Author: scooter
Date: 2010-12-30 11:18:28 -0800 (Thu, 30 Dec 2010)
New Revision: 23283
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/CommandUtils.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
Log:
Refactored to support submodels. Compiles, but not tested
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -72,7 +72,7 @@
// Chimera process
static Process chimera;
static private List<ChimeraModel> models;
- static private Map<Float,ChimeraModel> modelHash;
+ static private Map<Integer,ChimeraModel> modelHash;
static private ListenerThreads listener;
static private CyNetworkView networkView;
static private ModelNavigatorDialog mnDialog = null;
@@ -81,6 +81,8 @@
static Chimera staticPointer = null;
static CyLogger logger;
+ static int MAX_SUB_MODELS = 1000;
+
static public Chimera GetChimeraInstance(CyNetworkView networkView,
CyLogger logger) {
if (staticPointer != null) {
staticPointer.setNetworkView(networkView);
@@ -97,7 +99,7 @@
*/
protected Chimera(CyNetworkView networkView, CyLogger logger) {
models = new ArrayList<ChimeraModel>();
- modelHash = new HashMap<Float,ChimeraModel>();
+ modelHash = new HashMap<Integer,ChimeraModel>();
this.networkView = networkView;
this.logger = logger;
selectionList = new ArrayList<ChimeraStructuralObject>();
@@ -116,9 +118,10 @@
* @param model model number
* @return the corresponding model
*/
- public ChimeraModel getChimeraModel (Float model) {
- if (modelHash.containsKey(model))
- return modelHash.get(model);
+ public ChimeraModel getChimeraModel (int model, int subModel) {
+ Integer key = makeModelKey(model,subModel);
+ if (modelHash.containsKey(key))
+ return modelHash.get(key);
return null;
}
@@ -129,7 +132,7 @@
* @return the corresponding model
*/
public ChimeraModel getChimeraModel (int model) {
- return getChimeraModel(Float.valueOf((float)model));
+ return getChimeraModel(model, 0);
}
/**
@@ -205,38 +208,52 @@
public AlignStructuresDialog getAlignDialog() { return this.alDialog; }
/**
- * Test to see if we currently have a particular model open
+ * Test to see if we currently have a particular model open.
*
- * @param modelNumber the model number expressed as an Float object
+ * @param modelNumber the model number expressed as an integer
+ * @param subModelNumber the subModel number expressed as an integer
*/
- public boolean containsModel(Float modelNumber) {
- return modelHash.containsKey(modelNumber);
+ public boolean containsModel(int modelNumber, int subModelNumber) {
+ return modelHash.containsKey(makeModelKey(modelNumber,
subModelNumber));
}
/**
- * Test to see if we currently have a particular model open
+ * Test to see if we currently have a particular model open.
*
- * @param modelNumber the model number expressed as a float
+ * @param modelNumber the model number expressed as an int
*/
- public boolean containsModel(float modelNumber) {
- Float mn = new Float(modelNumber);
- return modelHash.containsKey(mn);
+ public boolean containsModel(int modelNumber) {
+ return containsModel(modelNumber, 0);
}
/**
* Return the ChimeraModel associated with the requested
* model number
*
- * @param modelNumber the model number expressed as a float
+ * @param modelNumber the model number expressed as an int
+ * @param subModelNumber the subModel number expressed as an int
* @return the ChimeraModel with a model number of modelNumber
*/
- public ChimeraModel getModel(float modelNumber) {
- Float mn = new Float(modelNumber);
- return (ChimeraModel)modelHash.get(mn);
+ public ChimeraModel getModel(int modelNumber, int subModelNumber) {
+ Integer key = makeModelKey(modelNumber, subModelNumber);
+ if (modelHash.containsKey(key))
+ return modelHash.get(key);
+ return null;
}
/**
* Return the ChimeraModel associated with the requested
+ * model number
+ *
+ * @param modelNumber the model number expressed as an int
+ * @return the ChimeraModel with a model number of modelNumber
+ */
+ public ChimeraModel getModel(int modelNumber) {
+ return getModel(modelNumber, 0);
+ }
+
+ /**
+ * Return the ChimeraModel associated with the requested
* model name
*
* @param modelName the model name expressed as a string
@@ -343,7 +360,7 @@
* @param structure the Structure to open
*/
public void open(Structure structure) {
- structure.setModelNumber(Structure.getNextModel());
+ structure.setModelNumber(Structure.getNextModel(), 0);
if (structure.getType() ==
Structure.StructureType.MODBASE_MODEL)
chimeraSend("listen stop models; listen stop selection;
open "+structure.modelNumber()+" modbase:"+structure.name());
else if (structure.getType() == Structure.StructureType.SMILES)
@@ -361,7 +378,7 @@
// Get our properties (default color scheme, etc.)
