Pyroprint.java

public class Pyroprint
   implements java.io.Serializable{
   private static final int RELEVANT_VALS = 93;
   private int lineNum;
   private int pyroId;
   private String isolateId;
   private String commonName;
   private String appliedRegion;
   double[] pHeightOrig;
   double[] pHeightComp;

   public Pyroprint(int lineNum, int pyroId, 
         String isolateId, 
         String commonName, 
         String appliedRegion,
         double[] pHeightIn){
      this.lineNum = lineNum;
      this.pyroId = pyroId;
      this.isolateId = isolateId;
      this.commonName = commonName;
      this.appliedRegion = appliedRegion;
      this.pHeightComp = new double[RELEVANT_VALS];
      this.pHeightOrig = new double[pHeightIn.length];

      for(int arrLoc = 0; arrLoc < RELEVANT_VALS; arrLoc++){
         this.pHeightComp[arrLoc] = pHeightIn[arrLoc];
         this.pHeightOrig[arrLoc] = pHeightIn[arrLoc];
      }
      for(int arrLoc = RELEVANT_VALS; arrLoc < pHeightIn.length; arrLoc++){
         this.pHeightOrig[arrLoc] = pHeightIn[arrLoc];
      }
   }
   //PYROPRINT STUFFS //==>
   public int getPyroId(){
      return pyroId;
   }
   public String getIsolateId(){
      return isolateId;
   }
   public String getCommonName(){
      return commonName;
   }
   public void setCommonName(String commonName){
      this.commonName = commonName;
   }
   public String getAppliedRegion(){
      return appliedRegion;
   }
   public int getNumPHeights(){
      return pHeightOrig.length;
   }
   static int getRelevantVals(){
      return RELEVANT_VALS;
   }
   public String toString(){
      return this.pyroId + ":" + this.isolateId + ":" 
         + this.commonName +":" + this.appliedRegion + ":[" + pHeightComp.length + "]";
   }
   public boolean equals(Object other){
      if(other == null) return false;
      if(this.getClass() != other.getClass()) return false;
      if(this.pyroId != ((Pyroprint)other).pyroId) return false;
      if(!this.appliedRegion.equals(((Pyroprint)other).appliedRegion)) 
         return false;
      return true;
   }//<==
   //MATHS
   public double pearsonDist(Pyroprint other){
      double covariance = covariance(this.pHeightComp,other.pHeightComp);
      double thisStandardDev = standardDev(this.pHeightComp);
      double otherStandardDev = standardDev(other.pHeightComp);

      return covariance/(thisStandardDev*otherStandardDev);
   }
   //PRIVATE HELPERS
   /**
    * Calculates the MEAN of the doubles values in a given array.
    *
    * @param double array containing values to calculate upon
    * @return double type mean of the given data
    */
   private double mean(double[] values){//==>
      double mean = 0;
      for(int dataLoc = 0; dataLoc < values.length; dataLoc++){
         mean += values[dataLoc];
      }
      mean /= values.length;
      return mean;
   }//<==

   /**
    * Calculates the covariance betwen two double arrays. For now, it chooses
    * the length of the x array to calculate over. In the future, we may need
    * to implement something to consider the smaller length and calculate over
    * only that one.
    */
   private double covariance(double[] x, double[] y){//==>
      if(x.length != y.length){
         throw new IncomparableVectorException("Vectors are not equal in length. x[ " 
               +x.length + "] y[" + y.length + "]");
      }
      double covariance = 0;
      double xMean = mean(x);
      double yMean = mean(y);
      double dataPoints = x.length;     
      for(int dataLoc = 0; dataLoc < dataPoints; dataLoc++){
         covariance += (x[dataLoc] - xMean)*(y[dataLoc] - yMean);
      }
      covariance /= dataPoints;
      
      return covariance;
   }//<==

   /**
    * Calculates the variance of the double values in a given array. Variance
    * here is defined as the average square of the difference between each
    * value and the mean.
    *
    * @param double array containing values to calculate upon
    * @return double type variance of the given data
    */
   private double variance(double[] values){//==>
      return covariance(values,values);
   }//<==

   /**
    * Calculates the standard deviation of a double type array using the 
    */
   private double standardDev(double[] values){//==>
      return Math.sqrt(variance(values));
   }

   /**
    * IncomparableVectorException is a RuntimeException class made for throwing
    * the program when two vectors cannot be compared, usually for the
    * difference in length.
    */
   public class IncomparableVectorException//==>
         extends RuntimeException{
         public IncomparableVectorException(){
         }
         public IncomparableVectorException(String msg){
            super(msg);
         }
   }//<==
}