From c6c6d32b462cd44d95a9b0e159e2d5cc8b4988d3 Mon Sep 17 00:00:00 2001
From: bthomas <bthomas@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Sep 2010 15:55:17 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/GenomeAnalysisEngine.java      | 10 ++++++++
 .../datasources/sample/SampleDataSource.java  | 23 ++++++++++++++++++-
 .../sample/SampleDataSourceUnitTest.java      |  7 ++++++
 3 files changed, 39 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 640f71d95..b0cb761fc 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/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);
+    }
+
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
index f8e923eb1..eedc15e7f 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
+++ b/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;
+    }
 
-}
\ No newline at end of file
+
+}
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
index 54b4f0658..8b4046e5c 100644
--- a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
+++ b/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...