// Make the molecule look decent
- chimeraSend("repr stick #"+newModel.getModelNumber());
+ chimeraSend("repr stick "+newModel.toSpec());
if (structure.getType() !=
Structure.StructureType.SMILES) {
// Create the information we need for the
navigator
@@ -372,7 +389,7 @@
models.add(newModel);
// Add it to the hash table
- modelHash.put(new
Float(newModel.getModelNumber()),newModel);
+
modelHash.put(makeModelKey(newModel.getModelNumber(),newModel.getSubModelNumber()),newModel);
}
chimeraSend("focus");
@@ -390,15 +407,17 @@
* @param structure the Structure to close
*/
public void close(Structure structure) {
- float model = structure.modelNumber();
- chimeraSend("listen stop models; listen stop select; close
#"+model);
- System.out.println("listen stop models; listen stop select;
close #"+model);
-
- ChimeraModel chimeraModel = (ChimeraModel)modelHash.get(new
Float(model));
- if (chimeraModel != null) {
+ int model = structure.modelNumber();
+ int subModel = structure.subModelNumber();
+ Integer modelKey = makeModelKey(model, subModel);
+ if (modelHash.containsKey(modelKey)) {
+ ChimeraModel chimeraModel = modelHash.get(modelKey);
+ chimeraSend("listen stop models; listen stop select;
close "+chimeraModel.toSpec());
models.remove(chimeraModel);
- modelHash.remove(new Float(model));
+ modelHash.remove(modelKey);
selectionList.remove(chimeraModel);
+ } else {
+ chimeraSend("listen stop models; listen stop select;
close #"+model+"."+subModel);
}
chimeraSend("listen start models; listen start select");
return;
@@ -464,7 +483,7 @@
*/
public void refresh() {
// Get a new model list
- HashMap newHash = new HashMap();
+ HashMap<Integer,ChimeraModel> newHash = new
HashMap<Integer,ChimeraModel>();
// Stop all of our listeners while we try to handle this
chimeraSend("listen stop select; listen stop models");
@@ -474,14 +493,17 @@
// Match them up -- assume that the model #'s haven't changed
for (ChimeraModel model: newModelList) {
- Float modelNumber = new Float(model.getModelNumber());
// Get the color (for our navigator)
model.setModelColor(getModelColor(model));
+ // Get our model info
+ int modelNumber = model.getModelNumber();
+ int subModelNumber = model.getSubModelNumber();
+
// If we already know about this model number, get the
Structure,
// which tells us about the associated CyNode
- if (modelHash.containsKey(modelNumber)) {
- ChimeraModel oldModel =
(ChimeraModel)modelHash.get(modelNumber);
+ if (containsModel(modelNumber, subModelNumber)) {
+ ChimeraModel oldModel = getModel(modelNumber,
subModelNumber);
Structure s = oldModel.getStructure();
if (s.getType() ==
Structure.StructureType.SMILES)
model.setModelName(s.name());
@@ -489,11 +511,11 @@
} else {
// This will return a new Structure if we don't
know about it
Structure s =
CyChimera.findStructureForModel(networkView, model.getModelName());
- s.setModelNumber(modelNumber);
+ s.setModelNumber(model.getModelNumber(),
model.getSubModelNumber());
model.setStructure(s);
}
- newHash.put(modelNumber,model);
+ newHash.put(makeModelKey(model.getModelNumber(),
model.getSubModelNumber()),model);
if (model.getStructure() != null &&
model.getStructure().getType() != Structure.StructureType.SMILES) {
// Get the residue information
@@ -502,7 +524,7 @@
}
// Replace the old model list
- models = (ArrayList)newModelList;
+ models = newModelList;
modelHash = newHash;
// Restart all of our listeners
@@ -534,31 +556,33 @@
* and update our list.
