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Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.

This commit is contained in:
Mark DePristo 2011-07-27 22:06:23 -04:00
parent 06374c91d7
commit f3ad4ec94b
4 changed files with 12 additions and 27 deletions
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13
public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
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@ -25,7 +25,6 @@
package net.sf.picard.reference;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSourceProgressListener;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;
@ -39,8 +38,8 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
* Produces fai file with same output as samtools faidx
*/
public class FastaSequenceIndexBuilder {
public File fastaFile;
ReferenceDataSourceProgressListener progress; // interface that provides a method for updating user on progress of reading file
final public File fastaFile;
final boolean printProgress;
// keep track of location in file
long bytesRead, endOfLastLine, lastTimestamp, fileLength; // initialized to -1 to keep 0-indexed position in file;
@ -55,10 +54,10 @@ public class FastaSequenceIndexBuilder {
public enum Status { NONE, CONTIG, FIRST_SEQ_LINE, SEQ_LINE, COMMENT }
Status status = Status.NONE; // keeps state of what is currently being read. better to use int instead of enum?
public FastaSequenceIndexBuilder(File fastaFile, ReferenceDataSourceProgressListener progress) {
this.progress = progress;
public FastaSequenceIndexBuilder(File fastaFile, boolean printProgress) {
this.fastaFile = fastaFile;
fileLength = fastaFile.length();
this.printProgress = printProgress;
}
/**
@ -252,8 +251,8 @@ public class FastaSequenceIndexBuilder {
if (System.currentTimeMillis() - lastTimestamp > 10000) {
int percentProgress = (int) (100*bytesRead/fileLength);
if (progress != null)
progress.percentProgress(percentProgress);
if (printProgress)
System.out.println(String.format("PROGRESS UPDATE: file is %d percent complete", percentProgress));
lastTimestamp = System.currentTimeMillis();
}
}

3
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -926,9 +926,6 @@ public class GenomeAnalysisEngine {
GenomeLocParser genomeLocParser,
ValidationExclusion.TYPE validationExclusionType) {
RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser,validationExclusionType);
// try and make the tracks given their requests
// create of live instances of the tracks
List<RMDTrack> tracks = new ArrayList<RMDTrack>();
List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
for (RMDTriplet fileDescriptor : referenceMetaDataFiles)

13
public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
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@ -41,7 +41,7 @@ import java.io.File;
* Loads reference data from fasta file
* Looks for fai and dict files, and tries to create them if they don't exist
*/
public class ReferenceDataSource implements ReferenceDataSourceProgressListener {
public class ReferenceDataSource {
private IndexedFastaSequenceFile index;
/** our log, which we want to capture anything from this class */
@ -75,7 +75,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
// get exclusive lock
if (!indexLock.exclusiveLock())
throw new UserException.CouldNotCreateReferenceIndexFileBecauseOfLock(dictFile);
FastaSequenceIndexBuilder faiBuilder = new FastaSequenceIndexBuilder(fastaFile, this);
FastaSequenceIndexBuilder faiBuilder = new FastaSequenceIndexBuilder(fastaFile, true);
FastaSequenceIndex sequenceIndex = faiBuilder.createIndex();
FastaSequenceIndexBuilder.saveAsFaiFile(sequenceIndex, indexFile);
}
@ -194,13 +194,4 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
public IndexedFastaSequenceFile getReference() {
return this.index;
}
/**
* Notify user of progress in creating fai file
* @param percent Percent of fasta file read as a percent
*/
public void percentProgress(int percent) {
System.out.println(String.format("PROGRESS UPDATE: file is %d percent complete", percent));
}
}

10
public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java
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@ -27,7 +27,6 @@ package net.sf.picard.reference;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSourceProgressListener;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@ -40,7 +39,6 @@ import java.io.FileNotFoundException;
public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
private FastaSequenceIndexBuilder builder;
private ReferenceDataSourceProgressListener progress;
private File fastaFile;
private FastaSequenceIndex controlIndex;
@ -58,7 +56,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
logger.warn("Executing unixFileTest");
fastaFile = new File(validationDataLocation + "exampleFASTA.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, progress);
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
@ -75,7 +73,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
logger.warn("Executing windowsFileTest");
fastaFile = new File(validationDataLocation + "exampleFASTA-windows.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, progress);
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr2", 7, 29, 7, 9,0));
@ -91,7 +89,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
logger.warn("Executing combinedWindowsUnix");
fastaFile = new File(validationDataLocation + "exampleFASTA-combined.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, progress);
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
controlIndex.add(new FastaSequenceIndexEntry("chr2", 101680, 29, 7, 9,1));
@ -108,7 +106,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
logger.warn("Executing threeVariableLengthContigs");
fastaFile = new File(validationDataLocation + "exampleFASTA-3contigs.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, progress);
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 17, 5, 6,0));
controlIndex.add(new FastaSequenceIndexEntry("chr2", 35, 21, 7, 8,1));