Author: scooter
Date: 2011-09-15 15:34:18 -0700 (Thu, 15 Sep 2011)
New Revision: 26829
Modified:
csplugins/trunk/ucsf/scooter/structureViz/build.xml
csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureCommands.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
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/ActionPopupMenu.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
Log:
Changes to Structure to allow multiple graph objects to be associated
with a single Chimera Model.
Modified: csplugins/trunk/ucsf/scooter/structureViz/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/structureViz/build.xml 2011-09-15 22:12:59 UTC
(rev 26828)
+++ csplugins/trunk/ucsf/scooter/structureViz/build.xml 2011-09-15 22:34:18 UTC
(rev 26829)
@@ -8,6 +8,7 @@
<property name = "lib" location = "../../../../cytoscape"/>
<property name = "jar" location = "jar"/>
<property name = "doc" location = "doc"/>
+ <property name="java.target_version" value="1.6" />
<property name="cytoscape.plugin" value="${lib}/plugins"/>
Modified: csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
2011-09-15 22:12:59 UTC (rev 26828)
+++ csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
2011-09-15 22:34:18 UTC (rev 26829)
@@ -13,7 +13,7 @@
pluginDescription=This plugin provides an interface to UCSF Chimera from
within Cytoscape, providing a linkage between the network view and the
structural view.
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=1.9
+pluginVersion=1.10
# Compatible Cytoscape version
cytoscapeVersion=2.8
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -41,6 +41,10 @@
import java.util.Properties;
// giny imports
+import giny.model.Edge;
+import giny.model.GraphObject;
+import giny.model.Node;
+import giny.view.EdgeView;
import giny.view.NodeView;
// Cytoscape imports
@@ -57,7 +61,9 @@
import structureViz.actions.Chimera;
import structureViz.model.Structure;
import structureViz.model.Sequence;
+import structureViz.model.ChimeraChain;
import structureViz.model.ChimeraModel;
+import structureViz.model.ChimeraResidue;
/**
@@ -76,7 +82,7 @@
private static CyAttributes cyAttributes;
private static CyLogger logger = null;
- static List<NodeView> selectedList = null;
+ static List<GraphObject> selectedList = null;
static {
String structureAttribute = getProperty("structureAttribute");
@@ -261,7 +267,7 @@
if (sList != null && sList.size() > 0)
return sList.get(0);
}
- Structure s = new Structure(name, null,
Structure.StructureType.PDB_MODEL);
+ Structure s = Structure.getStructure(name, (CyNode)null,
Structure.StructureType.PDB_MODEL);
pdbStructureMap.put(name, s);
return s;
}
@@ -339,14 +345,40 @@
* with ChimeraModels as the keys
* @param chimeraModels the list of ChimeraModels we currently have open
*/
- public static void selectCytoscapeNodes(CyNetworkView networkView,
Map<ChimeraModel,ChimeraModel> modelsToSelect,
+ public static void selectCytoscapeNodes(CyNetworkView networkView,
+ Map<ChimeraModel,ChimeraModel>
modelsToSelect,
List<ChimeraModel> chimeraModels) {
CyNetwork network = networkView.getNetwork();
- if (selectedList == null) selectedList = new
ArrayList<NodeView>();
+ if (selectedList == null) selectedList = new
ArrayList<GraphObject>();
+ // We need to do this in two passes since some parts of a
structure might be
+ // selected and some might not. Our selection model
(unfortunately) only tells
+ // us that something has changed, not what...