*/
public void updateSelection() {
- HashMap<Float,ChimeraModel>modelSelHash = new HashMap();
+ HashMap<Integer,ChimeraModel>modelSelHash = new
HashMap<Integer, ChimeraModel>();
clearSelectionList();
// Execute the command to get the list of models with selections
for (String modelLine: commandReply("lists level molecule")) {
ChimeraModel chimeraModel = new ChimeraModel(modelLine);
- modelSelHash.put(new
Float(chimeraModel.getModelNumber()), chimeraModel);
+ Integer modelKey =
makeModelKey(chimeraModel.getModelNumber(), chimeraModel.getSubModelNumber());
+ modelSelHash.put(modelKey, chimeraModel);
}
// Now get the residue-level data
for (String inputLine: commandReply("lists level residue")) {
ChimeraResidue r = new ChimeraResidue(inputLine);
- Float modelNumber = new Float(r.getModelNumber());
- if (modelSelHash.containsKey(modelNumber)) {
- ChimeraModel model =
(ChimeraModel)modelSelHash.get(modelNumber);
+ Integer modelKey = makeModelKey(r.getModelNumber(),
r.getSubModelNumber());
+ if (modelSelHash.containsKey(modelKey)) {
+ ChimeraModel model = modelSelHash.get(modelKey);
model.addResidue(r);
}
}
// Get the selected objects
for (ChimeraModel selectedModel: modelSelHash.values()) {
- float modelNumber = selectedModel.getModelNumber();
+ int modelNumber = selectedModel.getModelNumber();
+ int subModelNumber = selectedModel.getSubModelNumber();
// Get the corresponding "real" model
- if (containsModel(modelNumber)) {
- ChimeraModel dataModel = getModel(modelNumber);
+ if (containsModel(modelNumber, subModelNumber)) {
+ ChimeraModel dataModel = getModel(modelNumber,
subModelNumber);
if (dataModel.getResidueCount() ==
selectedModel.getResidueCount() ||
dataModel.getStructure().getType() ==
Structure.StructureType.SMILES) {
// Select the entire model
@@ -635,15 +659,16 @@
private List<ChimeraModel> getModelInfoList(Structure structure) {
String name = structure.name();
int modelNumber = structure.modelNumber();
+ int subModelNumber = structure.subModelNumber();
List<ChimeraModel>infoList = new ArrayList();
- for (String modelLine: commandReply("listm type molecule spec
#"+modelNumber)) {
+ for (String modelLine: commandReply("listm type molecule spec
#"+modelNumber+"."+subModelNumber)) {
// System.out.println("ModelList: "+modelLine);
- if (modelLine.contains("id #"+modelNumber)) {
+ if (modelLine.contains("id
#"+modelNumber+"."+subModelNumber)) {
// System.out.println("Found: "+name);
// got the right model, now get the model number
ChimeraModel chimeraModel = new
ChimeraModel(structure, modelLine);
-
structure.setModelNumber(chimeraModel.getModelNumber());
+
structure.setModelNumber(chimeraModel.getModelNumber(),
chimeraModel.getSubModelNumber());
// System.out.println("Identified model as
"+chimeraModel);
infoList.add(chimeraModel);
}
@@ -687,14 +712,26 @@
*
*/
private void getResidueInfo(ChimeraModel model) {
- float modelNumber = model.getModelNumber();
+ int modelNumber = model.getModelNumber();
+ int subModelNumber = model.getSubModelNumber();
// Get the list -- it will be in the reply log
- for (String inputLine: commandReply ("listr spec
#"+modelNumber)) {
+ for (String inputLine: commandReply ("listr spec
#"+modelNumber+"."+subModelNumber)) {
ChimeraResidue r = new ChimeraResidue(inputLine);
- if (r.getModelNumber() == modelNumber) {
+ if (r.getModelNumber() == modelNumber ||
r.getSubModelNumber() == subModelNumber) {
model.addResidue(r);
}
}
}
+
+ /**
+ * Create the key to use for forming the model/submodel key into the
modelHash
+ *
+ * @param model the model number
+ * @param subModel the submodel number
+ * @return the model key as an Integer
+ */
+ private Integer makeModelKey(int model, int subModel) {
