rod's now have names. Use getName() to access it. Next step is better interface to accessing rods

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a

doc/Genome Analysis TK plan.omniplan/contents.xml

@@ -28,9 +28,9 @@
 			<key>GanttGroupShading</key>
 			<false/>
 			<key>GanttVisibleRect</key>
-			<string>{{-35, 124}, {1025, 1033}}</string>
+			<string>{{-35, 141}, {1025, 1033}}</string>
 			<key>OutlineVisibleRect</key>
-			<string>{{0, 124}, {789, 1033}}</string>
+			<string>{{0, 141}, {789, 1033}}</string>
 			<key>ScaleWidths</key>
 			<dict>
 				<key>Automatic</key>
@@ -587,7 +587,7 @@
 	<key>taskDifferenceEngine</key>
 	<dict>
 		<key>nextId</key>
-		<integer>111</integer>
+		<integer>112</integer>
 	</dict>
 	<key>taskUserKeys</key>
 	<array/>
@@ -1373,6 +1373,7 @@
 				<integer>83</integer>
 				<integer>95</integer>
 				<integer>96</integer>
+				<integer>111</integer>
 			</array>
 			<key>objectId</key>
 			<integer>41</integer>
@@ -2391,6 +2392,18 @@
 			<key>workTime</key>
 			<real>8</real>
 		</dict>
+		<dict>
+			<key>effort</key>
+			<real>28800</real>
+			<key>objectId</key>
+			<integer>111</integer>
+			<key>task</key>
+			<string>Fix rodDBSNP</string>
+			<key>workSeconds</key>
+			<real>28800</real>
+			<key>workTime</key>
+			<real>8</real>
+		</dict>
 	</array>
 	<key>topResources</key>
 	<array>
@@ -2401,7 +2414,7 @@
 		<integer>-1</integer>
 	</array>
 	<key>uuid</key>
-	<string>E50852A9-C0BE-452A-A050-4FF83DEF06D7</string>
+	<string>85860500-DAB8-4D75-95EE-F86F00907D5D</string>
 	<key>version</key>
 	<integer>2</integer>
 </dict>

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

@@ -158,21 +158,21 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >();
 
         if ( TEST_ROD ) {
-            ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>(new File("trunk/data/gFFTest.gff"), rodGFF.class );
+            ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>("test", new File("trunk/data/gFFTest.gff"), rodGFF.class );
             gff.testMe();
 
             //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );
-            ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class );
+            ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>("dbSNP", new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class );
             //dbsnp.testMe();
             rods.add(dbsnp); // { gff, dbsnp };
         } else {
             if ( DBSNP_FILE != null ) {
-                ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File(DBSNP_FILE), rodDbSNP.class );
+                ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>("dbSNP", new File(DBSNP_FILE), rodDbSNP.class );
                 //dbsnp.testMe();
                 rods.add(dbsnp); // { gff, dbsnp };
             }
             if ( HAPMAP_FILE != null ) {
-                ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class );
+                ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>("hapmap", new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class );
                 //dbsnp.testMe();
                 rods.add(hapmap); // { gff, dbsnp };
             }

java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java

@@ -35,6 +35,9 @@ public class HapMapAlleleFrequenciesROD extends ReferenceOrderedDatum {
     public Integer varCounts; // maybe we don't need these?
     public Integer totalCounts; // maybe we don't need these?
 
+    public HapMapAlleleFrequenciesROD(String name) {
+        super(name);
+    }
 
     public GenomeLoc getLocation() { return loc; }
 

java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java

@@ -7,6 +7,8 @@ import java.io.FileNotFoundException;
 import java.util.Iterator;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
 
 import edu.mit.broad.picard.util.TabbedTextFileParser;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
@@ -23,12 +25,14 @@ import org.broadinstitute.sting.utils.Utils;
  * To change this template use File | Settings | File Templates.
  */
 public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<ROD> {
+    private String name;
     private File file = null;
     private Class<ROD> type = null; // runtime type information for object construction
 
-    public ReferenceOrderedData(File file, Class<ROD> type ) {
+    public ReferenceOrderedData(final String name, File file, Class<ROD> type ) {
         this.file = file;
         this.type = type;
+        this.name = name;
     }
 
     public RODIterator iterator() {
@@ -232,7 +236,9 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     ROD parseLine(final String[] parts) {
         //System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
         try {
-            ROD obj = type.newInstance();
+            //ROD obj = type.newInstance();
+            Constructor c = type.getConstructor(String.class);
+            ROD obj = (ROD)c.newInstance(name);
             obj.parseLine(parts);
             return obj;
         } catch ( java.lang.InstantiationException e ) {
@@ -241,6 +247,12 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         } catch ( java.lang.IllegalAccessException e ) {
             System.out.println(e);
             return null; // wow, unsafe!
-        }       
+        } catch ( java.lang.NoSuchMethodException e ) {
+            System.out.println(e);
+            return null; // wow, unsafe!
+        } catch ( InvocationTargetException e ) {
+            System.out.println(e);
+            return null; // wow, unsafe!
+        }
     }
 }

java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java

@@ -10,8 +10,13 @@ import org.broadinstitute.sting.utils.GenomeLoc;
  * To change this template use File | Settings | File Templates.
  */
 public abstract class ReferenceOrderedDatum implements Comparable<ReferenceOrderedDatum> {
+    protected String name;
 
-    public ReferenceOrderedDatum() { }
+    public ReferenceOrderedDatum(String name) {
+        this.name = name;
+    }
+
+    public String getName() { return this.name; }
 
     public abstract void parseLine(final String[] parts);
 

java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -52,7 +52,9 @@ public class rodDbSNP extends ReferenceOrderedDatum implements AllelicVariant {
     // Constructors
     //
     // ----------------------------------------------------------------------
-    public rodDbSNP() {}
+    public rodDbSNP(final String name) {
+        super(name);
+    }
 
     // ----------------------------------------------------------------------
     //

java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java

@@ -29,8 +29,8 @@ public class rodGFF extends ReferenceOrderedDatum {
     // Constructors
     //
     // ----------------------------------------------------------------------
-    public rodGFF() {
+    public rodGFF(final String name) {
-        
+        super(name);        
     }
 
     public void setValues(final String contig, final String source, final String feature,

java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java

@@ -49,7 +49,7 @@ public class PrepareROD extends CommandLineProgram {
 
         Class<? extends ReferenceOrderedDatum> rodClass = Types.get(ROD_TYPE.toLowerCase());
 
-        ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = new ReferenceOrderedData(new File(ROD_FILE), rodClass );
+        ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = new ReferenceOrderedData("ROD", new File(ROD_FILE), rodClass );
         try {
             rod.validateFile();
         } catch ( Exception e ) {
@@ -68,7 +68,7 @@ public class PrepareROD extends CommandLineProgram {
         }
 
         System.out.printf("Validating output file %s%n", rodData.size(), OUTPUT_FILE);
-        ReferenceOrderedData outputRod = new ReferenceOrderedData(new File(OUTPUT_FILE), rodClass );
+        ReferenceOrderedData outputRod = new ReferenceOrderedData("ROD", new File(OUTPUT_FILE), rodClass );
         try {
             outputRod.validateFile();
             //outputRod.hasSameContents(ROD_FILE);