+ List<GraphObject> graphObjectList = new
ArrayList<GraphObject>();
for (ChimeraModel model: chimeraModels) {
if (model == null) continue;
+ Structure st = model.getStructure();
+ if (!modelsToSelect.containsKey(model)) {
+ // Deselect everything in this structure
+ graphObjectList.addAll(st.getGraphObjectList());
+ }
+ }
+ setSelectedState(networkView, graphObjectList, false);
+ graphObjectList.clear();
+
+ for (ChimeraModel model: chimeraModels) {
+ if (model == null) continue;
+ Structure st = model.getStructure();
+ if (modelsToSelect.containsKey(model)) {
+ // Select the appropriate things
+ List<ChimeraResidue>residueList =
model.getSelectedResidues();
+
graphObjectList.addAll(st.getGraphObjectList(residueList));
+ }
+ }
+ setSelectedState(networkView, graphObjectList, true);
+
+/*
CyNode node = model.getStructure().node();
if (node == null) continue;
NodeView nodeView = networkView.getNodeView(node);
@@ -371,6 +403,7 @@
}
}
}
+*/
networkView.updateView();
}
@@ -416,7 +449,8 @@
return structure;
}
- private static List<Structure> getStructures(CyNode node,
List<Structure> structureList, String matchName) {
+ private static List<Structure> getStructures(CyNode node,
+ List<Structure>
structureList, String matchName) {
if (structureList == null) {
structureList = new ArrayList<Structure>();
}
@@ -425,7 +459,8 @@
if (chemStruct != null && chemStruct.length() > 0) {
String[] structList = chemStruct.split(",");
for (int i = 0; i < structList.length; i++) {
- Structure s = new
Structure(structList[i].trim() ,node , Structure.StructureType.SMILES);
+ Structure s =
Structure.getStructure(structList[i].trim(), node,
+
Structure.StructureType.SMILES);
smilesStructureMap.put(structList[i].trim(), s);
structureList.add(s);
}
@@ -444,10 +479,11 @@
if (sList != null && sList.length > 0) {
// It does, so add them all
for (int i = 0; i < sList.length; i++) {
- Structure s = new
Structure(sList[i].trim(),node, Structure.StructureType.PDB_MODEL);
+ Structure s =
Structure.getStructure(sList[i].trim(),node,
+
Structure.StructureType.PDB_MODEL);
pdbStructureMap.put(sList[i].trim(), s);
// System.out.println("Setting residue list for
"+s);
- s.setResidueList(residues);
+ s.setResidueList(node, residues);
if (matchName != null &&
matchName.equals(sList[i].trim())) {
structureList.add(s);
return structureList;
@@ -455,12 +491,25 @@
structureList.add(s);
}
} else if (structure != null) {
- Structure s = new Structure(structure,node,
Structure.StructureType.PDB_MODEL);
+ Structure s = Structure.getStructure(structure,node,
Structure.StructureType.PDB_MODEL);
pdbStructureMap.put(structure, s);
- s.setResidueList(residues);
+ s.setResidueList(node, residues);
if (matchName != null && matchName.equals(structure))
structureList.add(s);
}
return structureList;
}
+
+ private static void setSelectedState(CyNetworkView view,
List<GraphObject> goList, boolean state) {
+ for (GraphObject obj: goList) {
+ if (obj instanceof Node) {
+ // Handle secondary paint??
+ view.getNodeView((Node)obj).setSelected(state);
+ } else if (obj instanceof Edge) {
+ view.getEdgeView((Edge)obj).setSelected(state);
+ }
+ if (selectedList.contains(obj))
+ selectedList.remove(obj);
+ }
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureCommands.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureCommands.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureCommands.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -121,7 +121,7 @@
structureType = Structure.StructureType.SMILES;
}
- Structure st = new Structure(name, null, structureType);
+ Structure st = Structure.getStructure(name, (CyNode)null,
structureType);
chimera.open(st);
// To make sure, see if we can get the Chimera model
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -114,6 +114,24 @@
public boolean isSelected() { return selected; }
/**
+ * Return the list of selected residues
+ *
+ * @return all selected residues
+ */
+ public List<ChimeraResidue> getSelectedResidues() {
+ List<ChimeraResidue>residueList = new
ArrayList<ChimeraResidue>();
+ if (selected) {
+ residueList.addAll(getResidues());
+ } else {
+ for (ChimeraResidue residue: getResidues()) {
+ if (residue.isSelected())
+ residueList.add(residue);
+ }
+ }
+ return residueList;
+ }
+
+ /**
* Add a residue to the chain.
*
* @param residue the ChimeraResidue to add to the chain.
