Author: ruschein
Date: 2011-08-05 14:01:10 -0700 (Fri, 05 Aug 2011)
New Revision: 26391
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
Log:
Work in progress on Redmine bug #100.
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
2011-08-05 18:05:03 UTC (rev 26390)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
2011-08-05 21:01:10 UTC (rev 26391)
@@ -382,15 +382,16 @@
numGenes = geneNames.size();
for (int i = 0; i < geneNames.size(); i++) {
- if (geneNames.get(i) != null) {
- geneNameToIndex.put(geneNames.get(i),
Integer.valueOf(i));
- }
+ if (geneNames.get(i) != null)
+ geneNameToIndex.put(geneNames.get(i),
i);
}
/* trim capacity of data structures for efficiency */
geneNames.trimToSize();
geneDescripts.trimToSize();
allMeasurements.trimToSize();
+
+ copyToAttribs(taskMonitor);
} finally {
input.close();
}
@@ -629,194 +630,29 @@
} // getPvalueFromLambda
/**
- * Gets the Significance Type.
- *
- * @return one of NONE, UNKNOWN, PVAL, LAMBDA
- */
- public int getSignificanceType() {
- return this.significanceType;
- }
-
- /**
- * Sets a List of Gene Names. This clobbers the old list of gene names,
if
- * it exists.
- *
- * @param newNames Vector of String Objects.
- */
- public void setGeneNames(Vector<String> newNames) {
- geneNames = newNames;
- geneNameToIndex.clear();
-
- for (int i = 0; i < geneNames.size(); i++) {
- geneNameToIndex.put(geneNames.get(i),
Integer.valueOf(i));
- }
- }
-
- /**
- * Gets an Array of GeneDescriptors.
- *
- * @return Array of String Objects.
- */
- public String[] getGeneDescriptors() {
- return (String[]) geneDescripts.toArray(new String[0]);
- }
-
- /**
- * Gets a Vector Gene Descriptors.
- *
- * @return Vector of String Objects.
- */
- public Vector<String> getGeneDescriptorsVector() {
- return geneDescripts;
- }
-
- /**
- * Sets a List of Gene Descriptors. This clobbers the old list of gene
- * descriptors, if it exists.
- *
- * @param newDescripts Vector of String Objects.
- */
- public void setGeneDescriptors(Vector<String> newDescripts) {
- geneDescripts = newDescripts;
- }
-
- /**
* Gets an Array of All Experimental Conditions.
*
* @return Array of String Objects.
*/
- public String[] getConditionNames() {
+ private String[] getConditionNames() {
return (String[]) condNames.toArray(new String[0]);
}
/**
- * Gets the index value of the specified experimenal conditon.
- *
- * @param condition Name of experimental condition.
- * @return index value of the specified experimenal conditon.
- */
- public int getConditionIndex(String condition) {
- return ((Integer)
this.condNameToIndex.get(condition)).intValue();
- }
-
- /**
- * Gets the Gene Descriptor for the specified gene.
- *
- * @param gene Gene Name.
- * @return Gene Descriptor String.
- */
- public String getGeneDescriptor(String gene) {
- Integer geneIndex = (Integer) geneNameToIndex.get(gene);
-
- if (geneIndex == null) {
- return null;
- }
-
- return (String) geneDescripts.get(geneIndex.intValue());
- }
-
- /**
- * Indicates whether the expression data has significance values.
- *
- * @return true or false.
- */
- public boolean hasSignificanceValues() {
- return haveSigValues;
- }
-
- /**
- * Gets all Measurements.
- *
- * @return A Vector of Vectors. The embedded Vector contains
mRNAMeasurement
- * Objects.
- */
- public Vector<Vector<mRNAMeasurement>> getAllMeasurements() {
- return allMeasurements;
- }
-
- /**
- * Gets a List of All Gene Names. Same as getGeneNamesVector(), except
this
- * method returns an Array of String Objects.
- *
- * @return Array of Strings.
- */
- public String[] getGeneNames() {
- return (String[]) geneNames.toArray(new String[0]);
- }
-
- /**
- * Gets a List of All Gene Names. Same as getGeneNames(), except this
method
- * returns a Vector of String Objects.
- *
- * @return Vector of String Objects.
- */
- public Vector<String> getGeneNamesVector() {
- return geneNames;
- }
-
- /**
- * Gets Total Number of Experimental Conditions. This corresponds to the
- * number of condition columns in the original expression data file.
