Author: ruschein
Date: 2010-06-28 14:08:43 -0700 (Mon, 28 Jun 2010)
New Revision: 20693
Added:
cytoscape/trunk/src/cytoscape/data/readers/EqnAttrTracker.java
Removed:
cytoscape/trunk/src/cytoscape/data/readers/AttribEquation.java
Modified:
cytoscape/trunk/build.xml
cytoscape/trunk/src/cytoscape/Cytoscape.java
cytoscape/trunk/src/cytoscape/data/readers/CyAttributesReader.java
cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
cytoscape/trunk/src/cytoscape/data/readers/XGMMLParser.java
cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java
Log:
Completely reorganised equation loading to not error out when invalid equations
are encountered.
Modified: cytoscape/trunk/build.xml
===================================================================
--- cytoscape/trunk/build.xml 2010-06-28 20:32:09 UTC (rev 20692)
+++ cytoscape/trunk/build.xml 2010-06-28 21:08:43 UTC (rev 20693)
@@ -271,7 +271,7 @@
target="${java.target_version}"
optimize="on"
includeAntRuntime="false"
- deprecation="yes">
+ deprecation="no">
<classpath refid="classpath" />
<include name="cytoscape/**" />
<src path="${src.dir}" />
Modified: cytoscape/trunk/src/cytoscape/Cytoscape.java
===================================================================
--- cytoscape/trunk/src/cytoscape/Cytoscape.java 2010-06-28 20:32:09 UTC
(rev 20692)
+++ cytoscape/trunk/src/cytoscape/Cytoscape.java 2010-06-28 21:08:43 UTC
(rev 20693)
@@ -1,15 +1,8 @@
/*
File: Cytoscape.java
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -71,6 +64,7 @@
import cytoscape.data.Semantics;
import cytoscape.data.readers.BookmarkReader;
import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.data.readers.EqnAttrTracker;
import cytoscape.data.readers.GraphReader;
import cytoscape.data.readers.NestedNetworkReader;
import cytoscape.data.servers.BioDataServer;
@@ -451,6 +445,14 @@
return nullNetwork;
}
+ private static EqnAttrTracker eqnAttrTracker = null;
+
+ public static EqnAttrTracker getEqnAttrTracker() {
+ if (eqnAttrTracker == null)
+ eqnAttrTracker = new EqnAttrTracker();
+ return eqnAttrTracker;
+ }
+
/**
* Shuts down Cytoscape, after giving plugins time to react.
*
Deleted: cytoscape/trunk/src/cytoscape/data/readers/AttribEquation.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/AttribEquation.java
2010-06-28 20:32:09 UTC (rev 20692)
+++ cytoscape/trunk/src/cytoscape/data/readers/AttribEquation.java
2010-06-28 21:08:43 UTC (rev 20693)
@@ -1,60 +0,0 @@
-/*
- File: AttribEquation.java
-
- Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-package cytoscape.data.readers;
-
-
-/**
- * Utility class used by some readers to record equation attributes for later
evaluation.
- */
-class AttribEquation {
- private final String id;
- private final String attrName;
- private final String equation;
- private final byte dataType;
- private final int lineNumber;
-
- AttribEquation(final String id, final String attrName, final String
equation, final byte dataType, final int lineNumber) {
- this.id = id;
- this.attrName = attrName;
- this.equation = equation;
- this.dataType = dataType;
- this.lineNumber = lineNumber;
- }
-
- AttribEquation(final String id, final String attrName, final String
equation, final byte dataType) {
- this(id, attrName, equation, dataType, -1);
- }
-
- String getID() { return id; }
- String getAttrName() { return attrName; }
- String getEquation() { return equation; }
- byte getDataType() { return dataType; }
- int getLineNumber() { return lineNumber; }
-}
Modified: cytoscape/trunk/src/cytoscape/data/readers/CyAttributesReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/CyAttributesReader.java
2010-06-28 20:32:09 UTC (rev 20692)
+++ cytoscape/trunk/src/cytoscape/data/readers/CyAttributesReader.java
2010-06-28 21:08:43 UTC (rev 20693)
@@ -41,6 +41,7 @@
import java.util.Set;
import java.util.StringTokenizer;
+import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.attr.MultiHashMapDefinition;
import cytoscape.data.writers.CyAttributesWriter;
@@ -64,7 +65,6 @@
private int lineNum;
private boolean doDecoding;
final Map<String, Map<String, Class>> idsToAttribNameToTypeMapMap;
- private List<AttribEquation> attribEquations; // This is where we
collect equations for later addition.
