuItems() {
+ }
+
/**
* This method is called when a tree is expanded
*
@@ -290,8 +294,11 @@
selSpec = selSpec.concat(nodeInfo.toSpec());
modelsToSelect.put(model,model);
if (i < selectedObjects.size()-1) selSpec.concat("|");
- // Add the model to be selected (if it's not already)
+
}
+
+ enableMenuItems(selectedObjects.size());
+
if (!ignoreSelection && selected)
chimeraObject.select(selSpec);
else if (!ignoreSelection && selectedObjects.size() == 0) {
@@ -385,6 +392,7 @@
* in the dialog.
*/
private void initComponents() {
+ selectionDependentMenus = new ArrayList<JMenuItem>();
int modelCount = chimeraObject.getChimeraModels().size();
setDefaultCloseOperation(DISPOSE_ON_CLOSE);
@@ -422,28 +430,36 @@
chimeraMenu.add(new JSeparator());
JMenu clashMenu = new JMenu("Clash detection");
- addMenuItem(clashMenu, "Find all clashes", FINDCLASH,
"findclash sel continuous true");
- addMenuItem(clashMenu, "Find clashes within models", FINDCLASH,
"findclash sel test model continuous true");
+ JMenuItem item = addMenuItem(clashMenu, "Find all clashes",
FINDCLASH, "findclash sel continuous true");
+ selectionDependentMenus.add(item);
+ item = addMenuItem(clashMenu, "Find clashes within models",
FINDCLASH, "findclash sel test model continuous true");
+ selectionDependentMenus.add(item);
addMenuItem(clashMenu, "Clear clashes and contacts", COMMAND,
"~findclash");
chimeraMenu.add(clashMenu);
JMenu contactMenu = new JMenu("Contact detection");
- addMenuItem(contactMenu, "Find all contacts", FINDCLASH,
"findclash sel overlapCutoff -0.4 hbondAllowance 0.0");
- addMenuItem(contactMenu, "Find contacts within models",
FINDCLASH, "findclash sel test model overlapCutoff -0.4 hbondAllowance 0.0");
+ item = addMenuItem(contactMenu, "Find all contacts", FINDCLASH,
"findclash sel overlapCutoff -0.4 hbondAllowance 0.0");
+ selectionDependentMenus.add(item);
+ item = addMenuItem(contactMenu, "Find contacts within models",
FINDCLASH, "findclash sel test model overlapCutoff -0.4 hbondAllowance 0.0");
+ selectionDependentMenus.add(item);
addMenuItem(contactMenu, "Clear clashes and contacts", COMMAND,
"~findclash");
chimeraMenu.add(contactMenu);
JMenu hBondMenu = new JMenu("Hydrogen bond detection");
JMenu fHBondMenu = new JMenu("Find hydrogen bonds");
- addMenuItem(fHBondMenu, "Between models", FINDHBOND, "findhbond
selRestrict any intermodel true intramodel false");
- addMenuItem(fHBondMenu, "Within models", FINDHBOND, "findhbond
selRestrict any intermodel false intramodel true");
- addMenuItem(fHBondMenu, "Both", FINDHBOND, "findhbond
selRestrict any intermodel true intramodel true");
+ item = addMenuItem(fHBondMenu, "Between models", FINDHBOND,
"findhbond selRestrict any intermodel true intramodel false");
+ selectionDependentMenus.add(item);
+ item = addMenuItem(fHBondMenu, "Within models", FINDHBOND,
"findhbond selRestrict any intermodel false intramodel true");
+ selectionDependentMenus.add(item);
+ item = addMenuItem(fHBondMenu, "Both", FINDHBOND, "findhbond
selRestrict any intermodel true intramodel true");
+ selectionDependentMenus.add(item);
hBondMenu.add(fHBondMenu);
addMenuItem(hBondMenu, "Clear hydrogen bonds", COMMAND,
"~findhbond");
chimeraMenu.add(hBondMenu);
chimeraMenu.add(new JSeparator());
- addMenuItem(chimeraMenu, "Create interaction network from
structure...", CREATENETWORK, null);
+ item = addMenuItem(chimeraMenu, "Create interaction network
from structure...", CREATENETWORK, null);
+ selectionDependentMenus.add(item);
chimeraMenu.add(new JSeparator());
@@ -506,6 +522,8 @@
JScrollPane treeView = new JScrollPane(navigationTree);
setContentPane(treeView);
+
+ enableMenuItems(0);
}
/**
@@ -587,6 +605,14 @@
return;
}
+ private void enableMenuItems(int count) {
+ boolean enable = true;
+ if (count == 0) enable = false;
+ for (JMenuItem item: selectionDependentMenus) {
+ item.setEnabled(enable);
+ }
+ }
+
// Embedded classes
/**
@@ -681,7 +707,12 @@
"Nothing
Selected", JOptionPane.ERROR_MESSAGE);
}
} else if (type == CREATENETWORK) {
- launchNewNetworkDialog();
+ if (selectedObjects.size() > 0) {
+ launchNewNetworkDialog();
+ } else {
+ JOptionPane.showMessageDialog(dialog,
"You must select something to create a network",
+ "Nothing
Selected", JOptionPane.ERROR_MESSAGE);
+ }
} else {
residueDisplay = type;
treeModel.setResidueDisplay(type);
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