Initial support for reference ordered data sets

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@7 348d0f76-0448-11de-a6fe-93d51630548a

src/edu/mit/broad/sting/atk/AnalysisTK.java

@@ -6,6 +6,7 @@ import edu.mit.broad.picard.cmdline.Usage;
 import edu.mit.broad.picard.cmdline.Option;
 
 import edu.mit.broad.sting.atk.modules.*;
+import edu.mit.broad.sting.utils.ReferenceOrderedData;
 
 import java.io.*;
 import java.util.HashMap;
@@ -43,6 +44,9 @@ public class AnalysisTK extends CommandLineProgram {
     }
 
     protected int doWork() {
+        ReferenceOrderedData rod = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"));
+        rod.testMe();
+
         this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG);
 
         ValidationStringency strictness;

src/edu/mit/broad/sting/utils/ReferenceOrderedData.java

@@ -0,0 +1,93 @@
+package edu.mit.broad.sting.utils;
+
+import edu.mit.broad.sam.SAMRecord;
+import edu.mit.broad.sam.util.CloseableIterator;
+import edu.mit.broad.picard.util.TabbedTextFileParser;
+
+import java.io.File;
+import java.io.InputStream;
+import java.io.FileInputStream;
+import java.io.BufferedInputStream;
+import java.util.Iterator;
+import java.util.HashMap;
+
+/**
+ * Class for representing arbitrary reference ordered data sets
+ *
+ * User: mdepristo
+ * Date: Feb 27, 2009
+ * Time: 10:47:14 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ReferenceOrderedData implements Iterable<ReferenceOrderedDatum> {
+    private File file = null;
+
+    public ReferenceOrderedData(File file) {
+        this.file = file;
+    }
+
+    // ----------------------------------------------------------------------
+    //
+    // Iteration
+    //
+    // ----------------------------------------------------------------------
+    private class RODIterator implements Iterator<ReferenceOrderedDatum> {
+        TabbedTextFileParser parser = null;
+        public RODIterator() {
+            parser = new TabbedTextFileParser(true, file);
+        }
+
+        public boolean hasNext() {
+            return parser.hasNext();
+        }
+
+        public ReferenceOrderedDatum next() {
+            String parts[] = parser.next();
+            return parseGFFLine(parts);
+        }
+
+        public void remove () {
+            throw new UnsupportedOperationException();
+        }
+    }
+
+    public RODIterator iterator() {
+        return new RODIterator();
+    }
+
+    // ----------------------------------------------------------------------
+    //
+    // Testing
+    //
+    // ----------------------------------------------------------------------
+    public void testMe() {
+        for ( ReferenceOrderedDatum rec : this ) {
+            System.out.println(rec.toString());
+        }
+    }
+
+
+    // ----------------------------------------------------------------------
+    //
+    // Parsing
+    //
+    // ----------------------------------------------------------------------
+    ReferenceOrderedDatum parseGFFLine(final String[] parts) {
+        //System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
+
+        final String contig = parts[0];
+        final String source = parts[1];
+        final String feature = parts[2];
+        final long start = Long.parseLong(parts[3]);
+        final long stop = Long.parseLong(parts[4]);
+
+        double score = Double.NaN;
+        if ( ! parts[5].equals(".") )
+            score = Double.parseDouble(parts[5]);
+
+        final String strand = parts[6];
+        final String frame = parts[7];
+        HashMap<String, String> attributes = null;
+        return new ReferenceOrderedDatum(contig, source, feature, start, stop, score, strand, frame, attributes);
+    }
+}

src/edu/mit/broad/sting/utils/ReferenceOrderedDatum.java

@@ -0,0 +1,93 @@
+package edu.mit.broad.sting.utils;
+
+import java.util.HashMap;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mdepristo
+ * Date: Feb 27, 2009
+ * Time: 10:49:47 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ReferenceOrderedDatum {
+    private String contig, source, feature, strand, frame;
+    private long start, stop;
+    private double score;
+    private HashMap<String, String> attributes;
+
+    // ----------------------------------------------------------------------
+    //
+    // Constructors
+    //
+    // ----------------------------------------------------------------------
+    public ReferenceOrderedDatum(final String contig, final String source, final String feature,
+                                 final long start, final long stop, final double score,
+                                 final String strand, final String frame, HashMap<String, String> attributes) {
+        this.contig = contig;
+        this.source = source;
+        this.feature = feature;
+        this.start = start;
+        this.stop= stop;
+        this.score = score;
+        this.strand = strand;
+        this.frame = frame;
+        this.attributes = attributes;
+    }
+
+//    public ReferenceOrderedDatum(final String contig, final String source, final String feature,
+//                                 final long start, final long stop, final double score,
+//                                 final String strand, final String frame) {
+//        ReferenceOrderedDatum(contig, source, feature, start, stop, score, strand, frame, null);
+//    }
+
+    // ----------------------------------------------------------------------
+    //
+    // Accessors
+    //
+    // ----------------------------------------------------------------------
+    public String getContig() {
+        return this.contig;
+    }
+
+    public String getSource() {
+        return source;
+    }
+
+    public String getFeature() {
+        return feature;
+    }
+
+    public String getStrand() {
+        return strand;
+    }
+
+    public String getFrame() {
+        return frame;
+    }
+
+    public long getStart() {
+        return start;
+    }
+
+    public long getStop() {
+        return stop;
+    }
+
+    public double getScore() {
+        return score;
+    }
+
+    public String getAttribute(final String key) {
+        return attributes.get(key);
+    }
+
+    // ----------------------------------------------------------------------
+    //
+    // formatting
+    //
+    // ----------------------------------------------------------------------
+    public String toString() {
+        return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s", contig, source, feature, start, stop, score, strand, frame);
+    }
+
+}

src/edu/mit/broad/sting/utils/Utils.java

@@ -52,4 +52,15 @@ public class Utils {
         return flags;
     }
 
+    public static String join(String separator, String[] strings) {
+        if (strings.length == 0) {
+            return "";
+        }
+        StringBuilder ret = new StringBuilder(strings[0]);
+        for (int i = 1; i < strings.length; ++i) {
+            ret.append(separator);
+            ret.append(strings[i]);
+        }
+        return ret.toString();
+    }
 }