diff -u -r1.13 -r1.14
--- HPSSVTCalibrationConstants.java	21 Jun 2012 18:47:07 -0000	1.13
+++ HPSSVTCalibrationConstants.java	13 Jul 2012 23:02:57 -0000	1.14
@@ -1,7 +1,3 @@

-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */

 package org.lcsim.hps.recon.tracking;
 
 import java.io.BufferedReader;

@@ -18,36 +14,27 @@

 
 /**
  *

- * @author mgraham

+ * @author Mathew Graham <[log in to unmask]>
+ * $Id: HPSSVTCalibrationConstants.java,v 1.14 2012/07/13 23:02:57 omoreno Exp $

  */
 public class HPSSVTCalibrationConstants {
 

-    public static Map<Pair<Integer /*
-             * Hybrid
-             */, Integer /*
-             * FPGA
-             */>, double[] /*
-             * constants
-             */> noiseMap = new HashMap<Pair<Integer, Integer>, double[]>();
-    public static Map<Pair<Integer /*
-             * Hybrid
-             */, Integer /*
-             * FPGA
-             */>, double[] /*
-             * constants
-             */> pedestalMap = new HashMap<Pair<Integer, Integer>, double[]>();
-    public static Map<Pair<Integer /*
-             * Hybrid
-             */, Integer /*
-             * FPGA
-             */>, double[] /*
-             * constants
-             */> tpMap = new HashMap<Pair<Integer, Integer>, double[]>();

+	// TODO: Change all pairs such that FPGA is the fist value
+	// TODO: Change all map keys to type SiSensor?
+	
+    public static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, double[] /* constants */> noiseMap 
+    	= new HashMap<Pair<Integer, Integer>, double[]>();
+    public static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, double[] /* constants */> pedestalMap 
+    	= new HashMap<Pair<Integer, Integer>, double[]>();
+    public static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, double[] /* constants */> tpMap 
+    	= new HashMap<Pair<Integer, Integer>, double[]>();
+    public static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, Set<Integer> /* Bad channels */> badChannelMap
+    	= new HashMap<Pair<Integer, Integer>, Set<Integer>>();

     private static boolean pedestalLoaded = false;
     private static boolean tpLoaded = false;
 
     /**

-     * Default Constructor.

+     * Default Ctor

      */
     private HPSSVTCalibrationConstants() {
     }

@@ -55,6 +42,11 @@

     public static void loadCalibrationConstants() {
         loadCalibrationConstants(null);
     }

+    
+    public static void loadCalibrationConstants(Date date, int runNumber){
+    	loadCalibrationConstants(date);
+    	loadBadChannels(runNumber);
+    }

 
     public static void loadCalibrationConstants(Date date) {
         //write something here to read in constants from calibration file

@@ -126,7 +118,7 @@

                     double pedestal = Double.valueOf(lineTok.nextToken());
                     double noise = Double.valueOf(lineTok.nextToken());
 

-                    Pair<Integer, Integer> daqPair = new Pair(hybrid, fpga);

+                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);

 
                     double[] pedestals = pedestalMap.get(daqPair);
                     if (pedestals == null) {

@@ -182,7 +174,7 @@

                     double tp = Double.valueOf(lineTok.nextToken()) * 24.0 / 25.0; //FIXME: this is a hack to compensate for the calibrations we have that assumed 25 ns APV clock
                     double chisq = Double.valueOf(lineTok.nextToken());
 

-                    Pair<Integer, Integer> daqPair = new Pair(hybrid, fpga);

+                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);

 
                     double[] tps = tpMap.get(daqPair);
                     if (tps == null) {

@@ -199,6 +191,73 @@

     public static boolean tpLoaded() {
         return tpLoaded;
     }

+    
+    /**
+     * Load the bad channels for the specified run.  If there are no 
+     * bad channels specified, just load those found from QA.  Channels
+     * found to be bad from QA will always be loaded.
+     * 
+     * @param run number
+     */
+    public static void loadBadChannels(int runNumber){
+    	
+    	// Clear the previously loaded bad channels
+    	badChannelMap.clear();
+    	System.out.println("Loading the SVT bad channels for run " + runNumber);
+    	
+    	ConditionsManager conditions = ConditionsManager.defaultInstance();
+    	BufferedReader reader;
+    	
+    	// First load the bad channels found during QA (not run dependent)
+    	String filePath = "daqmap/svt_qa.badchannels";
+    	try{
+    		reader = new BufferedReader(conditions.getRawConditions(filePath).getReader());
+    		loadBadChannels(reader);
+    	} catch(IOException exception){
+    		throw new RuntimeException("Unable to load bad channels for list " + filePath , exception);
+    	}
+    	
+    	// Load the bad channels for the specified run number
+    	if(runNumber < 0) return;
+    	filePath = "daqmap/svt" + runNumber + ".badchannels";
+    	try{
+    		reader = new BufferedReader(conditions.getRawConditions(filePath).getReader());
+    		loadBadChannels(reader);
+    	} catch(IOException exception){
+    		// If the file isn't found, continue on with just the QA bad channels
+    		System.out.println("File " + filePath + " was not found! Continuing with only QA bad channels");
+    	}
+    }
+    
+    /**
+     * Load the bad channels from a file using the specified character stream.
+     * 
+     * @param reader : character stream of type Reader
+     */
+    public static void loadBadChannels(Reader reader){
+    	BufferedReader badChannelReader = new BufferedReader(reader);
+    	
+    	String line = null;
+    	try{
+    		while((line = badChannelReader.readLine()) != null){
+    			// If the line is a comment, skip it
+    			if(line.indexOf("#") != -1) continue;
+    			StringTokenizer stringTok = new StringTokenizer(line);
+    			while(stringTok.hasMoreTokens()){
+    				int badChannel = Integer.valueOf(stringTok.nextToken());
+    				int fpga       = Integer.valueOf(stringTok.nextToken());
+    				int hybrid     = Integer.valueOf(stringTok.nextToken());
+    				System.out.println("FPGA: " + fpga + " Hybrid: " + hybrid + " Bad Channel: " + badChannel);
+    				Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);
+    				if(!badChannelMap.containsKey(daqPair))
+    					badChannelMap.put(daqPair, new HashSet<Integer>());
+    				badChannelMap.get(daqPair).add(badChannel);
+    			}
+    		}
+    	} catch(IOException exception){
+    		throw new RuntimeException("Unable to parse SVT bad channel list", exception);
+    	}
+    }

 
     public static Double getNoise(SiSensor sensor, int channel) {
         Pair<Integer, Integer> daqPair = SvtUtils.getInstance().getDaqPair(sensor);

@@ -335,6 +394,20 @@

         return constants;
     }
 

+    /**
+     * Checks if a channel has been tagged as bad
+     * 
+     * @param daqPair : a Hybrid/FPGA pair defining which sensor the 
+     * 					channels in located on
+     * @param channel : The channel to be checked
+     * @return true if the channel is bad, false otherwise
+     */
+    public static boolean isBadChannel(SiSensor sensor, int channel){
+    	Pair<Integer, Integer> daqPair = SvtUtils.getInstance().getDaqPair(sensor);
+    	if(badChannelMap.get(daqPair) != null && badChannelMap.get(daqPair).contains(channel)) return true;
+    	else return false;
+    }
+    

     //class to hold calibration constants for a channel; leave fields NaN or null if not known
     public static class ChannelConstants {