Author: Christian Lopes
Date: 2011-05-12 14:50:04 -0700 (Thu, 12 May 2011)
New Revision: 25036
Modified:
core3/io-impl/trunk/pom.xml
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
Log:
XGMML reading: fixed error when parsing att tags that are equations (note:
equations are not being recreated from XGMML yet).
XGMML writing: serializing more visual properties as part of the graphics tag;
fixed code that serializes equations to att tags.
Modified: core3/io-impl/trunk/pom.xml
===================================================================
--- core3/io-impl/trunk/pom.xml 2011-05-12 21:40:45 UTC (rev 25035)
+++ core3/io-impl/trunk/pom.xml 2011-05-12 21:50:04 UTC (rev 25036)
@@ -123,6 +123,11 @@
<version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>equations-api</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
<groupId>com.lowagie.text</groupId>
<artifactId>com.springsource.com.lowagie.text</artifactId>
<version>2.0.8</version>
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-05-12 21:40:45 UTC (rev 25035)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-05-12 21:50:04 UTC (rev 25036)
@@ -275,36 +275,45 @@
public ParseState handleAttribute(Attributes atts, CyRow row) throws
SAXParseException {
String name = atts.getValue("name");
String type = atts.getValue("type");
+ String equationStr = atts.getValue("cy:equation");
+
ObjectType objType = typeMap.getType(type);
- Object obj = getTypedAttributeValue(objType, atts);
CyColumn column = row.getTable().getColumn(name);
- switch (objType) {
- case BOOLEAN:
- if (obj != null) setAttribute(row, name, (Boolean) obj);
- break;
- case REAL:
- if (obj != null) setAttribute(row, name, (Double) obj);
- break;
- case INTEGER:
- if (obj != null) setAttribute(row, name, (Integer) obj);
- break;
- case STRING:
- if (obj != null) setAttribute(row, name, (String) obj);
- break;
- // We need to be *very* careful. Because we duplicate attributes
for
- // each network we write out, we wind up reading and processing
each
- // attribute multiple times, once for each network. This isn't a
problem
- // for "base" attributes, but is a significant problem for
attributes
- // like LIST and MAP where we add to the attribute as we parse.
So, we
- // must make sure to clear out any existing values before we parse.
- case LIST:
- manager.currentAttributeID = name;
- if (column != null &&
List.class.isAssignableFrom(column.getType()))
- row.set(name, null);
- return ParseState.LISTATT;
+ if (equationStr == null) {
+ // Regular attribute value (NOT an equation)...
+ Object obj = getTypedAttributeValue(objType, atts);
+
+ switch (objType) {
+ case BOOLEAN:
+ if (obj != null && name != null) setAttribute(row, name,
(Boolean) obj);
+ break;
+ case REAL:
+ if (obj != null && name != null) setAttribute(row, name,
(Double) obj);
+ break;
+ case INTEGER:
+ if (obj != null && name != null) setAttribute(row, name,
(Integer) obj);
+ break;
+ case STRING:
+ if (obj != null && name != null) setAttribute(row, name,
(String) obj);
+ break;
+ // We need to be *very* careful. Because we duplicate
attributes for
+ // each network we write out, we wind up reading and
processing each
+ // attribute multiple times, once for each network. This isn't
a problem
+ // for "base" attributes, but is a significant problem for
attributes
+ // like LIST and MAP where we add to the attribute as we
parse. So, we
+ // must make sure to clear out any existing values before we
parse.
+ case LIST:
+ manager.currentAttributeID = name;
+ if (column != null &&
List.class.isAssignableFrom(column.getType())) row.set(name, null);
+ return ParseState.LISTATT;
+ }
+ } else {
+ // It is an equation...
+ if (name != null) manager.addEquation(name, row, equationStr);
+ if (objType.equals(ObjectType.LIST)) return ParseState.LISTATT;
}
-
+
return ParseState.NONE;
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-05-12 21:40:45 UTC (rev 25035)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-05-12 21:50:04 UTC (rev 25036)
@@ -189,4 +189,9 @@
public CyNetwork getNetwork() {
return this.network;
}
+
+ public void addEquation(String columnName, CyRow row, String equationStr) {
+ // TODO: should just store all the equation strings per columnName/row
+ // TODO: create all equations after all CyTables/CyColumns are loaded?