+ return new Integer(model*MAX_SUB_MODELS+subModel);
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -69,7 +69,7 @@
for (Structure openStructure: openStructs) {
if (structureName.equals(openStructure.name()))
{
// Map the model numbers
-
structure.setModelNumber(openStructure.modelNumber());
+
structure.setModelNumber(openStructure.modelNumber(),
openStructure.subModelNumber());
open = true;
break;
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/CommandUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/CommandUtils.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/CommandUtils.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -98,10 +98,20 @@
try {
if (spec.startsWith("#")) {
try {
- float f =
Float.parseFloat(spec.substring(1));
- m = chimera.getModel(f);
- if (m == null) {
- throw new
CyCommandException("No open model: "+f);
+ int decimalOffset =
spec.substring(1).indexOf('.'); // Do we have a sub-model?
+ if (decimalOffset > 0) {
+ int subModelNumber =
Integer.parseInt(spec.substring(decimalOffset+1));
+ int modelNumber =
Integer.parseInt(spec.substring(1, decimalOffset));
+ m =
chimera.getModel(modelNumber, subModelNumber);
+ if (m == null) {
+ throw new
CyCommandException("No open model: "+modelNumber+"."+subModelNumber);
+ }
+ } else {
+ int modelNumber =
Integer.parseInt(spec.substring(1));
+ m =
chimera.getModel(modelNumber, 0);
+ if (m == null) {
+ throw new
CyCommandException("No open model: "+modelNumber);
+ }
}
} catch (NumberFormatException e) {
throw new CyCommandException("Model
numbers must be numeric");
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -52,9 +52,10 @@
public class ChimeraChain implements ChimeraStructuralObject {
/**
- * The model number this chain is a part of
+ * The model/subModel number this chain is a part of
*/
- private float model;
+ private int modelNumber;
+ private int subModelNumber;
/**
* A pointer to the model this chain is a part of
@@ -86,10 +87,12 @@
* Constructor to create a new ChimeraChain
*
* @param model the model number this chain is part of
+ * @param subModel the subModel number this chain is part of
* @param chainId the chain ID for this chain
*/
- public ChimeraChain(float model, String chainId) {
- this.model = model;
+ public ChimeraChain(int model, int subModel, String chainId) {
+ this.modelNumber = model;
+ this.subModelNumber = subModel;
this.chainId = chainId;
residueList = new TreeMap();
}
@@ -185,9 +188,16 @@
*
* @return the model number
*/
- public float getModelNumber() { return model; }
+ public int getModelNumber() { return modelNumber; }
/**
+ * Get the sub-model number for this chain
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber() { return subModelNumber; }
+
+ /**
* Return a string representation of this chain as follows:
* Chain <i>chainId</i> (<i>residue_count</i> residues)
*
@@ -229,9 +239,9 @@
*/
public String toSpec() {
if (chainId.equals("_")) {
- return("#"+model+":.");
+ return("#"+modelNumber+"."+subModelNumber+":.");
} else {
- return("#"+model+":."+chainId);
+
return("#"+modelNumber+"."+subModelNumber+":."+chainId);
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -91,7 +91,7 @@
*/
public ChimeraModel (String inputLine) {
this.name = parseModelName(inputLine);
- this.identifier = parseModelNumber(inputLine);
+ this.modelNumber = parseModelNumber(inputLine);
this.chains = new TreeMap();
this.residues = new TreeMap();
this.residueMap = new HashMap();
@@ -107,7 +107,7 @@
public ChimeraModel (Structure structure, String inputLine) {
this.name = structure.name();
this.structure = structure;
- this.identifier = parseModelNumber(inputLine);
+ this.modelNumber = parseModelNumber(inputLine);