private final CyLogger logger;
@@ -73,7 +73,6 @@
lineNum = 0;
doDecoding =
Boolean.valueOf(System.getProperty(DECODE_PROPERTY, "true"));
idsToAttribNameToTypeMapMap = new HashMap<String, Map<String,
Class>>();
- attribEquations = new ArrayList<AttribEquation>();
}
/**
@@ -87,7 +86,6 @@
public static void loadAttributes(final CyAttributes cyAttrs, final
Reader fileIn) throws IOException {
CyAttributesReader ar = new CyAttributesReader();
ar.loadAttributesInternal(cyAttrs, fileIn);
- ar.addEquations(cyAttrs);
}
private Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
@@ -107,53 +105,7 @@
}
}
- private void addEquations(final CyAttributes cyAttrs) {
- final EqnCompiler compiler = new EqnCompiler();
- final String[] allAttribNames = cyAttrs.getAttributeNames();
- final Class[] allTypes = new Class[allAttribNames.length];
- int index = 0;
- for (final String attribName : allAttribNames) {
- final byte type = cyAttrs.getType(attribName);
- allTypes[index++] =
mapCytoscapeAttribTypeToEqnType(type);
- }
-
- for (final AttribEquation attribEquation : attribEquations) {
- Map<String, Class> attribNameToTypeMap =
idsToAttribNameToTypeMapMap.get(attribEquation.getID());
- if (attribNameToTypeMap == null)
- attribNameToTypeMap = new HashMap<String,
Class>();
- for (int i = 0; i < allAttribNames.length; ++i) {
- if (allTypes[i] != null)
-
attribNameToTypeMap.put(allAttribNames[i], allTypes[i]);
- }
-
- if (compiler.compile(attribEquation.getEquation(),
attribNameToTypeMap))
- cyAttrs.setAttribute(attribEquation.getID(),
attribEquation.getAttrName(), compiler.getEquation(),
-
attribEquation.getDataType());
- else {
- final String errorMessage =
compiler.getLastErrorMsg();
- logger.warn("bad equation on line " +
attribEquation.getLineNumber() + ": " + errorMessage);
- final Class eqnType =
mapCytoscapeAttribTypeToEqnType(attribEquation.getDataType());
- final Equation errorEquation =
Equation.getErrorEquation(attribEquation.getEquation(),
-
eqnType, errorMessage);
- cyAttrs.setAttribute(attribEquation.getID(),
attribEquation.getAttrName(), errorEquation,
-
attribEquation.getDataType());
- }
- }
- }
-
/**
- * Helper function for loadAttributesInternal().
- */
- private void updateMapToMaps(final String id, final String attribName,
final Class attribType,
- final Map<String, Map<String, Class>>
idsToAttribNameToTypeMapMap)
- {
- Map<String, Class> attribNameToTypeMap =
idsToAttribNameToTypeMapMap.get(id);
- if (attribNameToTypeMap == null)
- attribNameToTypeMap = new HashMap<String, Class>();
- attribNameToTypeMap.put(attribName, attribType);
- }
-
- /**
* DOCUMENT ME!
*
* @param cyAttrs DOCUMENT ME!
@@ -303,7 +255,6 @@
}
}
- updateMapToMaps(key, attributeName,
List.class, idsToAttribNameToTypeMapMap);
cyAttrs.setListAttribute(key,
attributeName, elmsBuff);
} else { // Not a list.