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -77,9 +77,9 @@
this.modelNumber = structure.modelNumber();
this.subModelNumber = structure.subModelNumber();
}
- this.chains = new TreeMap();
- this.residues = new TreeMap();
- this.residueMap = new HashMap();
+ this.chains = new TreeMap<String,ChimeraChain>();
+ this.residues = new TreeMap<String,ChimeraResidue>();
+ this.residueMap = new HashMap<String,ChimeraResidue>();
this.structure = structure;
this.modelColor = color;
}
@@ -114,9 +114,9 @@
this.structure =
structure.makeSubModel(this.subModelNumber);
this.structure.setModelNumber(this.modelNumber,
this.subModelNumber);
- this.chains = new TreeMap();
- this.residues = new TreeMap();
- this.residueMap = new HashMap();
+ this.chains = new TreeMap<String,ChimeraChain>();
+ this.residues = new TreeMap<String,ChimeraResidue>();
+ this.residueMap = new HashMap<String,ChimeraResidue>();
}
/**
@@ -136,6 +136,23 @@
public boolean isSelected() { return selected; }
/**
+ * Return the list of selected residues
+ *
+ * @return all selected residues
+ */
+ public List<ChimeraResidue> getSelectedResidues() {
+ List<ChimeraResidue>residueList = new
ArrayList<ChimeraResidue>();
+ if (selected) {
+ residueList.addAll(getResidues());
+ } else {
+ for (ChimeraChain chain: getChains())
+ residueList.addAll(chain.getSelectedResidues());
+ }
+ return residueList;
+
+ }
+
+ /**
* Get the list of chain names associated with this model
*
* @return return the list of chain names for this model
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -213,6 +213,56 @@
}
/**
+ * Return true if this residue is included in the atom
+ * spec passed to it...
+ *
+ * @param atomSpec the Chimera atom spec
+ * @return true if this residue is addressed by this atom spec
+ */
+ public boolean matchesAtomSpec(String atomSpec) {
+ // We need to parse the atom spec to see if it includes this
residue
+ // Possibilities:
+ // 1) Atom spec is just a residue -- compare and return
result
+ // 2) Atom spec is a range, need to see if this residue is
in that range
+ // 3) Atom spec is a chain -- see if this residue is part
of that chain
+ if (atomSpec.charAt(0) == '.') {
+ // System.out.println("Chain match: chainId =
"+chainId+" atomSpec = "+atomSpec);
+ // We have a chain
+ if (atomSpec.substring(1).equalsIgnoreCase(chainId))
+ return true;
+ } else if (atomSpec.indexOf("-") > 0) {
+ // We have a range
+ String range[] = atomSpec.split("-");
+ if (range[1].indexOf('.') > 0) {
+ String chainSpec[] = range[1].split("\\.");
+ if (!chainSpec[1].equalsIgnoreCase(chainId))
+ return false;
+ range[1] = chainSpec[0];
+ }
+ // System.out.println("Residue match: index = "+index+"
range = "+range[0]+"-"+range[1]);
+ int thisResidue = Integer.parseInt(index);
+ int rangeStart = Integer.parseInt(range[0]);
+ int rangeEnd = Integer.parseInt(range[1]);
+ if (rangeStart <= thisResidue && rangeEnd >=
thisResidue)
+ return true;
+ } else {
+ // Residue
+ if (atomSpec.indexOf('.') > 0) {
+ // We've got a chain -- make sure it's our chain
+ // System.out.println("Chain match: chainId =
"+chainId+" atomSpec = "+atomSpec);
+ String chainSpec[] = atomSpec.split("\\.");
+ if (!chainSpec[1].equalsIgnoreCase(chainId))
+ return false;
+ atomSpec = chainSpec[0];
+ }
+ // System.out.println("Residue match: index = "+index+"
atomSpec = "+atomSpec);
+ if (index.equals(atomSpec))
+ return true;
+ }
+ return false;
+ }
+
+ /**
* Get the index of this residue
*
* @return residue index
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -32,21 +32,26 @@
*/
package structureViz.model;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
-import java.util.ArrayList;
+import java.util.Map;
import cytoscape.CyNode;
+import giny.model.GraphObject;
+import structureViz.model.ChimeraResidue;
+
/**
* The Structure class provides a link between the Chimera data
* and the Cytoscape data.
