From bc125f104a9accedb89ef52238fea84af1f3fee8 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 10 Aug 2011 10:23:33 -0400
Subject: [PATCH] TrainingSets class is obsolete now.

---
 .../variantrecalibration/TrainingSet.java     | 71 -------------------
 .../VariantDataManager.java                   |  2 -
 2 files changed, 73 deletions(-)
 delete mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
deleted file mode 100755
index 6c1a7ddbc..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright (c) 2011 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.walkers.variantrecalibration;
-
-import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.Tags;
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: 3/12/11
- */
-
-public class TrainingSet {
-
-    public String name;
-    public boolean isKnown = false;
-    public boolean isTraining = false;
-    public boolean isAntiTraining = false;
-    public boolean isTruth = false;
-    public boolean isConsensus = false;
-    public double prior = 0.0;
-
-    protected final static Logger logger = Logger.getLogger(TrainingSet.class);
-
-    public TrainingSet( final String name, final Tags tags ) {
-        this.name = name;
-
-        // Parse the tags to decide which tracks have which properties
-        if( tags != null ) {
-            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
-            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
-            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
-            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
-            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
-            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
-        }
-
-        // Report back to the user which tracks were found and the properties that were detected
-        if( !isConsensus && !isAntiTraining ) {
-            logger.info( String.format( "Found %s track: \tKnown = %s \tTraining = %s \tTruth = %s \tPrior = Q%.1f", this.name, isKnown, isTraining, isTruth, prior) );
-        } else if( isConsensus ) {
-            logger.info( String.format( "Found consensus track: %s", this.name) );
-        } else {
-            logger.info( String.format( "Found bad sites training track: %s", this.name) );
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 08026a45e..cb4d94332 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -52,7 +52,6 @@ public class VariantDataManager {
     private final double[] meanVector;
     private final double[] varianceVector; // this is really the standard deviation
     public final ArrayList<String> annotationKeys;
-    private final ExpandingArrayList<TrainingSet> trainingSets;
     private final VariantRecalibratorArgumentCollection VRAC;
     protected final static Logger logger = Logger.getLogger(VariantDataManager.class);
 
@@ -63,7 +62,6 @@ public class VariantDataManager {
         this.VRAC = VRAC;
         meanVector = new double[this.annotationKeys.size()];
         varianceVector = new double[this.annotationKeys.size()];
-        trainingSets = new ExpandingArrayList<TrainingSet>();
     }
 
     public void setData( final ExpandingArrayList<VariantDatum> data ) {