Quickly adding a new convenience method for retreiving a group of samples. The method is getSamples(Collection<String>) and returns a set of sample objects. There's also a test there.

Ryan is using this to modify VCF code today...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4303 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1037,4 +1037,14 @@ public class GenomeAnalysisEngine {
         return sampleDataSource.getChildren(sample);
     }
 
+    /**
+     * Takes a list of sample names and returns their corresponding sample objects
+     *
+     * @param sampleNameList List of sample names
+     * @return Corresponding set of samples
+     */
+    public Set<Sample> getSamples(Collection<String> sampleNameList) {
+	return sampleDataSource.getSamples(sampleNameList);
+    }
+
 }

java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java

@@ -19,6 +19,8 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.ArrayList;
+import java.util.Collection;
 
 /**
  * Created by IntelliJ IDEA.
@@ -464,5 +466,24 @@ public class SampleDataSource {
         return children;
     }
 
+    /**
+     * Takes a collection of sample names and returns their corresponding sample objects
+     * Note that, since a set is returned, if you pass in a list with duplicates names there will not be any duplicates in the returned set
+     * @param sampleNameList Set of sample names
+     * @return Corresponding set of samples
+     */
+    public Set<Sample> getSamples(Collection<String> sampleNameList) {
+	HashSet<Sample> samples = new HashSet<Sample>();
+        for (String name : sampleNameList) {
+            try {
+                samples.add(getSampleById(name));
+            }
+            catch (Exception e) {
+                throw new StingException("Could not get sample with the following ID: " + name, e);
+            }
+        }
+        return samples;
+    }
 
-}
+
+}

java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java

@@ -46,6 +46,13 @@ public class SampleDataSourceUnitTest extends BaseTest {
         Assert.assertTrue(family.size() == 2);
         Assert.assertTrue(family.contains(sampleA));
         Assert.assertTrue(family.contains(sampleB));
+
+	// make sure getSamples(List names) works
+	ArrayList<String> names = new ArrayList<String>();
+	names.add("sampleA");
+	names.add("sampleB");
+	Set<Sample> testList = s.getSamples(names);
+	Assert.assertTrue(testList.size() == 2);
     }
 
     // but that file should fail if it has an extra character in it...