*/
public class Structure {
- static int nStructures = 0;
static int nextModel = 0;
+ static Map<String, Structure> structureMap = new HashMap<String,
Structure>();
String structureName;
- List<String> residueList;
- CyNode cytoscapeNode;
+ Map<GraphObject, List<String>> residueMap;
+ List<GraphObject> graphObjectList;
int modelNumber;
int subModelNumber;
StructureType type;
@@ -60,24 +65,38 @@
*/
public static int getNextModel() {return nextModel++;}
+ public static Structure getStructure(String name, CyNode node,
StructureType type) {
+ if (structureMap.containsKey(name)) {
+ Structure s = structureMap.get(name);
+ s.addGraphObject(node);
+ return s;
+ }
+ return new Structure(name, node, type);
+ }
+
/**
* Create a new Structure
*
* @param name the name of the structure
* @param node the CyNode that this structure points to
*/
- public Structure (String name, CyNode node, StructureType type) {
+ protected Structure (String name, CyNode node, StructureType type) {
+ this(name, new ArrayList<GraphObject>(), type);
+ if (node != null)
+ this.setNode(node);
+ }
+
+ protected Structure (String name, List<GraphObject> nodeList,
StructureType type) {
this.structureName = name;
- this.cytoscapeNode = node;
this.modelNumber = nextModel;
this.subModelNumber = 0;
- this.residueList = null;
+ this.residueMap = new HashMap<GraphObject, List<String>>();
this.type = type;
+ this.graphObjectList = nodeList;
}
public Structure makeSubModel(int subModelNumber) {
- System.out.println("Makeing sub-model");
- Structure st = new Structure(this.structureName,
this.cytoscapeNode, this.type);
+ Structure st = new Structure(this.structureName,
this.graphObjectList, this.type);
st.setModelNumber(this.modelNumber, subModelNumber);
return st;
}
@@ -94,16 +113,65 @@
*
* @return the CyNode this structure is an attribute of
*/
- public CyNode node() {return this.cytoscapeNode;}
+ public CyNode node() {
+ if (graphObjectList.get(0) instanceof CyNode)
+ return (CyNode)graphObjectList.get(0);
+ return null;
+ }
/**
* Set the CyNode this structure is associated with
*
* @param node the CyNode this structure is an attribute of
*/
- public void setNode(CyNode node) {this.cytoscapeNode = node;}
+ public void setNode(CyNode node) {this.graphObjectList.add(0,node);}
/**
+ * Add a CyNode or CyEdge to the list of graph objects this structure
is associated with
+ *
+ * @param node the GraphObject this structure is an attribute of
+ */
+ public void addGraphObject(GraphObject go)
{this.graphObjectList.add(go);}
+
+ /**
+ * Remove a Graph Object from the list of objects this structure is
associated with
+ *
+ * @param node the Graph Object to remove from this structure's list
+ */
+ public void removeGraphObject(GraphObject go) {
+ if (graphObjectList.contains(go))
+ graphObjectList.remove(go);
+ }
+
+ /**
+ * Get the list of GraphObjects for this structure
+ *
+ * @return objList the GraphObjects this structure is an attribute of
+ */
+ public List<GraphObject> getGraphObjectList() {return
this.graphObjectList;}
+
+ /**
+ * Get the list of GraphObjects for this structure that match a list
+ * of residues.
+ *
+ * @param residueList the list of residues we're matching
+ * @return objList the GraphObjects this structure is an attribute of
+ */
+ public List<GraphObject> getGraphObjectList(List<ChimeraResidue>
residueList) {
+ List<GraphObject>goList = new ArrayList<GraphObject>();
+ if (residueList == null || residueList.size() == 0)
+ return goList;
+
+ for (GraphObject obj: graphObjectList) {
+ if (residuesMatch(obj, residueList)) {
+ // System.out.println("Found match for
"+obj.getIdentifier());
+ goList.add(obj);
+ }
+ }
+ return goList;
+ }
+
+ /**
* Get the modelNumber for this structure
*
* @return the model number as an int
@@ -132,12 +200,15 @@
* Get the identifier of the cytoscape node this structure
* is an attribute of.
