SampleDataSource -> SampleDB

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -34,8 +34,7 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.reads.*;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.samples.Sample;
+import org.broadinstitute.sting.gatk.samples.SampleDB;
-import org.broadinstitute.sting.gatk.samples.SampleDataSource;
 import org.broadinstitute.sting.gatk.executive.MicroScheduler;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
@@ -51,7 +50,6 @@ import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.*;
@@ -88,7 +86,7 @@ public class GenomeAnalysisEngine {
     /**
      * Accessor for sample metadata
      */
-    private SampleDataSource sampleDataSource = null;
+    private SampleDB sampleDB = null;
 
     /**
      * Accessor for sharded reference-ordered data.
@@ -688,7 +686,7 @@ public class GenomeAnalysisEngine {
         for (ReadFilter filter : filters)
             filter.initialize(this);
 
-        sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
+        sampleDB = new SampleDB(getSAMFileHeader(), argCollection.sampleFiles);
 
         // set the sequence dictionary of all of Tribble tracks to the sequence dictionary of our reference
         rodDataSources = getReferenceOrderedDataSources(referenceMetaDataFiles,referenceDataSource.getReference().getSequenceDictionary(),genomeLocParser,argCollection.unsafe);
@@ -953,8 +951,8 @@ public class GenomeAnalysisEngine {
     //
     // -------------------------------------------------------------------------------------
 
-    public SampleDataSource getSampleDB() {
+    public SampleDB getSampleDB() {
-        return this.sampleDataSource;
+        return this.sampleDB;
     }
 
     public Map<String,String> getApproximateCommandLineArguments(Object... argumentProviders) {

public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java

@@ -4,7 +4,6 @@ import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.samples.SampleDataSource;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;

public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java

@@ -138,17 +138,17 @@ public class PedReader {
 
     public PedReader() { }
 
-    public final List<Sample> parse(File source, EnumSet<MissingPedField> missingFields, SampleDataSource sampleDB) throws FileNotFoundException  {
+    public final List<Sample> parse(File source, EnumSet<MissingPedField> missingFields, SampleDB sampleDB) throws FileNotFoundException  {
         logger.info("Reading PED file " + source + " with missing fields: " + missingFields);
         return parse(new FileReader(source), missingFields, sampleDB);
     }
 
-    public final List<Sample> parse(final String source, EnumSet<MissingPedField> missingFields, SampleDataSource sampleDB) {
+    public final List<Sample> parse(final String source, EnumSet<MissingPedField> missingFields, SampleDB sampleDB) {
         logger.warn("Reading PED string: \"" + source + "\" with missing fields: " + missingFields);
         return parse(new StringReader(source.replace(";", String.format("%n"))), missingFields, sampleDB);
     }
 
-    public final List<Sample> parse(Reader reader, EnumSet<MissingPedField> missingFields, SampleDataSource sampleDB) {
+    public final List<Sample> parse(Reader reader, EnumSet<MissingPedField> missingFields, SampleDB sampleDB) {
         final List<String> lines = new XReadLines(reader).readLines();
 
         // What are the record offsets?
@@ -245,7 +245,7 @@ public class PedReader {
             return string;
     }
 
-    private final Sample maybeAddImplicitSample(SampleDataSource sampleDB, final String id, final String familyID, final Gender gender) {
+    private final Sample maybeAddImplicitSample(SampleDB sampleDB, final String id, final String familyID, final Gender gender) {
         if ( id != null && sampleDB.getSample(id) == null ) {
             Sample s = new Sample(id, sampleDB, familyID, null, null, gender, Affection.UNKNOWN, Sample.UNSET_QT);
             sampleDB.addSample(s);

public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java

@@ -14,12 +14,12 @@ public class Sample implements java.io.Serializable {
     final private double quantitativePhenotype;
     final private Affection affection;
     final private String ID;
-    final private SampleDataSource dataSource;
+    final private SampleDB infoDB;
     final private Map<String, Object> properties = new HashMap<String, Object>();
 
     public final static double UNSET_QT = Double.NaN;
 
