Working on reference ordered data; added build.xml for ant!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@14 348d0f76-0448-11de-a6fe-93d51630548a

java/build.xml

@@ -0,0 +1,38 @@
+<project name="AnalysisTK" default="dist" basedir=".">
+    <description>
+        simple build file
+    </description>
+  <!-- set global properties for this build -->
+  <property name="src" location="trunk/java/"/>
+  <property name="build" location="out/production/AnalysisTK"/>
+  <property name="dist"  location="dist"/>
+
+  <target name="init">
+    <!-- Create the time stamp -->
+    <tstamp/>
+    <!-- Create the build directory structure used by compile -->
+    <mkdir dir="${build}"/>
+  </target>
+
+  <target name="compile" depends="init"
+        description="compile the source " >
+    <!-- Compile the java code from ${src} into ${build} -->
+    <javac srcdir="${src}" destdir="${build}"/>
+  </target>
+
+  <target name="dist" depends="compile"
+        description="generate the distribution" >
+    <!-- Create the distribution directory -->
+    <mkdir dir="${dist}/lib"/>
+
+    <!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->
+    <jar jarfile="${dist}/AnalysisTK-${DSTAMP}.jar" basedir="${build}"/>
+  </target>
+
+  <target name="clean"
+        description="clean up" >
+    <!-- Delete the ${build} and ${dist} directory trees -->
+    <delete dir="${build}"/>
+    <delete dir="${dist}"/>
+  </target>
+</project>

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

@@ -25,6 +25,7 @@ public class AnalysisTK extends CommandLineProgram {
     @Option(shortName="B", doc="Debugging output", optional=true) public String DEBUGGING_STR = null;
     @Option(shortName="L", doc="Genome region to operation on: from chr:start-end", optional=true) public String REGION_STR = null;
     @Option(shortName="T", doc="Type of analysis to run") public String Analysis_Name = null;
+    @Option(shortName="DBSNP", doc="DBSNP file", optional=true) public String DBSNP_FILE = null;
     
     public static HashMap<String, Object> MODULES = new HashMap<String,Object>();
     public static void addModule(final String name, final Object walker) {
@@ -60,6 +61,11 @@ public class AnalysisTK extends CommandLineProgram {
             //dbsnp.testMe();
             rods = new ReferenceOrderedData[] { dbsnp }; // { gff, dbsnp };
         }
+        else if ( DBSNP_FILE != null ) {
+            ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class );
+            //dbsnp.testMe();
+            rods = new ReferenceOrderedData[] { dbsnp }; // { gff, dbsnp };
+        }
         else {
             rods = new ReferenceOrderedData[] {}; // { gff, dbsnp };
         }

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

@@ -2,6 +2,7 @@ package edu.mit.broad.sting.utils;
 
 import java.io.File;
 import java.util.Iterator;
+import edu.mit.broad.picard.util.TabbedTextFileParser;
 
 /**
  * Class for representing arbitrary reference ordered data sets
@@ -30,9 +31,14 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     //
     // ----------------------------------------------------------------------
     public void testMe() {
+        ReferenceOrderedDatum last = null;
         for ( ReferenceOrderedDatum rec : this ) {
-            System.out.println(rec.toString());
+            if ( last == null || ! last.getContig().equals(rec.getContig()) ) {
+                System.out.println(rec.toString());
+            }
+            last = rec;
         }
+        System.exit(1);
     }
 
     // ----------------------------------------------------------------------
@@ -41,10 +47,11 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     //
     // ----------------------------------------------------------------------
     private class SimpleRODIterator implements Iterator<ROD> {
-        private WhitespaceTextFileParser parser = null;
+        //private WhitespaceTextFileParser parser = null;
+        private TabbedTextFileParser parser = null;
 
         public SimpleRODIterator() {
-            parser = new WhitespaceTextFileParser(true, file);
+            parser = new TabbedTextFileParser(true, file);
         }
 
         public boolean hasNext() {
@@ -81,9 +88,11 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         // Otherwise we return the first object who's start is at pos
         //
         public ROD seekForward(final String contigName, final int pos) {
+            final boolean DEBUG = false; 
+        
             ROD result = null;
             
-            //System.out.printf("  *** starting seek to %s %d %s%n", contigName, pos, prev);
+            if ( DEBUG ) System.out.printf("  *** starting seek to %s %d %s%n", contigName, pos, prev);
             while ( hasNext() ) {
                 ROD current = next();
                 //System.out.printf("    -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart());
@@ -102,18 +111,20 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
                     }
                 }
                 else if ( strCmp < 0 ) {
+                    if ( DEBUG ) System.out.printf("    -> Jumping to contig %s%n", contigName);
                     // We've gone past the desired contig, break
                     break;
                 }
             }
 
-            /*
+            if ( DEBUG ) {
-            if ( result == null )
+                if ( result == null )
-                ;
+                    ;
-                //System.out.printf("    --- seek result to %s %d is NULL%n", contigName, pos);
+                    //System.out.printf("    --- seek result to %s %d is NULL%n", contigName, pos);
-            else
+                else
-                System.out.printf("    ### Found %s %d%n", result.getContig(), result.getStart());
+                    System.out.printf("    ### Found %s %d%n", result.getContig(), result.getStart());
-            */
+            }
+            
 
              // we ran out of elements or found something
             return result;