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generic declarations added here and there to eliminate a few annoying warnings; no consequential changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@268 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-02 20:53:01 +00:00
parent 4bc035d919
commit 5d9b068b8b
7 changed files with 25 additions and 26 deletions
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15
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -8,6 +8,7 @@ import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF; import org.broadinstitute.sting.gatk.refdata.rodGFF;
import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD; import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
@ -155,26 +156,24 @@ public class GenomeAnalysisTK extends CommandLineProgram {
protected int execute() { protected int execute() {
final boolean TEST_ROD = false; final boolean TEST_ROD = false;
List<ReferenceOrderedData> rods = new ArrayList<ReferenceOrderedData>(); List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >();
if ( TEST_ROD ) { if ( TEST_ROD ) {
ReferenceOrderedData gff = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"), rodGFF.class ); ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>(new File("trunk/data/gFFTest.gff"), rodGFF.class );
gff.testMe(); gff.testMe();
//ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class ); //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );
ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class ); ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class );
//dbsnp.testMe(); //dbsnp.testMe();
rods.add(dbsnp); // { gff, dbsnp }; rods.add(dbsnp); // { gff, dbsnp };
} else { } else {
if ( DBSNP_FILE != null ) { if ( DBSNP_FILE != null ) {
ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class ); ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File(DBSNP_FILE), rodDbSNP.class );
//dbsnp.testMe(); //dbsnp.testMe();
rods.add(dbsnp); // { gff, dbsnp }; rods.add(dbsnp); // { gff, dbsnp };
} }
if ( HAPMAP_FILE != null ) { if ( HAPMAP_FILE != null ) {
ReferenceOrderedData hapmap = new ReferenceOrderedData(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class ); ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class );
//dbsnp.testMe(); //dbsnp.testMe();
rods.add(hapmap); // { gff, dbsnp }; rods.add(hapmap); // { gff, dbsnp };
} }
@ -182,7 +181,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
initializeOutputStreams(); initializeOutputStreams();
Walker my_walker = null; Walker<?,?> my_walker = null;
try { try {
my_walker = walkerManager.createWalkerByName( Analysis_Name ); my_walker = walkerManager.createWalkerByName( Analysis_Name );
} }

16
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -30,10 +30,10 @@ import java.util.*;
public abstract class TraversalEngine { public abstract class TraversalEngine {
// list of reference ordered data objects // list of reference ordered data objects
protected List<ReferenceOrderedData> rods = null; protected List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = null;
// Iterator over rods // Iterator over rods
List<ReferenceOrderedData.RODIterator> rodIters; List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> rodIters;
// How strict should we be with SAM/BAM parsing? // How strict should we be with SAM/BAM parsing?
protected ValidationStringency strictness = ValidationStringency.STRICT; protected ValidationStringency strictness = ValidationStringency.STRICT;
@ -112,7 +112,7 @@ public abstract class TraversalEngine {
* @param ref Reference file in FASTA format, assumes a .dict file is also available * @param ref Reference file in FASTA format, assumes a .dict file is also available
* @param rods Array of reference ordered data sets * @param rods Array of reference ordered data sets
*/ */
public TraversalEngine(File reads, File ref, List<ReferenceOrderedData> rods) { public TraversalEngine(File reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
readsFile = reads; readsFile = reads;
refFileName = ref; refFileName = ref;
this.rods = rods; this.rods = rods;
@ -411,10 +411,10 @@ public abstract class TraversalEngine {
* *
* @return A list of ROD iterators for getting data from each ROD * @return A list of ROD iterators for getting data from each ROD
*/ */
protected List<ReferenceOrderedData.RODIterator> initializeRODs() { protected List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> initializeRODs() {
// set up reference ordered data // set up reference ordered data
rodIters = new ArrayList<ReferenceOrderedData.RODIterator>(); rodIters = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator>();
for (ReferenceOrderedData data : rods) { for (ReferenceOrderedData<? extends ReferenceOrderedDatum> data : rods) {
rodIters.add(data.iterator()); rodIters.add(data.iterator());
} }
return rodIters; return rodIters;
@ -459,10 +459,10 @@ public abstract class TraversalEngine {
* @param loc The location to get the rods at * @param loc The location to get the rods at
* @return A list of ReferenceOrderDatum at loc. ROD without a datum at loc will be null in the list * @return A list of ReferenceOrderDatum at loc. ROD without a datum at loc will be null in the list
*/ */
protected List<ReferenceOrderedDatum> getReferenceOrderedDataAtLocus(List<ReferenceOrderedData.RODIterator> rodIters, protected List<ReferenceOrderedDatum> getReferenceOrderedDataAtLocus(List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> rodIters,
final GenomeLoc loc) { final GenomeLoc loc) {
List<ReferenceOrderedDatum> data = new ArrayList<ReferenceOrderedDatum>(); List<ReferenceOrderedDatum> data = new ArrayList<ReferenceOrderedDatum>();
for (ReferenceOrderedData.RODIterator iter : rodIters) { for (ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator iter : rodIters) {
data.add(iter.seekForward(loc)); data.add(iter.seekForward(loc));
} }
return data; return data;