val = decodeString(val);
@@ -336,39 +287,40 @@
}
if (equation) {
- final Class javaType;
+ final Class eqnReturnType;
switch (type) {
- case
MultiHashMapDefinition.TYPE_INTEGER:
- javaType = Long.class;
+ case CyAttributes.TYPE_INTEGER:
+ eqnReturnType =
Long.class;
break;
- case
MultiHashMapDefinition.TYPE_FLOATING_POINT:
- javaType = Double.class;
+ case CyAttributes.TYPE_FLOATING:
+ eqnReturnType =
Double.class;
break;
- case
MultiHashMapDefinition.TYPE_BOOLEAN:
- javaType =
Boolean.class;
+ case CyAttributes.TYPE_BOOLEAN:
+ eqnReturnType =
Boolean.class;
break;
- case
MultiHashMapDefinition.TYPE_STRING:
- javaType = String.class;
+ case CyAttributes.TYPE_STRING:
+ eqnReturnType =
String.class;
break;
+ case
CyAttributes.TYPE_SIMPLE_LIST:
+ eqnReturnType =
List.class;
+ break;
default:
- throw new
IllegalStateException("don't know which type to register on line " + lineNum +
"!");
+ final String message =
"don't know which equation return type to register on line " + lineNum + "!";
+
System.err.println(message);
+ logger.warn(message);
+ continue;
}
- updateMapToMaps(key,
attributeName, javaType, idsToAttribNameToTypeMapMap);
- attribEquations.add(new
AttribEquation(key, attributeName, val, type, lineNum));
+ final EqnAttrTracker
eqnAttrTracker = Cytoscape.getEqnAttrTracker();
+
eqnAttrTracker.recordEquation(cyAttrs, key, attributeName, val, eqnReturnType);
}
- else if (type ==
MultiHashMapDefinition.TYPE_INTEGER) {
- updateMapToMaps(key,
attributeName, Long.class, idsToAttribNameToTypeMapMap);
+ else if (type ==
MultiHashMapDefinition.TYPE_INTEGER)
cyAttrs.setAttribute(key,
attributeName, new Integer(val));
- } else if (type ==
MultiHashMapDefinition.TYPE_BOOLEAN) {
- updateMapToMaps(key,
attributeName, Boolean.class, idsToAttribNameToTypeMapMap);
+ else if (type ==
MultiHashMapDefinition.TYPE_BOOLEAN)
cyAttrs.setAttribute(key,
attributeName, new Boolean(val));
- } else if (type ==
MultiHashMapDefinition.TYPE_FLOATING_POINT) {
- updateMapToMaps(key,
attributeName, Double.class, idsToAttribNameToTypeMapMap);
+ else if (type ==
MultiHashMapDefinition.TYPE_FLOATING_POINT)
cyAttrs.setAttribute(key,
attributeName, new Double(val));
- } else {
- updateMapToMaps(key,
attributeName, String.class, idsToAttribNameToTypeMapMap);
+ else
cyAttrs.setAttribute(key,
attributeName, val);
- }
}
}
} catch (Exception e) {
Modified: cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2010-06-28 20:32:09 UTC (rev 20692)
+++ cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2010-06-28 21:08:43 UTC (rev 20693)
@@ -1,15 +1,8 @@
/*
File: CytoscapeSessionReader.java
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -396,7 +389,10 @@
Cytoscape.getDesktop().getVizMapperUI().initializeTableState();
try {
+ final EqnAttrTracker eqnAttrTracker =
Cytoscape.getEqnAttrTracker();
+ eqnAttrTracker.reset();
unzipSessionFromURL(true);
+ eqnAttrTracker.addAllEquations();
} catch (cytoscape.visual.DuplicateCalculatorNameException
dcne) {
logger.warn("Duplicate VS name found. It will be
ignored...", dcne);
}
@@ -507,7 +503,7 @@
* @throws IOException
* @throws JAXBException
*/
- private void unzipSessionFromURL(boolean loadVizmap) throws
IOException, JAXBException, Exception {
+ private void unzipSessionFromURL(final boolean loadVizmap) throws
IOException, JAXBException, Exception {
extractEntry();
logger.info("extractEntry: " + (System.currentTimeMillis() -
start) + " msec.");
@@ -681,14 +677,13 @@
final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
InputStream is = null;
- try {
+ try {
is = URLUtil.getBasicInputStream(cysessionFileURL);
- session = (Cysession) unmarshaller.unmarshal(is);
- }
- finally {
- if (is != null) {
+ session = (Cysession) unmarshaller.unmarshal(is);
+ }
