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Updated to the new readHeader(..) api 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3391 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-19 04:06:34 +00:00
parent 984c51efd3
commit 46ba88018d
1 changed files with 28 additions and 30 deletions
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58
java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/AnnotatorInputTableCodec.java
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@ -1,15 +1,17 @@
package org.broadinstitute.sting.gatk.refdata.features.sampileup;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import org.apache.log4j.Logger;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.util.AsciiLineReader;
import org.broad.tribble.util.LineReader;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.text.XReadLines;
public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTableFeature> {
@ -19,24 +21,20 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
private ArrayList<String> header;
private File file;
/**
* We use this to parse out the header.
* Parses the header.
*
* @param f the file
* @param reader
*
* @return 0. Since we just read the header, the number of lines left to skip is 0.
* @return The # of header lines for this file.
*/
public int headerLineCount(File f) {
this.file = f;
public int readHeader(LineReader reader)
{
int[] lineCounter = new int[1];
try {
header = readHeader(f, lineCounter);
header = readHeader(reader, lineCounter);
} catch(IOException e) {
throw new IllegalArgumentException("Unable to read from file " + f, e);
throw new IllegalArgumentException("Unable to read from file.", e);
}
return lineCounter[0];
}
@ -79,7 +77,12 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
* @throws IOException
*/
public static ArrayList<String> readHeader(final File source) throws IOException {
return readHeader(source, null);
FileInputStream is = new FileInputStream(source);
try {
return readHeader(new AsciiLineReader(is), null);
} finally {
is.close();
}
}
@ -90,28 +93,23 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
* @return The header fields.
* @throws IOException
*/
private static ArrayList<String> readHeader(final File source, int[] lineCounter) throws IOException {
private static ArrayList<String> readHeader(final LineReader source, int[] lineCounter) throws IOException {
ArrayList<String> header = null;
int numLines = 0;
final XReadLines reader = new XReadLines(source);
try {
//find the 1st line that's non-empty and not a comment
for ( String line : reader ) {
numLines++;
line = line.trim();
if ( line.isEmpty() || line.startsWith("#") ) {
continue;
}
//parse the header
header = Utils.split(line, DELIMITER);
break;
//find the 1st line that's non-empty and not a comment
String line = null;
while( (line = source.readLine()) != null ) {
numLines++;
line = line.trim();
if ( line.isEmpty() || line.startsWith("#") ) {
continue;
}
}
finally {
reader.close();
//parse the header
header = Utils.split(line, DELIMITER);
break;
}
// check that we found the header