+ }
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-05-12 21:40:45 UTC (rev 25035)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-05-12 21:50:04 UTC (rev 25036)
@@ -30,17 +30,15 @@
import java.awt.Color;
import java.awt.Font;
import java.awt.Paint;
-import java.awt.geom.Point2D;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
-import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
-import java.util.Map;
import java.util.Set;
+import org.cytoscape.equations.Equation;
import org.cytoscape.io.write.CyWriter;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
@@ -55,51 +53,16 @@
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+import org.cytoscape.view.presentation.property.RichVisualLexicon;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
-enum GraphicsType {
- ARC("arc"),
- BITMAP("bitmap"),
- IMAGE("image"),
- LINE("line"),
- OVAL("oval"),
- POLYGON("polygon"),
- RECTANGLE("rectangle"),
- TEXT("text"),
- BOX("box"),
- CIRCLE("circle"),
- VER_ELLIPSIS("ver_ellipsis"),
- HOR_ELLIPSIS("hor_ellipsis"),
- RHOMBUS("rhombus"),
- TRIANGLE("triangle"),
- PENTAGON("pentagon"),
- HEXAGON("hexagon"),
- OCTAGON("octagon"),
- ELLIPSE("ellipse"),
- DIAMOND("diamond"),
- PARALLELOGRAM("parallelogram"),
- ROUNDED_RECTANGLE("rounded_rectangle");
-
- private final String value;
-
- GraphicsType(String v) {
- value = v;
- }
-
- String value() {
- return value;
- }
-}
-
enum ObjectType {
LIST("list"),
STRING("string"),
REAL("real"),
INTEGER("integer"),
- BOOLEAN("boolean"),
- MAP("map"),
- COMPLEX("complex");
+ BOOLEAN("boolean");
private final String value;
@@ -516,12 +479,13 @@
for (VisualProperty vp : visualProperties) {
if (!vp.getTargetDataType().isAssignableFrom(element.getClass()))
continue;
-
+
String key = getGraphicsKey(vp);
Object value = view.getVisualProperty(vp);
if (key != null && value != null) {
- writeAttributePair(key, vp.toSerializableString(value));
+ value = vp.toSerializableString(value);
+ if (value != null) writeAttributePair(key, value);
}
}
@@ -559,24 +523,24 @@
if (vp.equals(MinimalVisualLexicon.NODE_WIDTH)) return "w";
if (vp.equals(MinimalVisualLexicon.NODE_HEIGHT)) return "h";
if (vp.equals(MinimalVisualLexicon.NODE_FILL_COLOR)) return "fill";
- // TODO: Visual Lexicon has to expose these properties
- // if (vp.equals(TwoDVisualLexicon.NODE_SHAPE)) return "type";
- // if (vp.equals(TwoDVisualLexicon.NODE_)) return "wth";
- // if (vp.equals(TwoDVisualLexicon.NODE_)) return "outline";
- // if (vp.equals(TwoDVisualLexicon.NODE_)) return
"cy:nodeTransparency";
- // if (vp.equals(TwoDVisualLexicon.NODE_)) return
"cy:borderLineType";
- // if (vp.equals(TwoDVisualLexicon.NODE_)) return
"cy:nodeLabelFont";
+ if (vp.equals(RichVisualLexicon.NODE_SHAPE)) return "type";
+ if (vp.equals(RichVisualLexicon.NODE_BORDER_WIDTH)) return "width";
+ if (vp.equals(RichVisualLexicon.NODE_BORDER_PAINT)) return "outline";
+ if (vp.equals(RichVisualLexicon.NODE_TRANSPARENCY)) return
"cy:nodeTransparency";
+ if (vp.equals(RichVisualLexicon.NODE_BORDER_LINE_TYPE)) return
"cy:borderLineType";
+ if (vp.equals(RichVisualLexicon.NODE_LABEL)) return "cy:nodeLabelFont";
// Edges
if (vp.equals(MinimalVisualLexicon.EDGE_WIDTH)) return "width";
- if (vp.equals(MinimalVisualLexicon.EDGE_PAINT)) return "fill";
+ if (vp.equals(RichVisualLexicon.EDGE_STROKE_UNSELECTED_PAINT)) return
"fill";
+ if (vp.equals(MinimalVisualLexicon.EDGE_LABEL)) return
"cy:edgeLabelFont";
+ if (vp.equals(RichVisualLexicon.EDGE_LINE_TYPE)) return
"cy:edgeLineType";
// TODO:
// "cy:sourceArrow"
// "cy:targetArrow"
// "cy:sourceArrowColor"
// "cy:targetArrowColor"
- // "cy:edgeLabelFont"
- // "cy:edgeLineType"
+ // "cy:curved"
return null;
}
@@ -600,53 +564,49 @@
if (column == null) return;
final Class<?> attType = column.getType();
- String value = null;