+ finally {
+ if (is != null)
is.close();
- }
}
/*
@@ -698,15 +693,13 @@
sessionID = session.getId();
netMap = new HashMap<String, Network>();
- for (Network curNet : session.getNetworkTree().getNetwork()) {
+ for (Network curNet : session.getNetworkTree().getNetwork())
netMap.put(curNet.getId(), curNet);
- }
walkTree(netMap.get(NETWORK_ROOT), null, cysessionFileURL);
}
private void restoreDesktopState() {
-
// Restore Desktop size
Cytoscape.getDesktop()
.setSize(session.getSessionState().getDesktop().getDesktopSize().getWidth()
@@ -725,18 +718,18 @@
.getComponents();
for (int i = 0; i < desktopFrames.length; i++) {
- Component cmp;
+ Component cmp;
- cmp = desktopFrames[i];
- if (cmp instanceof JInternalFrame) {
- JInternalFrame frame = (JInternalFrame)cmp;
- NetworkFrame nFrame = frameMap.get(frame.getTitle());
+ cmp = desktopFrames[i];
+ if (cmp instanceof JInternalFrame) {
+ JInternalFrame frame = (JInternalFrame)cmp;
+ NetworkFrame nFrame =
frameMap.get(frame.getTitle());
- if (nFrame != null) {
- frame.setSize(nFrame.getWidth().intValue(),
nFrame.getHeight().intValue());
- frame.setLocation(nFrame.getX().intValue(),
nFrame.getY().intValue());
- }
- }
+ if (nFrame != null) {
+
frame.setSize(nFrame.getWidth().intValue(), nFrame.getHeight().intValue());
+
frame.setLocation(nFrame.getX().intValue(), nFrame.getY().intValue());
+ }
+ }
}
}
@@ -750,7 +743,8 @@
* @throws IOException
*/
private void walkTree(final Network currentNetwork, final CyNetwork
parent,
- final Object sessionSource) throws JAXBException,
IOException {
+ final Object sessionSource) throws JAXBException,
IOException
+ {
// Get the list of children under this root
final List<Child> children = currentNetwork.getChild();
@@ -796,14 +790,12 @@
reader = new XGMMLReader(networkStream);
new_network =
Cytoscape.createNetwork(reader, false, parent);
- }
- finally {
- if (networkStream != null) {
+ } finally {
+ if (networkStream != null)
networkStream.close();
- }
}
- } catch (Exception e) {
- String message = "Unable to read XGMML file:
"+childNet.getFilename()+". "+e.getMessage();
+ } catch (final Exception e) {
+ final String message = "Unable to read XGMML
file: " + childNet.getFilename() + ". " + e.getMessage();
logger.error(message, e);
Cytoscape.destroyNetwork(new_network);
if (taskMonitor != null)
@@ -864,9 +856,8 @@
setSelectedEdges(new_network, (SelectedEdges)
childNet.getSelectedEdges());
// Load child networks
- if (childNet.getChild().size() != 0) {
+ if (childNet.getChild().size() != 0)
walkTree(childNet, new_network,
sessionSource);
- }
}
}
}
Copied: cytoscape/trunk/src/cytoscape/data/readers/EqnAttrTracker.java (from
rev 20677, cytoscape/trunk/src/cytoscape/data/readers/XGMMLParser.java)
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/EqnAttrTracker.java
(rev 0)
+++ cytoscape/trunk/src/cytoscape/data/readers/EqnAttrTracker.java
2010-06-28 21:08:43 UTC (rev 20693)
@@ -0,0 +1,198 @@
+/*
+ File: EqnAttrTracker.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.Equation;
+
+
+public class EqnAttrTracker {
+ private enum AttrClass {
+ NODES(Cytoscape.getNodeAttributes()),
+ EDGES(Cytoscape.getEdgeAttributes()),
+ NETWORKS(Cytoscape.getNetworkAttributes());
+
+ private CyAttributes attribs;
+
+ AttrClass(final CyAttributes attribs) { this.attribs = attribs;
}
+
+ CyAttributes getAttribs() { return attribs; }
+ };
+
+
+ private static class AttrInfo {
+ private String id;
+ private String attrName;
+ private String equation;
+ private Class returnType;
+
+ AttrInfo(final String id, final String attrName, final String
equation, final Class returnType) {
+ this.id = id;
+ this.attrName = attrName;
+ this.equation = equation;
+ this.returnType = returnType;
+ }
+
+ String getID() { return id; }