5
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
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@ -31,14 +31,13 @@ import edu.mit.broad.picard.filter.FilteringIterator;
*/ */
public class TraverseByLoci extends TraversalEngine { public class TraverseByLoci extends TraversalEngine {
public TraverseByLoci(File reads, File ref, List<ReferenceOrderedData> rods) { public TraverseByLoci(File reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
super(reads, ref, rods); super(reads, ref, rods);
} }
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) { public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
if ( walker instanceof LocusWalker ) { if ( walker instanceof LocusWalker ) {
Walker x = walker; LocusWalker<M, T> locusWalker = (LocusWalker<M, T>)walker;
LocusWalker<?, ?> locusWalker = (LocusWalker<?, ?>)x;
return (T)this.traverseByLoci(locusWalker, locations); return (T)this.traverseByLoci(locusWalker, locations);
} else { } else {
throw new IllegalArgumentException("Walker isn't a loci walker!"); throw new IllegalArgumentException("Walker isn't a loci walker!");

2
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
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@ -29,7 +29,7 @@ import edu.mit.broad.picard.filter.FilteringIterator;
*/ */
public class TraverseByLociByReference extends TraverseByLoci { public class TraverseByLociByReference extends TraverseByLoci {
public TraverseByLociByReference(File reads, File ref, List<ReferenceOrderedData> rods) { public TraverseByLociByReference(File reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
super(reads, ref, rods); super(reads, ref, rods);
} }

3
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator; import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
@ -26,7 +27,7 @@ import net.sf.samtools.SAMRecord;
*/ */
public class TraverseByReads extends TraversalEngine { public class TraverseByReads extends TraversalEngine {
public TraverseByReads(File reads, File ref, List<ReferenceOrderedData> rods) { public TraverseByReads(File reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
super(reads, ref, rods); super(reads, ref, rods);
} }

2
java/src/org/broadinstitute/sting/playground/ValidateSAM.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.playground; package org.broadinstitute.sting.playground;
import net.sf.samtools.*; import net.sf.samtools.*;
import net.sf.samtools.SAMFileReader.ValidationStringency; import net.sf.samtools.SAMFileReader.ValidationStringency;

8
java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
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@ -24,8 +24,8 @@ public class PrepareROD extends CommandLineProgram {
@Option(shortName="RODNAME", doc="Name of the data") public String ROD_NAME = null; @Option(shortName="RODNAME", doc="Name of the data") public String ROD_NAME = null;
@Option(shortName="RODTYPE", doc="Referenced Ordered Data type") public String ROD_TYPE = null; @Option(shortName="RODTYPE", doc="Referenced Ordered Data type") public String ROD_TYPE = null;
public static HashMap<String, Class> Types = new HashMap<String,Class>(); public static HashMap<String, Class<? extends ReferenceOrderedDatum>> Types = new HashMap<String,Class<? extends ReferenceOrderedDatum>>();
public static void addModule(final String name, final Class rodType) { public static void addModule(final String name, final Class<? extends ReferenceOrderedDatum> rodType) {
System.out.printf("* Adding rod class %s%n", name); System.out.printf("* Adding rod class %s%n", name);
Types.put(name.toLowerCase(), rodType); Types.put(name.toLowerCase(), rodType);
} }
@ -47,9 +47,9 @@ public class PrepareROD extends CommandLineProgram {
final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG); final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
GenomeLoc.setupRefContigOrdering(refFile); GenomeLoc.setupRefContigOrdering(refFile);
Class rodClass = Types.get(ROD_TYPE.toLowerCase()); Class<? extends ReferenceOrderedDatum> rodClass = Types.get(ROD_TYPE.toLowerCase());
ReferenceOrderedData rod = new ReferenceOrderedData(new File(ROD_FILE), rodClass ); ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = new ReferenceOrderedData(new File(ROD_FILE), rodClass );
try { try {
rod.validateFile(); rod.validateFile();
} catch ( Exception e ) { } catch ( Exception e ) {