- String type = null;
+ Equation equation = null;
+ Object rawValue = row.getRaw(attName);
+ if (rawValue instanceof Equation) equation = (Equation) rawValue;
- // TODO: Equations
- // final Equation equation = row.getEquation(id, attributeName);
-
if (attType == Double.class) {
- // if (equation != null) {
- // writeEquationAttributeXML(attName,
ObjectType.REAL, equation.toString(),
- // true, hidden,
editable);
- // } else {
- Double dAttr = row.get(attName, Double.class);
- writeAttributeXML(attName, ObjectType.REAL, dAttr, true);
- // }
+ if (equation != null) {
+ writeEquationAttributeXML(attName, ObjectType.REAL,
equation.toString(), true);
+ } else {
+ Double dAttr = row.get(attName, Double.class);
+ writeAttributeXML(attName, ObjectType.REAL, dAttr, true);
+ }
} else {
if (attType == Integer.class) {
- // if (equation != null) {
- // writeEquationAttributeXML(attName,
ObjectType.INTEGER, equation.toString(), true, hidden, editable);
- // } else {
- Integer iAttr = row.get(attName, Integer.class);
- writeAttributeXML(attName, ObjectType.INTEGER, iAttr, true);
- // }
+ if (equation != null) {
+ writeEquationAttributeXML(attName, ObjectType.INTEGER,
equation.toString(), true);
+ } else {
+ Integer iAttr = row.get(attName, Integer.class);
+ writeAttributeXML(attName, ObjectType.INTEGER, iAttr,
true);
+ }
} else if (attType == String.class) {
- // if (equation != null) {
- // writeEquationAttributeXML(attName,
ObjectType.STRING, equation.toString(),
- // true, hidden,
editable);
- // } else {
- String sAttr = row.get(attName, String.class);
- // Protect tabs and returns
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
+ if (equation != null) {
+ writeEquationAttributeXML(attName, ObjectType.STRING,
equation.toString(), true);
+ } else {
+ String sAttr = row.get(attName, String.class);
+ // Protect tabs and returns
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
+ // TODO: nested networks
+ // if
(attName.equals(CyNode.NESTED_NETWORK_ID_ATTR)) {
+ // // This is a special attribute for
nested network.
+ // sAttr =
Cytoscape.getNetwork(sAttr).getTitle();
+ // }
+ writeAttributeXML(attName, ObjectType.STRING, sAttr, true);
}
- // TODO: nested networks
- // if
(attName.equals(CyNode.NESTED_NETWORK_ID_ATTR)) {
- // // This is a special attribute for
nested network.
- // sAttr =
Cytoscape.getNetwork(sAttr).getTitle();
- // }
- writeAttributeXML(attName, ObjectType.STRING, sAttr, true);
- // }
} else if (attType == Boolean.class) {
- // if (equation != null) {
- // writeEquationAttributeXML(attName,
ObjectType.BOOLEAN, equation.toString(), true, hidden, editable);
- // } else {
- Boolean bAttr = row.get(attName, Boolean.class);
- writeAttributeXML(attName, ObjectType.BOOLEAN, bAttr, true);
- // }
+ if (equation != null) {
+ writeEquationAttributeXML(attName, ObjectType.BOOLEAN,
equation.toString(), true);
+ } else {
+ Boolean bAttr = row.get(attName, Boolean.class);
+ writeAttributeXML(attName, ObjectType.BOOLEAN, bAttr,
true);
+ }
} else if (attType == List.class) {
final List<?> listAttr = row.getList(attName,
column.getListElementType());
writeAttributeXML(attName, ObjectType.LIST, null, false);
@@ -667,162 +627,11 @@
depth--;
}
writeAttributeXML(null, null, null, true);
- } else if (attType == Map.class) {
- // process SIMPLE MAP
- // get the attribute map
- final Map mapAttr = row.get(attName, Map.class);
- writeAttributeXML(attName, ObjectType.MAP, null, false);
-
- if (mapAttr != null) {
- depth++;
- // interate through the map
- for (Object obj : mapAttr.keySet()) {
- // get the attribute from the map
- String key = (String) obj;
- Object val = mapAttr.get(key);
- String sAttr = val.toString();
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
- }
-
- writeAttributeXML(key, checkType(val), sAttr, true);
- }
- depth--;