+ String getAttrName() { return attrName; }
+ String getEquation() { return equation; }
+ Class getReturnType() { return returnType; }
+ }
+
+ private CyLogger logger;
+ private List<AttrInfo> nodeAttrs, edgeAttrs, networkAttrs;
+
+ public EqnAttrTracker() {
+ logger = CyLogger.getLogger(EqnAttrTracker.class);
+ nodeAttrs = new ArrayList<AttrInfo>();
+ edgeAttrs = new ArrayList<AttrInfo>();
+ networkAttrs = new ArrayList<AttrInfo>();
+ }
+
+ void reset() {
+ nodeAttrs.clear();
+ edgeAttrs.clear();
+ networkAttrs.clear();
+ }
+
+ void recordEquation(final CyAttributes attribs, final String id, final
String attrName,
+ final String equation, final Class returnType)
+ {
+ if (attribs == AttrClass.NODES.getAttribs())
+ nodeAttrs.add(new AttrInfo(id, attrName, equation,
returnType));
+ else if (attribs == AttrClass.EDGES.getAttribs())
+ edgeAttrs.add(new AttrInfo(id, attrName, equation,
returnType));
+ else if (attribs == AttrClass.NETWORKS.getAttribs())
+ networkAttrs.add(new AttrInfo(id, attrName, equation,
returnType));
+ else
+ throw new IllegalArgumentException("unkown
CyAttributes!");
+
+ if (returnType == Double.class)
+ registerFloat(attribs, id, attrName);
+ else if (returnType == Long.class)
+ registerInteger(attribs, id, attrName);
+ else if (returnType == String.class)
+ registerString(attribs, id, attrName);
+ else if (returnType == Boolean.class)
+ registerBoolean(attribs, id, attrName);
+ else if (returnType == List.class)
+ registerList(attribs, id, attrName);
+ else
+ throw new IllegalArgumentException("unknown retuyrn
type: " + returnType + "!");
+ }
+
+ void addAllEquations() {
+ addEquations(AttrClass.NODES.getAttribs(), nodeAttrs);
+ addEquations(AttrClass.EDGES.getAttribs(), edgeAttrs);
+ addEquations(AttrClass.NETWORKS.getAttribs(), networkAttrs);
+ }
+
+ private void addEquations(final CyAttributes attribs, final
List<AttrInfo> attrInfos) {
+ final EqnCompiler compiler = new EqnCompiler();
+ final String[] allAttribNames = attribs.getAttributeNames();
+ final Class[] allTypes = new Class[allAttribNames.length];
+ final Map<String, Class> attribNameToTypeMap = new
HashMap<String, Class>();
+ int index = 0;
+ for (final String attribName : allAttribNames) {
+ final byte type = attribs.getType(attribName);
+ final Class eqnType =
mapCytoscapeAttribTypeToEqnType(type);
+ if (eqnType != null)
+ attribNameToTypeMap.put(attribName, eqnType);
+ }
+
+ for (final AttrInfo attrInfo : attrInfos) {
+ attribNameToTypeMap.remove(attrInfo.getAttrName());
+
+ if (compiler.compile(attrInfo.getEquation(),
attribNameToTypeMap))
+ attribs.setAttribute(attrInfo.getID(),
attrInfo.getAttrName(), compiler.getEquation());
+ else {
+ final String errorMessage =
compiler.getLastErrorMsg();
+ logger.warn("bad equation on import: " +
errorMessage);
+ final Equation errorEquation =
Equation.getErrorEquation(attrInfo.getEquation(),
+
attrInfo.getReturnType(), errorMessage);
+ attribs.setAttribute(attrInfo.getID(),
attrInfo.getAttrName(), errorEquation);
+ }
+
+ attribNameToTypeMap.put(attrInfo.getAttrName(),
attrInfo.getReturnType());
+ }
+ }
+
+ private static Class mapCytoscapeAttribTypeToEqnType(final byte
attribType) {
+ switch (attribType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.class;
+ case CyAttributes.TYPE_INTEGER:
+ return Long.class;
+ case CyAttributes.TYPE_FLOATING:
+ return Double.class;
+ case CyAttributes.TYPE_STRING:
+ return String.class;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return List.class;
+ default:
+ throw new IllegalStateException("can't map Cytoscape
type " + attribType + " to equation return type!");
+ }
+ }
+
+ private static void registerFloat(final CyAttributes attrs, final
String id, final String attrName) {