-    public Sample(final String ID, final SampleDataSource dataSource,
+    public Sample(final String ID, final SampleDB infoDB,
                   final String familyID, final String paternalID, final String maternalID,
                   final Gender gender, final Affection affection, final double quantitativePhenotype) {
         this.familyID = familyID;
@@ -29,7 +29,7 @@ public class Sample implements java.io.Serializable {
         this.quantitativePhenotype = quantitativePhenotype;
         this.affection = affection;
         this.ID = ID;
-        this.dataSource = dataSource;
+        this.infoDB = infoDB;
     }
 
     protected Sample(final String ID,
@@ -45,17 +45,17 @@ public class Sample implements java.io.Serializable {
     }
 
 
-    public Sample(final String ID, final SampleDataSource dataSource,
+    public Sample(final String ID, final SampleDB infoDB,
                   final String familyID, final String paternalID, final String maternalID, final Gender gender) {
-        this(ID, dataSource, familyID, paternalID, maternalID, gender, Affection.UNKNOWN, UNSET_QT);
+        this(ID, infoDB, familyID, paternalID, maternalID, gender, Affection.UNKNOWN, UNSET_QT);
     }
 
-    public Sample(final String ID, final SampleDataSource dataSource, final Affection affection, final double quantitativePhenotype) {
+    public Sample(final String ID, final SampleDB infoDB, final Affection affection, final double quantitativePhenotype) {
-        this(ID, dataSource, null, null, null, Gender.UNKNOWN, affection, quantitativePhenotype);
+        this(ID, infoDB, null, null, null, Gender.UNKNOWN, affection, quantitativePhenotype);
     }
 
-    public Sample(String id, SampleDataSource dataSource) {
+    public Sample(String id, SampleDB infoDB) {
-        this(id, dataSource, null, null, null,
+        this(id, infoDB, null, null, null,
                 Gender.UNKNOWN, Affection.UNKNOWN, UNSET_QT);
     }
 
@@ -98,7 +98,7 @@ public class Sample implements java.io.Serializable {
      * @return sample object with relationship mother, if exists, or null
      */
     public Sample getMother() {
-        return dataSource.getSample(maternalID);
+        return infoDB.getSample(maternalID);
     }
 
     /**
@@ -106,7 +106,7 @@ public class Sample implements java.io.Serializable {
      * @return sample object with relationship father, if exists, or null
      */
     public Sample getFather() {
-        return dataSource.getSample(paternalID);
+        return infoDB.getSample(paternalID);
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java

@@ -24,7 +24,7 @@ import java.util.*;
  * wants to access sample data, it asks GenomeAnalysis to fetch this data from its SampleDataSource.
  *
  */
-public class SampleDataSource {
+public class SampleDB {
     /**
      * This is where Sample objects are stored. Samples are usually accessed by their ID, which is unique, so
      * this is stored as a HashMap.
@@ -34,11 +34,11 @@ public class SampleDataSource {
     /**
      * Constructor takes both a SAM header and sample files because the two must be integrated.
      */
-    public SampleDataSource() {
+    public SampleDB() {
 
     }
 
-    public SampleDataSource(final SAMFileHeader header, final List<File> sampleFiles) {
+    public SampleDB(final SAMFileHeader header, final List<File> sampleFiles) {
         this();
         addSamples(header);
         addSamples(sampleFiles);
@@ -55,7 +55,7 @@ public class SampleDataSource {
     /**
      * Hallucinates sample objects for all the samples in the SAM file and stores them
      */
-    protected SampleDataSource addSamples(SAMFileHeader header) {
+    protected SampleDB addSamples(SAMFileHeader header) {
         for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
             if (getSample(sampleName) == null) {
                 Sample newSample = new Sample(sampleName, this);
@@ -65,7 +65,7 @@ public class SampleDataSource {
         return this;
     }
 
-    protected SampleDataSource addSamples(final List<File> sampleFiles) {
+    protected SampleDB addSamples(final List<File> sampleFiles) {
         // add files consecutively
         for (File file : sampleFiles) {
             addSamples(file);
@@ -77,7 +77,7 @@ public class SampleDataSource {
      * Parse one sample file and integrate it with samples that are already there
      * Fail quickly if we find any errors in the file
      */
-    protected SampleDataSource addSamples(File sampleFile) {
+    protected SampleDB addSamples(File sampleFile) {
         return this;
     }
 