- }
- writeAttributeXML(null, null, null, true);
}
}
-
- // TODO: process COMPLEX MAP
- // else if (attType == CyAttributes.TYPE_COMPLEX) {
- // MultiHashMap mmap = attributes.getMultiHashMap();
- // MultiHashMapDefinition mmapDef =
attributes.getMultiHashMapDefinition();
- //
- // // get the number & types of dimensions
- // byte[] dimTypes =
mmapDef.getAttributeKeyspaceDimensionTypes(attName);
- //
- // // Check to see if id has value assigned to attribute
- // if (!objectHasKey(id, attributes, attName)) {
- // return;
- // }
- // // Output the first <att>
- // writeAttributeXML(attName, ObjectType.COMPLEX,
String.valueOf(dimTypes.length), false, hidden, editable);
- //
- // // grab the complex attribute structure
- // Map complexAttributeStructure =
getComplexAttributeStructure(mmap, id, attributeName, null,
- //
0, dimTypes.length);
- //
- // // determine val type, get its string equivalent to
store in XGMML
- // ObjectType valType =
getType(mmapDef.getAttributeValueType(attributeName));
- //
- // depth++;
- // // walk the structure
- // writeComplexAttribute(complexAttributeStructure,
valType, dimTypes, 0);
- // depth--;
- // // Close
- // writeAttributeXML(null, null, null, true);
- // }
}
/**
- * Returns a map where the key(s) are each key in the attribute key space,
- * and the value is another map or the attribute value.
- *
- * For example, if the following key:
- *
- * {externalref1}{authors}{1} pointed to the following value:
- *
- * "author 1 name",
- *
- * Then we would have a Map where the key is externalref1, the value is a
- * Map where the key is {authors}, the value is a Map where the key is {1},
- * the value is "author 1 name".
- *
- * @param mmap -
- * reference to MultiHashMap used by CyAttributes
- * @param id -
- * id of node, edge or network
- * @param attributeName -
- * name of attribute
- * @param keys -
- * array of objects which store attribute keys
- * @param keysIndex -
- * index into keys array we should add the next key
- * @param numKeyDimensions -
- * the number of keys used for given attribute name
- * @return Map - ref to Map interface
- private Map<Object,Object> getComplexAttributeStructure(MultiHashMap mmap,
String id, String attributeName,
- Object[] keys, int keysIndex, int
numKeyDimensions) {
- // are we done?
- if (keysIndex == numKeyDimensions)
- return null;
-
- // the hashmap to return
- Map<Object,Object> keyHashMap = new HashMap<Object,Object>();
-
- // create a new object array to store keys for this interation
- // copy all existing keys into it
- Object[] newKeys = new Object[keysIndex + 1];
-
- for (int lc = 0; lc < keysIndex; lc++) {
- newKeys[lc] = keys[lc];
- }
-
- // get the key span
- Iterator keyspan = mmap.getAttributeKeyspan(id, attributeName, keys);
-
- while (keyspan.hasNext()) {
- Object newKey = keyspan.next();
- newKeys[keysIndex] = newKey;
-
- Map nextLevelMap = getComplexAttributeStructure(mmap, id,
attributeName, newKeys,
- keysIndex + 1,
numKeyDimensions);
- Object objectToStore = (nextLevelMap == null)
- ? mmap.getAttributeValue(id,
attributeName, newKeys) : nextLevelMap;
- keyHashMap.put(newKey, objectToStore);
- }
- return keyHashMap;
- }
- */
-
- /**
- * This method is a recursive routine to output a complex attribute.
- *
- * @param complexAttributeStructure the structure of the attribute
- * @param type the type of the attribute
- * @param dimTypes the array of dimension types
- * @param dimTypesIndex which dimType we're working on
- private void writeComplexAttribute(Map complexAttributeStructure,
ObjectType type,
- byte[] dimTypes, int dimTypesIndex)
throws IOException {
- for (Object key: complexAttributeStructure.keySet()) {
- Object possibleAttributeValue =
complexAttributeStructure.get(key);
-
- // Is this a leaf or are we still dealing with maps?