this.chains = new TreeMap();
this.residues = new TreeMap();
this.residueMap = new HashMap();
@@ -214,16 +214,30 @@
*
* @return integer model number
*/
- public float getModelNumber () { return this.identifier; }
+ public int getModelNumber () { return this.modelNumber; }
/**
+ * Get the sub-model number of this model
+ *
+ * @return integer sub-model number
+ */
+ public int getSubModelNumber () { return this.subModelNumber; }
+
+ /**
* Set the model number of this model
*
* @param modelNumber integer model number
*/
- public void setModelNumber (float modelNumber) { this.identifier =
modelNumber; }
+ public void setModelNumber (int modelNumber) { this.modelNumber =
modelNumber; }
/**
+ * Set the sub-model number of this model
+ *
+ * @param subModelNumber integer model number
+ */
+ public void setSubModelNumber (int subModelNumber) {
this.subModelNumber = subModelNumber; }
+
+ /**
* Get the ChimeraModel (required for ChimeraStructuralObject interface)
*
* @return ChimeraModel
@@ -302,7 +316,7 @@
public void addResidue(String chainId, ChimeraResidue residue) {
ChimeraChain chain = null;
if (!chains.containsKey(chainId)) {
- chain = new ChimeraChain(this.identifier, chainId);
+ chain = new ChimeraChain(this.modelNumber,
this.subModelNumber, chainId);
chain.setChimeraModel(this);
chains.put(chainId, chain);
} else {
@@ -326,32 +340,42 @@
if (name.length() > 14)
displayName = name.substring(0,13)+"...";
if (getChainCount() > 0) {
- return ("Node "+nodeName+" [Model #"+identifier+"
"+displayName+" ("+getChainCount()+" chains, "+getResidueCount()+"
residues)]");
+ return ("Node "+nodeName+" [Model "+toSpec()+"
"+displayName+" ("+getChainCount()+" chains, "+getResidueCount()+"
residues)]");
} else if (getResidueCount() > 0) {
- return ("Node "+nodeName+" [Model #"+identifier+"
"+displayName+" ("+getResidueCount()+" residues)]");
+ return ("Node "+nodeName+" [Model "+toSpec()+"
"+displayName+" ("+getResidueCount()+" residues)]");
} else {
- return ("Node "+nodeName+" [Model #"+identifier+"
"+displayName+"]");
+ return ("Node "+nodeName+" [Model "+toSpec()+"
"+displayName+"]");
}
}
/**
* Return the Chimera specification for this model
*/
- public String toSpec() { return ("#"+identifier); }
+ public String toSpec() {
+ if (subModelNumber == 0)
+ return ("#"+modelNumber);
+ return ("#"+modelNumber+"."+subModelNumber);
+ }
/**
* Parse the model number returned by Chimera and return
- * the float value
+ * the int value
*/
- private float parseModelNumber(String inputLine) {
+ private int parseModelNumber(String inputLine) {
int hash = inputLine.indexOf('#');
int space = inputLine.indexOf(' ',hash);
+ int decimal = inputLine.substring(hash+1,space).indexOf('.');
// model number is between hash+1 and space
try {
- Float modelNumber = new
Float(inputLine.substring(hash+1,space));
- return modelNumber.floatValue();
+ subModelNumber = 0;
+ if (decimal > 0) {
+ subModelNumber =
Integer.parseInt(inputLine.substring(decimal+1, space));
+ space = decimal;
+ }
+ modelNumber =
Integer.parseInt(inputLine.substring(hash+1, space));
+ return modelNumber;
} catch (Exception e) {
-
cytoscape.logger.CyLogger.getLogger(ChimeraResidue.class).error("Unexpected
return from Chimera: "+inputLine);
+
cytoscape.logger.CyLogger.getLogger(ChimeraModel.class).error("Unexpected
return from Chimera: "+inputLine);
return -1;
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -57,7 +57,8 @@
private String type; // Residue type
private String index; // Residue index
private String chainId; // ChainID for this residue
- private float modelNumber; // model number for this residue
+ private int modelNumber; // model number for this residue
