Author: Christian Lopes
Date: 2011-06-30 12:57:00 -0700 (Thu, 30 Jun 2011)
New Revision: 25986
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
Log:
closes #302 (XGMML Export: equations should not be exported)
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
2011-06-30 19:47:49 UTC (rev 25985)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-06-30 19:57:00 UTC (rev 25986)
@@ -39,7 +39,6 @@
import java.util.List;
import java.util.Map;
-import org.cytoscape.equations.Equation;
import org.cytoscape.io.internal.util.UnrecognizedVisualPropertyManager;
import org.cytoscape.io.write.CyWriter;
import org.cytoscape.model.CyColumn;
@@ -612,79 +611,58 @@
* @throws IOException
*/
private void writeAttribute(final CyRow row, final String attName) throws
IOException {
- // create an attribute and its type:
- final CyColumn column = row.getTable().getColumn(attName);
- if (column == null) return;
- final Class<?> attType = column.getType();
+ // create an attribute and its type:
+ final CyColumn column = row.getTable().getColumn(attName);
+ if (column == null) return;
+ final Class<?> attType = column.getType();
- Equation equation = null;
- Object rawValue = row.getRaw(attName);
- if (rawValue instanceof Equation) equation = (Equation) rawValue;
+ if (attType == Double.class) {
+ Double dAttr = row.get(attName, Double.class);
+ writeAttributeXML(attName, ObjectType.REAL, dAttr,
true);
+ } else {
+ if (attType == Integer.class) {
+ Integer iAttr = row.get(attName, Integer.class);
+ writeAttributeXML(attName, ObjectType.INTEGER,
iAttr, true);
+ } else if (attType == String.class) {
+ 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);
+ } else if (attType == Boolean.class) {
+ 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);
- if (attType == Double.class) {
- if (equation != null) {
- // TODO: Should Cy3 still save equations when exporting to
XGMML?
- 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);
- } 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);
- } 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);
- }
- } else if (attType == Boolean.class) {
- 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);
+ if (listAttr != null) {
+ depth++;
+ // interate through the list
+ for (Object obj : listAttr) {
+ // Protect tabs and returns (if
necessary)
+ String sAttr = obj.toString();
+ if (sAttr != null) {
+ sAttr =
sAttr.replace("\n", "\\n");
+ sAttr =
sAttr.replace("\t", "\\t");
+ }
+ // set child attribute value &
label
+ writeAttributeXML(attName,
checkType(obj), sAttr, true);
+ }
+ depth--;
+ }
+ writeAttributeXML(null, null, null, true);
+ }
+ }
+ }
- if (listAttr != null) {
- depth++;
- // interate through the list
- for (Object obj : listAttr) {
- // Protect tabs and returns (if necessary)
- String sAttr = obj.toString();
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
- }
- // set child attribute value & label
- writeAttributeXML(attName, checkType(obj), sAttr,
true);
- }
- depth--;
- }
- writeAttributeXML(null, null, null, true);
- }
- }
- }
-
/**
* writeAttributeXML outputs an XGMML attribute
*
@@ -738,37 +716,6 @@
}
/**
- * writeEquationAttributeXML outputs an XGMML attribute
- *
- * @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 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");
- }
- }
-
- /**
* Convert color (paint) to RGB string.<br>
*
* @param paint Paint object to be converted.
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