- if (possibleAttributeValue instanceof Map) {
- // Another map
- writeAttributeXML(key.toString(),
getType(dimTypes[dimTypesIndex]),
- String.valueOf(((Map)
possibleAttributeValue).size()), false);
- // Recurse
- depth++;
- writeComplexAttribute((Map)possibleAttributeValue,
type, dimTypes, dimTypesIndex+1);
- depth--;
- // Close
- writeAttributeXML(null, null, null, true);
- } else {
- // Final key
- writeAttributeXML(key.toString(),
getType(dimTypes[dimTypesIndex]),
- String.valueOf(1), false);
- depth++;
- writeAttributeXML(null, type,
possibleAttributeValue.toString(), true);
- depth--;
- writeAttributeXML(null, null, null, true);
- }
- }
- }
- */
-
- /**
* writeAttributeXML outputs an XGMML attribute
*
* @param name is the name of the attribute we are outputting
@@ -875,35 +684,33 @@
}
/**
- * Convert enumerated shapes into human-readable string.<br>
+ * writeEquationAttributeXML outputs an XGMML attribute
*
- * @param type
- * Enumerated node shape.
- * @return Shape in string.
+ * @param name is the name of the attribute we are outputting
+ * @param type is the XGMML type of the attribute
+ * @param equation is the textual representation of the formula we're
outputting
+ * @param end is a flag to tell us if the attribute should include a tag
end
+ * @param hidden is a flag to tell us if the attribute should be hidden
+ * @param editable is a flag to tell us if the attribute should be user
editable
+ *
+ * @throws IOException
*/
- private GraphicsType number2shape(final int type) {
- switch (type) {
- // TODO:
- // case NodeView.ELLIPSE:
- // return GraphicsType.ELLIPSE;
- // case NodeView.RECTANGLE:
- // return GraphicsType.RECTANGLE;
- // case NodeView.ROUNDED_RECTANGLE:
- // return GraphicsType.ROUNDED_RECTANGLE;
- // case NodeView.DIAMOND:
- // return GraphicsType.DIAMOND;
- // case NodeView.HEXAGON:
- // return GraphicsType.HEXAGON;
- // case NodeView.OCTAGON:
- // return GraphicsType.OCTAGON;
- // case NodeView.PARALELLOGRAM:
- // return GraphicsType.PARALLELOGRAM;
- // case NodeView.TRIANGLE:
- // return GraphicsType.TRIANGLE;
- // case NodeView.VEE:
- // return GraphicsType.VEE;
- default:
- return null;
+ private void writeEquationAttributeXML(final String name,
+ final ObjectType type,
+ final String equation,
+ final boolean end) throws
IOException {
+ if (name == null && type == null)
+ writeElement("</att>\n");
+ else {
+ writeElement("<att type=" + quote(type.toString()));
+ if (name != null) writer.write(" name=" + quote(name));
+ writer.write(" value=" + quote(equation));
+ writer.write(" cy:equation=\"true\"");
+
+ if (end)
+ writer.write("/>\n");
+ else
+ writer.write(">\n");
}
}
@@ -962,31 +769,6 @@
}
}
- /**
- * Given a byte describing a MultiHashMapDefinition TYPE_*, return the
- * proper XGMMLWriter type.
- *
- * @param dimType -
- * byte as described in MultiHashMapDefinition
- * @return the type pointed to by this dim
- private ObjectType getType(final byte dimType) {
- if (dimType == MultiHashMapDefinition.TYPE_BOOLEAN)
- return ObjectType.BOOLEAN;
-
- if (dimType == MultiHashMapDefinition.TYPE_FLOATING_POINT)
- return ObjectType.REAL;
-
- if (dimType == MultiHashMapDefinition.TYPE_INTEGER)
- return ObjectType.INTEGER;
-
- if (dimType == MultiHashMapDefinition.TYPE_STRING)
- return ObjectType.STRING;
-
- // houston we have a problem
- return null;
- }
- */
-
private String getNetworkName(CyNetwork network) {
String name = encode(network.getCyRow().get("name", String.class));
if (name == null) name = "UNDEFINED";
@@ -1049,29 +831,4 @@
private String quote(String str) {
return '"' + encode(str) + '"';
}
-
- /**
- * Determines if object has key in multihashmap
- *
- * @param id -
- * node, edge, network id
- * @param attributes -
- * CyAttributes ref
- * @param attributeName -
- * attribute name
- *
- * @return boolean
- private boolean objectHasKey(String id, CyAttributes attributes, String
attributeName) {
- MultiHashMap mmap = attributes.getMultiHashMap();
-
- for (Iterator keysIt = mmap.getObjectKeys(attributeName);
keysIt.hasNext();) {
- String thisKey = (String) keysIt.next();
-
- if ((thisKey != null) && thisKey.equals(id)) {
- return true;
- }
- }
- return false;
- }
- */
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