+ attrs.setAttribute(id, attrName, 0.0);
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerString(final CyAttributes attrs, final
String id, final String attrName) {
+ attrs.setAttribute(id, attrName, "");
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerInteger(final CyAttributes attrs, final
String id, final String attrName) {
+ attrs.setAttribute(id, attrName, 0);
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerBoolean(final CyAttributes attrs, final
String id, final String attrName) {
+ attrs.setAttribute(id, attrName, true);
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerList(final CyAttributes attrs, final String
id, final String attrName) {
+ attrs.setListAttribute(id, attrName, new ArrayList());
+ attrs.deleteAttribute(id, attrName);
+ }
+}
Modified: cytoscape/trunk/src/cytoscape/data/readers/XGMMLParser.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/XGMMLParser.java 2010-06-28
20:32:09 UTC (rev 20692)
+++ cytoscape/trunk/src/cytoscape/data/readers/XGMMLParser.java 2010-06-28
21:08:43 UTC (rev 20693)
@@ -43,9 +43,6 @@
import cytoscape.util.intr.IntEnumerator;
import cytoscape.logger.CyLogger;
-import org.cytoscape.equations.EqnCompiler;
-import org.cytoscape.equations.Equation;
-
import org.xml.sax.helpers.DefaultHandler;
import org.xml.sax.helpers.AttributesImpl;
import org.xml.sax.Attributes;
@@ -118,78 +115,6 @@
class XGMMLParser extends DefaultHandler {
- private enum AttrClass {
- NODES(Cytoscape.getNodeAttributes()),
- EDGES(Cytoscape.getEdgeAttributes()),
- NETWORKS(Cytoscape.getNetworkAttributes());
-
- private CyAttributes attribs;
-
- AttrClass(final CyAttributes attribs) { this.attribs = attribs;
}
-
- CyAttributes getAttribs() { return attribs; }
- };
-
- class AttrNameToTypeMaps {
- private final Map<String, Class> attribNameToTypeMapForNodes;
- private final Map<String, Class> attribNameToTypeMapForEdges;
- private final Map<String, Class> attribNameToTypeMapForNetworks;
-
- AttrNameToTypeMaps() {
- attribNameToTypeMapForNodes = new HashMap<String,
Class>();
- attribNameToTypeMapForEdges = new HashMap<String,
Class>();
- attribNameToTypeMapForNetworks = new HashMap<String,
Class>();
- }
-
- void put(final String attrName, final Class attrType, final
AttrClass attrClass) {
- switch (attrClass) {
- case NODES:
- attribNameToTypeMapForNodes.put(attrName,
attrType);
- break;
- case EDGES:
- attribNameToTypeMapForEdges.put(attrName,
attrType);
- break;
- case NETWORKS:
- attribNameToTypeMapForNetworks.put(attrName,
attrType);
- break;
- }
- }
-
- Map<String, Class> getAttribNameToTypeMapForNodes() { return
attribNameToTypeMapForNodes; }
- Map<String, Class> getAttribNameToTypeMapForEdges() { return
attribNameToTypeMapForEdges; }
- Map<String, Class> getAttribNameToTypeMapForNetworks() { return
attribNameToTypeMapForNetworks; }
- }
-
- class AttrEqnLists {
- private final List<AttribEquation> nodeEquations;
- private final List<AttribEquation> edgeEquations;
- private final List<AttribEquation> networkEquations;
-
- AttrEqnLists() {
- nodeEquations = new ArrayList<AttribEquation>();
- edgeEquations = new ArrayList<AttribEquation>();
- networkEquations = new ArrayList<AttribEquation>();
- }
-
- void add(final AttribEquation equation, final AttrClass
attrClass) {
- switch (attrClass) {
- case NODES:
- nodeEquations.add(equation);
- break;
- case EDGES:
- edgeEquations.add(equation);
- break;
- case NETWORKS:
- networkEquations.add(equation);
- break;
- }
- }
-
- List<AttribEquation> getNodeEquations() { return nodeEquations;
}
- List<AttribEquation> getEdgeEquations() { return edgeEquations;
}
- List<AttribEquation> getNetworkEquations() { return
networkEquations; }
- }
-
