Author: ruschein
Date: 2011-08-04 08:10:45 -0700 (Thu, 04 Aug 2011)
New Revision: 26373
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
Log:
Work in progress.
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
2011-08-03 23:38:59 UTC (rev 26372)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java
2011-08-04 15:10:45 UTC (rev 26373)
@@ -1,15 +1,8 @@
/*
File: ExpressionData.java
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2011, 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
@@ -34,19 +27,13 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-
-//ExpressionData.java
-
-//--------------------------------------------------------------------
-// $Revision: 13142 $
-// $Date: 2008-02-21 22:25:56 -0800 (Thu, 21 Feb 2008) $
-// $Author: mes $
-//--------------------------------------------------------------------
package org.cytoscape.io.internal.read.expression;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
+import java.io.FileReader;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
@@ -58,6 +45,7 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.work.TaskMonitor;
@@ -149,7 +137,7 @@
* Significance value: UNKNOWN.
*/
public static final int UNKNOWN = 3;
- private static final String DEFAULT_KEY_ATTRIBUTE = "ID";
+ private static final String DEFAULT_KEY_ATTRIBUTE = CyTableEntry.NAME;
protected int significanceType = 3;
/*
@@ -174,7 +162,6 @@
double minSig;
double maxSig;
Vector<Vector<mRNAMeasurement>> allMeasurements;
-/// FileUtil fileUtil;
/**
* Constructor. Creates an empty Expression Data object with no data.
@@ -353,42 +340,45 @@
if (filename == null)
return false;
+ final BufferedReader input = new BufferedReader(new
FileReader(filename));
boolean mappingByKeyAttribute = false;
- if (!keyAttributeName.equals(DEFAULT_KEY_ATTRIBUTE)) {
+ if (keyAttributeName != DEFAULT_KEY_ATTRIBUTE) {
mappingByKeyAttribute = true;
attributeToId = getAttributeToIdList(keyAttributeName);
}
- // TODO parser not implemented - needs to read an input stream
- String rawText = ""; //fileUtil.getInputString(filename);
- String[] lines =
rawText.split(System.getProperty("line.separator"));
-
int lineCount = 0;
+ String line;
// allow file to start with an arbitrary number
// of comment lines starting with '#' symbol
- while (lines[lineCount].startsWith("#")) ++lineCount;
+ while ((line = input.readLine()) != null &&
line.startsWith("#"))
+ ++lineCount;
- String headerLine = lines[lineCount++];
+ String headerLine = input.readLine();
+ ++lineCount;
- if ((headerLine == null) || (headerLine.length() == 0))
+ if (headerLine == null || headerLine.length() == 0)
return false;
if (isHeaderLineMTXHeader(headerLine)) {
// for sure we know that the file contains lambdas
- this.significanceType = this.LAMBDA;
- headerLine = lines[lineCount++];
+ significanceType = LAMBDA;
+ headerLine = input.readLine();
+ ++lineCount;
+ if (headerLine == null)
+ return false;
}
- boolean hasCOMMON = doesHeaderLineHasCOMMON(headerLine);
- boolean expectPvals = doesHeaderLineHaveDuplicates(headerLine,
hasCOMMON);
+ final boolean hasCOMMON = doesHeaderLineHasCOMMON(headerLine);
+ final boolean expectPvals =
doesHeaderLineHaveDuplicates(headerLine, hasCOMMON);
- if ((this.significanceType != this.LAMBDA) && !expectPvals) {
+ if ((significanceType != LAMBDA) && !expectPvals) {
// we know that we don't have a lambda header and we
don't
// have significance values
- this.significanceType = this.NONE;
+ significanceType = NONE;
}
StringTokenizer headerTok = new StringTokenizer(headerLine);
@@ -429,7 +419,7 @@
}
// Since COMMON is optional, it may not exist
- if (!hasCOMMON) {
+ if (!hasCOMMON) {
if (expectPvals) {
if (tmpI == tmpF) {
numberOfConditions = (numTokens - 2) /
2;
@@ -442,11 +432,11 @@
numberOfConditions = numTokens - 1;
}
}
-
+
/* eat the first two tokens from the header line */
headerTok.nextToken();
if (hasCOMMON) {
- headerTok.nextToken();
+ headerTok.nextToken();
}
/* the next numConds tokens are the condition names */
@@ -461,48 +451,46 @@
*/
if (expectPvals) {
for (int i = 0; i < numberOfConditions; i++) {
- String title = headerTok.nextToken();
+ final String title = headerTok.nextToken();
- if (!(title.equals(cNames.get(i)))) {
- StringBuffer msg = new StringBuffer();
- msg.append("Expecting both ratios and
p-values.\n");
- msg.append("Condition name mismatch in