*
- * @return identifier of the CyNode as a String
+ * @return identifier of the Graph Object as a String
*/
public String getIdentifier() {
- if (cytoscapeNode == null)
+ if (graphObjectList == null || graphObjectList.size() == 0)
return "(none)";
- return cytoscapeNode.getIdentifier();
+ else if (graphObjectList.size() == 1)
+ return graphObjectList.get(0).getIdentifier();
+ else
+ return constructListOfGraphObjects(graphObjectList);
}
/**
@@ -159,11 +230,27 @@
}
/**
- * Return the "active site" or "special" residues
+ * Return the "active site" or "special" residues for a single node or
edge
*
+ * @param graphObject the Graph Object this list applies to
* @return String representation of the residues (comma separated)
*/
+ public List<String> getResidueList(GraphObject obj) {
+ if (residueMap.containsKey(obj))
+ return residueMap.get(obj);
+ return null;
+ }
+
+ /**
+ * Return the "active site" or "special" residues for all nodes or edges
+ *
+ * @return String representation of the residues (comma separated)
+ */
public List<String> getResidueList() {
+ List<String> residueList = new ArrayList<String>();
+ for (GraphObject obj: residueMap.keySet()) {
+ residueList.addAll(getResidueList(obj));
+ }
return residueList;
}
@@ -172,8 +259,8 @@
*
* @param residues String representation of the residues (comma
separated)
*/
- public void setResidueList(String residues) {
- this.residueList = new ArrayList<String>();
+ public void setResidueList(GraphObject obj, String residues) {
+ List<String> residueList = new ArrayList<String>();
if (residues == null) {
return;
}
@@ -194,21 +281,59 @@
if (residue == null || residue.equals("") ||
residue.length() == 0)
continue;
String[] range = residue.split("-",2);
+ String chain = null;
for (int res = 0; res < range.length; res++) {
- if (res == 1) resRange = resRange.concat("-");
+ if (res == 1) {
+ resRange = resRange.concat("-");
+ if (chain != null &&
range[res].indexOf('.') == -1)
+ range[res] =
range[res].concat("."+chain);
+ }
+
+ if (res == 0 && range.length >= 2 &&
range[res].indexOf('.') > 0) {
+ // This is a range spec with the
leading residue containing a chain spec
+ String[] resChain =
range[res].split("\\.");
+ chain = resChain[1];
+ range[res] = resChain[0];
+ }
// Convert to legal atom-spec
- if (Character.isDigit(residue.charAt(0))) {
+ if (Character.isDigit(range[res].charAt(0))) {
resRange = resRange.concat(range[res]);
- } else if
(Character.isDigit(residue.charAt(1))) {
+ } else if
(Character.isDigit(range[res].charAt(1))) {
resRange =
resRange.concat(range[res].substring(1));
- } else if (residue.charAt(0) == '.') {
+ } else if (range[res].charAt(0) == '.') {
// Do we have a chain spec?
resRange = resRange.concat(range[res]);
} else {
resRange =
resRange.concat(range[res].substring(3));
}
}
- this.residueList.add(resRange);
+ residueList.add(resRange);
}
+ residueMap.put(obj, residueList);
}
+
+ private String constructListOfGraphObjects(List<GraphObject> objList) {
+ String list = null;
+ for (GraphObject obj: objList) {
+ if (list == null)
+ list = ""+obj.getIdentifier();
+ else
+ list += ";"+obj.getIdentifier();
+ }
+ return list;
+ }
+
+ private boolean residuesMatch(GraphObject obj,
List<ChimeraResidue>residueList) {
+ if (!residueMap.containsKey(obj))
+ return true;
+
+ List<String>residues = residueMap.get(obj);
+ for (ChimeraResidue res: residueList) {
+ for (String atomSpec: residues) {
+ if (res.matchesAtomSpec(atomSpec))
+ return true;
+ }
+ }
+ return false;
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -434,7 +434,7 @@
ChimeraModel model =
obj.getChimeraModel();
List<String> residueL =
model.getStructure().getResidueList();
if (residueL == null) return;
- // The residue list is of the form
RRRnnn,RRRnnn. We want
+ // The residue list may be of the form
RRRnnn,RRRnnn. We want
// to reformat this to nnn,nnn
String residues = new String();
for (String residue: residueL) {
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -125,8 +125,8 @@
* this dialog
*/
protected ModelNavigatorDialog (Frame parent, Chimera object) {
- // super(parent, false);
- super(Cytoscape.getDesktop(), "Cytoscape Molecular Structure
Navigator");
+ // super(Cytoscape.getDesktop(), "Cytoscape Molecular Structure
Navigator");
+ super((Frame)null, "Cytoscape Molecular Structure Navigator");
chimeraObject = object;
initComponents();
status = false;
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
2011-09-15 22:12:59 UTC (rev 26828)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
2011-09-15 22:34:18 UTC (rev 26829)
@@ -185,7 +185,7 @@
String ident = node.getIdentifier();
if (ident.startsWith("gi"))
ident = ident.substring(2);
- Structure struct = new Structure(ident, node,
Structure.StructureType.MODBASE_MODEL);
+ Structure struct = Structure.getStructure(ident, node,
Structure.StructureType.MODBASE_MODEL);
userData = struct;
openAction(ident, null, false);
}
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