a utility class; turns string iterator into GenomeLoc iterator

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3542 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java

@@ -0,0 +1,74 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.refdata.utils;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.bed.BedParser;
+
+import java.util.Iterator;
+
+/**
+ * Created by IntelliJ IDEA.
+* User: asivache
+* Date: Jun 11, 2010
+* Time: 2:25:42 PM
+* To change this template use File | Settings | File Templates.
+*/
+
+/**
+ * Wrap this adapter around Iterator<String> to get Iterator<GenomLoc>. Each string coming from the underlying
+ * iterator is parsed and converted to GenomeLoc on the fly and the latter is returned on each call to next().
+ * Two string formats are currently supported: BED and GATK. This iterator will throw an exception if it fails
+ * to parse a string.
+ */
+public class StringToGenomeLocIteratorAdapter implements Iterator<GenomeLoc> {
+    private Iterator<String> it = null;
+
+    public enum FORMAT { BED, GATK };
+
+    FORMAT myFormat = FORMAT.GATK;
+
+    public StringToGenomeLocIteratorAdapter(Iterator<String> it, FORMAT format) {
+        this.it = it;
+        myFormat = format;
+    }
+
+    public StringToGenomeLocIteratorAdapter(Iterator<String> it ) {
+        this(it,FORMAT.GATK);
+    }
+
+    public boolean hasNext() { return it.hasNext(); }
+
+    public GenomeLoc next() {
+        if ( myFormat == FORMAT.GATK ) return GenomeLocParser.parseGenomeInterval( it.next() );
+        return BedParser.parseLocation( it.next() );
+    }
+
+    public void remove() {
+        throw new UnsupportedOperationException("method 'remove' is not supported by this iterator");
+    }
+}