header line" + " of data file "
- + filename + ": " +
cNames.get(i) + " vs. " + title);
- throw new IOException(msg.toString());
- } // if !title
- } // for i
- } // if expectPvals
+ if (!title.equals(cNames.get(i))) {
+ final String msg = "Expecting both
ratios and p-values.\n"
+ +"Condition name
mismatch in header line" + " of data file "
+ + filename + ": " +
cNames.get(i) + " vs. " + title;
+ throw new IOException(msg);
+ }
+ }
+ }
- /* OK, we have a reasonable header; clobber all old information
*/
+ /*
+ * OK, we have a reasonable header; clobber all old information
+ */
this.filename = filename;
this.numConds = numberOfConditions;
this.extraTokens = haveExtraTokens;
this.haveSigValues = expectPvals;
+
/* wipe old data */
initDataStructures();
+
/* store condition names */
condNames = cNames;
- for (int i = 0; i < numConds; i++) {
+ for (int i = 0; i < numConds; i++)
condNameToIndex.put(condNames.get(i),
Integer.valueOf(i));
- }
/* parse rest of file line by line */
- if (taskMonitor != null) {
+ if (taskMonitor != null)
taskMonitor.setStatusMessage("Reading in Data...");
- }
- for (int ii = lineCount; ii < lines.length; ii++) {
- if (taskMonitor != null) {
- double percentComplete = ((double) ii /
lines.length) * 100.0;
- taskMonitor.setProgress(percentComplete);
- }
-
- parseOneLine(lines[ii], ii, expectPvals,
mappingByKeyAttribute, attributeToId, hasCOMMON);
+ while ((line = input.readLine()) != null) {
+ ++lineCount;
+ parseOneLine(line, lineCount, expectPvals,
mappingByKeyAttribute, attributeToId, hasCOMMON);
}
+ taskMonitor.setProgress(100.0);
/* save numGenes and build hash of gene names to indices */
- this.numGenes = geneNames.size();
+ numGenes = geneNames.size();
for (int i = 0; i < geneNames.size(); i++) {
if (geneNames.get(i) != null) {
@@ -557,15 +545,15 @@
}
headerTok.nextToken();
- String secondColHeader = headerTok.nextToken();
-
+ String secondColHeader = headerTok.nextToken();
+
if
(secondColHeader.equalsIgnoreCase("COMMON")||secondColHeader.equalsIgnoreCase("DESCRIPT"))
{
return true;
}
- return false;
+ return false;
}
-
+
private boolean doesHeaderLineHaveDuplicates(String hline, boolean
hasCOMMON) {
boolean retval = false;
@@ -574,14 +562,14 @@
int minTokens =2;
if (hasCOMMON) {
- minTokens =3;
+ minTokens =3;
}
if (numTokens < minTokens) {
retval = false;
} else {
headerTok.nextToken();
if (hasCOMMON) {
- headerTok.nextToken();
+ headerTok.nextToken();
}
HashMap<Object,Object> names = new
HashMap<Object,Object>();
@@ -635,7 +623,7 @@
private void parseOneLine(String oneLine, int lineCount, boolean
sig_vals,
boolean mappingByAttribute,
Map<String,List<String>> attributeToId, boolean hasCOMMON)
throws IOException {
- //
+ //
// Step 1: divide the line into input tokens, and parse through
// the input tokens.
//
@@ -653,7 +641,7 @@
return;
}
- int numPreCols = 2; // Number of columns before data columns
+ int numPreCols = 2; // Number of columns before data columns
if (!hasCOMMON) {
numPreCols = 1;
}
@@ -667,7 +655,7 @@
if (hasCOMMON) {
geneDescript = strtok.nextToken();
}
-
+
String[] expData = new String[numConds];
for (int i = 0; i < numConds; i++) {
@@ -734,7 +722,7 @@
}
if ((this.significanceType != this.LAMBDA) && sig_vals
&& (minSig > 0)) {
- // We are probably not looking at lambdas,
since no
+ // We are probably not looking at lambdas,
since no
// significance value was > 1
// and the header is not a LAMBDA header
this.significanceType = this.PVAL;
@@ -752,8 +740,8 @@
for ( mRNAMeasurement m : v ) {
double pval =
ExpressionData.getPvalueFromLambda(m.getSignificance());
m.setSignificance(pval);
- }
- }
+ }
+ }
} // convertPValsToLambdas
/**
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-08-03 23:38:59 UTC (rev 26372)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-08-04 15:10:45 UTC (rev 26373)
@@ -80,7 +80,11 @@
@Override
public void run(TaskMonitor tm) throws IOException {
try {
+System.err.println("$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ in
SIFNetworkReader.run(), before readInput()");
+long start=System.currentTimeMillis();
readInput(tm);
+long end=System.currentTimeMillis();
+System.err.println("$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ in
SIFNetworkReader.run(), before readInput()="+(end-start)+"ms");
} finally {
if (inputStream != null) {
inputStream.close();
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