final static String XLINK = "http://www.w3.org/1999/xlink";;
final static String RDF = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";;
final static String DUBLINCORE = "http://purl.org/dc/elements/1.1/";;
@@ -245,10 +170,7 @@
private ParseState attState = ParseState.NONE;
private String currentAttributeID = null;
private CyAttributes currentAttributes = null;
- private AttrClass currentAttrClass = null;
private String objectTarget = null;
- private AttrNameToTypeMaps attrNameToTypeMaps;
- private AttrEqnLists attrEqnLists;
/* Complex attribute data */
private int level = 0;
@@ -268,6 +190,8 @@
/* Y handle */
private String edgeBendY = null;
+ private EqnAttrTracker eqnAttrTracker = null;
+
/**
* Main parse table. This table controls the state machine, and follows
* the standard format for a state machine:
@@ -586,8 +510,7 @@
nodeGraphicsMap = new HashMap();
edgeGraphicsMap = new HashMap();
idMap = new HashMap();
- attrNameToTypeMaps = new AttrNameToTypeMaps();
- attrEqnLists = new AttrEqnLists();
+ eqnAttrTracker = Cytoscape.getEqnAttrTracker();
}
@@ -617,19 +540,6 @@
}
- void compileAndAddEquationAttribs() {
- compileAndAddEquationAttribs(attrEqnLists.getNodeEquations(),
-
attrNameToTypeMaps.getAttribNameToTypeMapForNodes(),
- Cytoscape.getNodeAttributes());
- compileAndAddEquationAttribs(attrEqnLists.getEdgeEquations(),
-
attrNameToTypeMaps.getAttribNameToTypeMapForEdges(),
- Cytoscape.getEdgeAttributes());
- compileAndAddEquationAttribs(attrEqnLists.getNetworkEquations(),
-
attrNameToTypeMaps.getAttribNameToTypeMapForNetworks(),
- Cytoscape.getNetworkAttributes());
- }
-
-
private Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
switch (attribType) {
case CyAttributes.TYPE_BOOLEAN:
@@ -648,31 +558,6 @@
}
- private void compileAndAddEquationAttribs(final List<AttribEquation>
attribEquations,
- final Map<String, Class>
attribNameToTypeMap,
- final CyAttributes attribs)
- {
- attribNameToTypeMap.put("ID", String.class);
- final EqnCompiler compiler = new EqnCompiler();
- for (final AttribEquation attribEquation : attribEquations) {
- if (compiler.compile(attribEquation.getEquation(),
attribNameToTypeMap))
- attribs.setAttribute(attribEquation.getID(),
attribEquation.getAttrName(),
- compiler.getEquation(),
attribEquation.getDataType());
- else {
- final String errorMessage =
compiler.getLastErrorMsg();
- logger.warn("failed to compile an equation in
an XGMML input file ("
- + errorMessage + ")!");
- final Equation errorEquation =
-
Equation.getErrorEquation(attribEquation.getEquation(),
-
mapCytoscapeAttribTypeToEqnType(attribEquation.getDataType()),
- errorMessage);
- attribs.setAttribute(attribEquation.getID(),
attribEquation.getAttrName(),
- errorEquation,
attribEquation.getDataType());
- }
- }
- }
-
-
HashMap<CyNode, Attributes> getNodeGraphics() {
return nodeGraphicsMap;
}
@@ -891,7 +776,6 @@
class HandleNetworkAttribute implements Handler {
public ParseState handle(String tag, Attributes atts,
ParseState current) throws SAXException {
currentAttributes = Cytoscape.getNetworkAttributes();
- currentAttrClass = AttrClass.NETWORKS;
attState = current;
ParseState nextState = current;
// Look for "special" network attributes
@@ -964,7 +848,6 @@
}
currentAttributes = Cytoscape.getNodeAttributes();
- currentAttrClass = AttrClass.NODES;
objectTarget = currentNode.getIdentifier();
ParseState nextState = handleAttribute(atts,
currentAttributes, objectTarget);
@@ -1042,20 +925,7 @@
class handleEdgeAttribute implements Handler {
public ParseState handle(String tag, Attributes atts,
ParseState current) throws SAXException {
attState = current;
- // logger.debug("Edge attribute:
"+printAttribute(atts));
- /*
- if (atts.getValue("name").startsWith("edge.")) {
- // Yes, add it to our nodeGraphicsMap