@@ -85,7 +85,7 @@ public class SampleDataSource {
      * Add a sample to the collection
      * @param sample to be added
      */
-    protected SampleDataSource addSample(Sample sample) {
+    protected SampleDB addSample(Sample sample) {
         samples.put(sample.getID(), sample);
         return this;
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.filters.MalformedReadFilter;
 import org.broadinstitute.sting.gatk.samples.Sample;
-import org.broadinstitute.sting.gatk.samples.SampleDataSource;
+import org.broadinstitute.sting.gatk.samples.SampleDB;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -88,7 +88,7 @@ public abstract class Walker<MapType, ReduceType> {
         return getToolkit().getMasterSequenceDictionary();
     }
 
-    protected SampleDataSource getSampleDB() {
+    protected SampleDB getSampleDB() {
         return getToolkit().getSampleDB();
     }
 

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java

@@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.executive.WindowMaker;
-import org.broadinstitute.sting.gatk.samples.SampleDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.LocusShard;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java

@@ -33,14 +33,12 @@ import org.broadinstitute.sting.gatk.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.samples.SampleDataSource;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
-import java.io.File;
 import java.util.Collections;
 import java.util.Iterator;
 

public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java

@@ -32,7 +32,6 @@ import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.StringReader;
-import java.lang.reflect.Array;
 import java.util.*;
 
 /**
@@ -186,7 +185,7 @@ public class PedReaderUnitTest extends BaseTest {
     private static final void runTest(PedReaderTest test, String myFileContents, EnumSet<PedReader.MissingPedField> missing) {
         logger.warn("Test " + test);
         PedReader reader = new PedReader();
-        SampleDataSource sampleDB = new SampleDataSource();
+        SampleDB sampleDB = new SampleDB();
         List<Sample> readSamples = reader.parse(myFileContents, missing, sampleDB);
         Assert.assertEquals(new HashSet<Sample>(test.expectedSamples), new HashSet<Sample>(readSamples), "Parsed incorrect number of samples");
     }
@@ -272,7 +271,7 @@ public class PedReaderUnitTest extends BaseTest {
         final String contents = sliceContents(test.missingFields, test.fileContents);
         logger.warn("Test " + test);
         PedReader reader = new PedReader();
-        SampleDataSource sampleDB = new SampleDataSource();
+        SampleDB sampleDB = new SampleDB();
         reader.parse(new StringReader(contents), test.missingDesc, sampleDB);
         final Sample missingSample = sampleDB.getSample("kid");
         Assert.assertEquals(test.expected, missingSample, "Missing field value not expected value for " + test);

public/java/test/org/broadinstitute/sting/gatk/samples/SampleDataSourceUnitTest.java

@@ -1,12 +1,7 @@
 package org.broadinstitute.sting.gatk.samples;
 
 import net.sf.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import org.testng.annotations.Test;
 
@@ -29,6 +24,6 @@ public class SampleDataSourceUnitTest extends BaseTest {
     // make sure samples are created from the SAM file correctly
     @Test()
     public void loadSAMSamplesTest() {
-        SampleDataSource s = new SampleDataSource(header, Collections.<File>emptyList());
+        SampleDB s = new SampleDB(header, Collections.<File>emptyList());
     }
 }

public/java/test/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java

@@ -13,14 +13,14 @@ import org.testng.annotations.Test;
  * Time: 8:21:00 AM
  */
 public class SampleUnitTest extends BaseTest {
-    SampleDataSource db;
+    SampleDB db;
     static Sample fam1A, fam1B, fam1C;
     static Sample s1, s2;
     static Sample trait1, trait2, trait3, trait4;
 
     @BeforeClass
     public void init() {
-        db = new SampleDataSource();
+        db = new SampleDB();
 
         fam1A = new Sample("1A", db, "fam1", "1B", "1C", Gender.UNKNOWN);
         fam1B = new Sample("1B", db, "fam1", null, null, Gender.MALE);