- *
- * @return total number of experimental conditions.
- */
- public int getNumberOfConditions() {
- return numConds;
- }
-
- /**
- * Gets Total Number of Genes. This corresponds to the number of rows of
- * data in the original expression data file.
- *
- * @return total number of genes.
- */
- public int getNumberOfGenes() {
- return numGenes;
- }
-
- /**
- * Returns a 2D Matrix of Extreme Values. The matrix is set to the
- * following:
- * <p/>
- * <PRE>
- * <p/>
- * maxVals[0][0] = minExp; maxVals[0][1] = maxExp; maxVals[1][0] =
minSig;
- * maxVals[0][1] = maxSig;
- * <p/>
- * </PRE>
- *
- * @return a 2D Matrix of double values.
- */
- public double[][] getExtremeValues() {
- double[][] maxVals = new double[2][2];
- maxVals[0][0] = minExp;
- maxVals[0][1] = maxExp;
- maxVals[1][0] = minSig;
- maxVals[1][1] = maxSig;
-
- return maxVals;
- }
-
- /**
* Gets a Vector of all Measurements associated with the specified gene.
*
* @param gene Gene Name.
* @return Vector of mRNAMeasurement Objects.
*/
- public Vector<mRNAMeasurement> getMeasurements(String gene) {
- if (gene == null) {
+ private Vector<mRNAMeasurement> getMeasurements(String gene) {
+ if (gene == null)
return null;
- }
- Integer geneIndex = geneNameToIndex.get(gene);
-
- if (geneIndex == null) {
+ final Integer geneIndex = geneNameToIndex.get(gene);
+ if (geneIndex == null)
return null;
- }
- Vector<mRNAMeasurement> measurements =
this.getAllMeasurements().get(geneIndex.intValue());
-
- return measurements;
+ return allMeasurements.get(geneIndex);
}
/**
@@ -828,7 +664,7 @@
* expression data file.)
* @return an mRNAMeasurement Object.
*/
- public mRNAMeasurement getMeasurement(String gene, String condition) {
+ private mRNAMeasurement getMeasurement(String gene, String condition) {
Integer condIndex = condNameToIndex.get(condition);
if (condIndex == null) {
@@ -852,7 +688,7 @@
* @param nodeAttribs Node Attributes CyTable.
* @param taskMonitor Task Monitor. Can be null.
*/
- public void copyToAttribs(CyTable table, TaskMonitor taskMonitor) {
+ private void copyToAttribs(TaskMonitor taskMonitor) {
String[] condNames = getConditionNames();
// first set up the columns
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-08-05 18:05:03 UTC (rev 26390)
+++
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-08-05 21:01:10 UTC (rev 26391)
@@ -190,31 +190,40 @@
</osgi:service>
<osgi:service id="vizmapPropertiesReaderFactoryService"
ref="vizmapPropertiesReaderFactory"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
<entry key="serviceType" value="vizmapPropertiesReaderFactory" />
<entry key="readerId" value="vizmapPropertiesReaderFactory" />
<entry key="readerDescription" value="Vizmap Properties File
Reader" />
- </osgi:service-properties>
- </osgi:service>
+ </osgi:service-properties>
+ </osgi:service>
<osgi:service id="vizmapXMLReaderFactoryService"
ref="vizmapXMLReaderFactory"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
<entry key="serviceType" value="vizmapXMLReaderFactory" />
<entry key="readerId" value="vizmapXMLReaderFactory" />
<entry key="readerDescription" value="Vizmap XML File Reader" />
- </osgi:service-properties>
- </osgi:service>
-
+ </osgi:service-properties>
+ </osgi:service>
+
<osgi:service id="sessionTableReaderFactoryService"
ref="sessionTableReaderFactory"
interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
+ <osgi:service-properties>
<entry key="serviceType" value="sessionTableReaderFactory" />
<entry key="readerId" value="sessionTableReaderFactory" />
<entry key="readerDescription" value="Session Table File Reader" />
- </osgi:service-properties>
- </osgi:service>
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="expressionMatrixReaderFactoryService"
ref="expressionReaderFactory"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType" value="attrsDataReaderFactory" />
+ <entry key="readerId" value="expressionMatrixReader" />
+ <entry key="readerDescription" value="Expression Matrix File
Reader" />
+ </osgi:service-properties>
+ </osgi:service>
<osgi:service id="sessionWriterFactoryService"
ref="sessionWriterFactory">
<interfaces>
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