- String name =
atts.getValue("name").substring(5);
- String value = atts.getValue("value");
- if (!edgeGraphicsMap.containsKey(currentEdge)) {
- edgeGraphicsMap.put(currentEdge, new
AttributesImpl());
- }
-
((AttributesImpl)edgeGraphicsMap.get(currentEdge)).addAttribute("", "", name,
"string", value);
- }
- */
currentAttributes = Cytoscape.getEdgeAttributes();
- currentAttrClass = AttrClass.EDGES;
if (currentEdge != null)
objectTarget = currentEdge.getIdentifier();
else
@@ -1071,7 +941,6 @@
class handleEdgeGraphics implements Handler {
public ParseState handle(String tag, Attributes atts,
ParseState current) throws SAXException {
- // logger.debug("Atts for
"+currentEdge.getIdentifier()+": "+printAttributes(atts));
if (tag.equals("graphics")) {
if (edgeGraphicsMap.containsKey(currentEdge)) {
addAttributes(edgeGraphicsMap.get(currentEdge),atts);
@@ -1550,36 +1419,32 @@
switch (objType) {
case BOOLEAN:
if (obj != null && name != null && id != null) {
- attrNameToTypeMaps.put(name, Boolean.class,
currentAttrClass);
if (equation)
- attrEqnLists.add(new AttribEquation(id,
name, (String)obj, MultiHashMapDefinition.TYPE_BOOLEAN), currentAttrClass);
+ eqnAttrTracker.recordEquation(cyAtts,
id, name, (String)obj, Boolean.class);
else
cyAtts.setAttribute(id, name,
(Boolean)obj);
}
break;
case REAL:
if (obj != null && name != null && id != null) {
- attrNameToTypeMaps.put(name, Double.class,
currentAttrClass);
if (equation)
- attrEqnLists.add(new AttribEquation(id,
name, (String)obj, MultiHashMapDefinition.TYPE_FLOATING_POINT),
currentAttrClass);
+ eqnAttrTracker.recordEquation(cyAtts,
id, name, (String)obj, Double.class);
else
cyAtts.setAttribute(id, name,
(Double)obj);
}
break;
case INTEGER:
if (obj != null && name != null && id != null) {
- attrNameToTypeMaps.put(name, Long.class,
currentAttrClass);
if (equation)
- attrEqnLists.add(new AttribEquation(id,
name, (String)obj, MultiHashMapDefinition.TYPE_INTEGER), currentAttrClass);
+ eqnAttrTracker.recordEquation(cyAtts,
id, name, (String)obj, Long.class);
else
cyAtts.setAttribute(id, name,
(Integer)obj);
}
break;
case STRING:
if (obj != null && name != null && id != null) {
- attrNameToTypeMaps.put(name, String.class,
currentAttrClass);
if (equation)
- attrEqnLists.add(new AttribEquation(id,
name, (String)obj, MultiHashMapDefinition.TYPE_STRING), currentAttrClass);
+ eqnAttrTracker.recordEquation(cyAtts,
id, name, (String)obj, String.class);
else
cyAtts.setAttribute(id, name,
(String)obj);
}
@@ -1593,22 +1458,16 @@
// must make sure to clear out any existing values before we
parse.
case LIST:
currentAttributeID = name;
- if (id != null && cyAtts.hasAttribute(id, name)) {
+ if (id != null && cyAtts.hasAttribute(id, name))
cyAtts.deleteAttribute(id,name);
- if (name != null)
- attrNameToTypeMaps.put(name,
List.class, currentAttrClass);
- }
listAttrHolder = new ArrayList();
return ParseState.LISTATT;
case MAP:
currentAttributeID = name;
- if (id != null && cyAtts.hasAttribute(id, name)) {
+ if (id != null && cyAtts.hasAttribute(id, name))
cyAtts.deleteAttribute(id,name);
- if (name != null)
- attrNameToTypeMaps.put(name,
Map.class, currentAttrClass);
- }
mapAttrHolder = new HashMap();
Modified: cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java 2010-06-28
20:32:09 UTC (rev 20692)
+++ cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java 2010-06-28
21:08:43 UTC (rev 20693)
@@ -303,7 +303,6 @@
pa.setErrorHandler(parser);
pa.parse(new
InputSource(networkStream));
networkName = parser.getNetworkName();
- parser.compileAndAddEquationAttribs();
} catch (OutOfMemoryError oe) {
/*
* It's not generally a good idea to
catch OutOfMemoryErrors, but in
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