+ private int subModelNumber; // sub-model number for this residue
private ChimeraModel chimeraModel; // ChimeraModel thie residue is part
of
private Object userData; // user data to associate with this residue
private static HashMap aaNames = null; // a map of amino acid names
@@ -71,10 +72,23 @@
* @param index the index of the residue
* @param modelNumber the model number this residue is part of
*/
- public ChimeraResidue (String type, String index, float modelNumber) {
+ public ChimeraResidue (String type, String index, int modelNumber) {
+ this(type, index, modelNumber, 0);
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type the residue type
+ * @param index the index of the residue
+ * @param modelNumber the model number this residue is part of
+ * @param subModelNumber the sub-model number this residue is part of
+ */
+ public ChimeraResidue (String type, String index, int modelNumber, int
subModelNumber) {
this.type = type;
this.index = index;
this.modelNumber = modelNumber;
+ this.subModelNumber = subModelNumber;
if (aaNames == null)
initNames();
}
@@ -89,11 +103,21 @@
String[] split1 = line.split(":");
+ // TODO: this should be merged with the parse line code in
+ // ChimeraModel
+
// First half has model number -- get the number
int numberOffset = split1[0].indexOf('#');
String model = split1[0].substring(numberOffset+1);
+ int decimalOffset = model.indexOf('.'); // Do we have a
sub-model?
try {
- this.modelNumber = (new Float(model)).floatValue();
+ this.subModelNumber = 0;
+ if (decimalOffset > 0) {
+ this.subModelNumber =
Integer.parseInt(model.substring(decimalOffset+1));
+ this.modelNumber =
Integer.parseInt(model.substring(0, decimalOffset));
+ } else {
+ this.modelNumber = Integer.parseInt(model);
+ }
} catch (Exception e) {
cytoscape.logger.CyLogger.getLogger(ChimeraResidue.class).error("Unexpected
return from Chimera in ChimeraResidue: "+model);
this.modelNumber = -1;
@@ -214,9 +238,16 @@
*
* @return the model number
*/
- public float getModelNumber () { return this.modelNumber; }
+ public int getModelNumber () { return this.modelNumber; }
/**
+ * Get the sub-model number for this residue
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber () { return this.subModelNumber; }
+
+ /**
* Get the model this residue is part of
*
* @return the ChimeraModel
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2010-12-30 17:51:24 UTC (rev 23282)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2010-12-30 19:18:28 UTC (rev 23283)
@@ -48,6 +48,7 @@
List<String> residueList;
CyNode cytoscapeNode;
int modelNumber;
+ int subModelNumber;
StructureType type;
public enum StructureType {PDB_MODEL, MODBASE_MODEL, SMILES};
@@ -69,6 +70,7 @@
this.structureName = name;
this.cytoscapeNode = node;
this.modelNumber = nextModel;
+ this.subModelNumber = 0;
this.residueList = null;
this.type = type;
}
@@ -97,18 +99,25 @@
/**
* Get the modelNumber for this structure
*
- * @return the model number as a float
+ * @return the model number as an int
*/
public int modelNumber() {return this.modelNumber;}
/**
+ * Get the subModelNumber for this structure
+ *
+ * @return the subModel number as an int
+ */
+ public int subModelNumber() {return this.subModelNumber;}
+
+ /**
* Set the modelNumber for this structure
*
* @param number the model number
*/
- public void setModelNumber (float number) {
- Float floatNumber = new Float(number);
- this.modelNumber = floatNumber.intValue();
+ public void setModelNumber (int number, int subNumber) {
+ this.modelNumber = number;
+ this.subModelNumber = subNumber;
if (this.modelNumber >= nextModel) nextModel =
this.modelNumber+1;
}
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