/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.analysis;
-import jalview.datamodel.*;
-
import java.util.*;
+import jalview.datamodel.*;
/**
* Calculates conservation values for a given set of sequences
*/
public class Conservation
{
- SequenceI [] sequences;
- int start;
- int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
- int maxLength = 0; // used by quality calcs
- boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
- Hashtable [] total;
-
- /** Stores calculated quality values */
- public Vector quality;
-
- /** Stores maximum and minimum values of quality values */
- public Double[] qualityRange = new Double[2];
- String consString = "";
- Sequence consSequence;
- Hashtable propHash;
- int threshold;
- String name = "";
- int[][] cons2;
-
- /**
- * Creates a new Conservation object.
- *
- * @param name Name of conservation
- * @param propHash DOCUMENT ME!
- * @param threshold to count the residues in residueHash(). commonly used value is 3
- * @param sequences sequences to be used in calculation
- * @param start start residue position
- * @param end end residue position
- */
- public Conservation(String name, Hashtable propHash, int threshold,
- Vector sequences, int start, int end)
+ SequenceI[] sequences;
+ int start;
+ int end;
+ Vector seqNums; // vector of int vectors where first is sequence checksum
+ int maxLength = 0; // used by quality calcs
+ boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
+ Hashtable[] total;
+
+ /** Stores calculated quality values */
+ public Vector quality;
+
+ /** Stores maximum and minimum values of quality values */
+ public Double[] qualityRange = new Double[2];
+ String consString = "";
+ Sequence consSequence;
+ Hashtable propHash;
+ int threshold;
+ String name = "";
+ int[][] cons2;
+
+ /**
+ * Creates a new Conservation object.
+ *
+ * @param name Name of conservation
+ * @param propHash DOCUMENT ME!
+ * @param threshold to count the residues in residueHash(). commonly used value is 3
+ * @param sequences sequences to be used in calculation
+ * @param start start residue position
+ * @param end end residue position
+ */
+ public Conservation(String name, Hashtable propHash, int threshold,
+ Vector sequences, int start, int end)
+ {
+
+ this.name = name;
+ this.propHash = propHash;
+ this.threshold = threshold;
+ this.start = start;
+ this.end = end;
+
+ maxLength = end - start + 1; // default width includes bounds of calculation
+
+ int s, sSize = sequences.size();
+ SequenceI[] sarray = new SequenceI[sSize];
+ this.sequences = sarray;
+
+ for (s = 0; s < sSize; s++)
{
-
- this.name = name;
- this.propHash = propHash;
- this.threshold = threshold;
- this.start = start;
- this.end = end;
-
- maxLength=end-start+1; // default width includes bounds of calculation
-
- int s, sSize = sequences.size();
- SequenceI[] sarray = new SequenceI[sSize];
- this.sequences = sarray;
-
- for (s = 0; s < sSize; s++)
- {
- sarray[s] = (SequenceI) sequences.elementAt(s);
- if(sarray[s].getLength()>maxLength)
- maxLength = sarray[s].getLength();
- }
+ sarray[s] = (SequenceI) sequences.elementAt(s);
+ if (sarray[s].getLength() > maxLength)
+ {
+ maxLength = sarray[s].getLength();
+ }
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ private void calcSeqNum(int i)
+ {
+ String sq = null; // for dumb jbuilder not-inited exception warning
+ int[] sqnum = null;
+ int sSize = sequences.length;
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- private void calcSeqNum(int i)
+ if ( (i > -1) && (i < sSize))
{
- String sq = null; // for dumb jbuilder not-inited exception warning
- int[] sqnum = null;
+ sq = sequences[i].getSequenceAsString();
+
+ if (seqNums.size() <= i)
+ {
+ seqNums.addElement(new int[sq.length() + 1]);
+ }
- int sSize = sequences.length;
+ if (sq.hashCode() != ( (int[]) seqNums.elementAt(i))[0])
+ {
+ int j;
+ int len;
+ seqNumsChanged = true;
+ len = sq.length();
- if ((i > -1) && (i < sSize))
+ if (maxLength < len)
{
- sq = sequences[i].getSequenceAsString();
+ maxLength = len;
+ }
- if (seqNums.size() <= i)
- {
- seqNums.addElement(new int[sq.length() + 1]);
- }
+ sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
+ sqnum[0] = sq.hashCode();
- if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
- {
- int j;
- int len;
- seqNumsChanged = true;
- len = sq.length();
+ for (j = 1; j <= len; j++)
+ {
+ sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charAt(j - 1)];
+ }
- if (maxLength < len)
- {
- maxLength = len;
- }
+ seqNums.setElementAt(sqnum, i);
+ }
+ else
+ {
+ System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+ }
+ }
+ else
+ {
+ // JBPNote INFO level debug
+ System.err.println(
+ "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+ }
+ }
+
+ /**
+ * Calculates the conservation values for given set of sequences
+ */
+ public void calculate()
+ {
+ Hashtable resultHash, ht;
+ int thresh, j, jSize = sequences.length;
+ int[] values; // Replaces residueHash
+ String type, res = null;
+ char c;
+ Enumeration enumeration2;
+
+ total = new Hashtable[maxLength];
+
+ for (int i = start; i <= end; i++)
+ {
+ values = new int[255];
- sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
- sqnum[0] = sq.hashCode();
+ for (j = 0; j < jSize; j++)
+ {
+ if (sequences[j].getLength() > i)
+ {
+ c = sequences[j].getCharAt(i);
- for (j = 1; j <= len; j++)
- {
- sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charAt(j-1)];
- }
+ // No need to check if its a '-'
+ if (c == '.' || c == ' ')
+ {
+ c = '-';
+ }
+ if ('a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
- seqNums.setElementAt(sqnum, i);
- }
- else
- System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+ values[c]++;
}
else
{
- // JBPNote INFO level debug
- System.err.println(
- "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+ values['-']++;
}
- }
+ }
- /**
- * Calculates the conservation values for given set of sequences
- */
- public void calculate()
- {
- Hashtable resultHash, ht;
- int thresh, j, jSize = sequences.length;
- int[] values; // Replaces residueHash
- String type, res=null;
- char c;
- Enumeration enumeration2;
+ //What is the count threshold to count the residues in residueHash()
+ thresh = (threshold * (jSize)) / 100;
- total = new Hashtable[maxLength];
+ //loop over all the found residues
+ resultHash = new Hashtable();
+ for (char v = '-'; v < 'Z'; v++)
+ {
- for (int i = start; i <= end; i++)
+ if (values[v] > thresh)
{
- values = new int[255];
+ res = String.valueOf(v);
- for (j = 0; j < jSize; j++)
- {
- if (sequences[j].getLength() > i)
- {
- c = sequences[j].getCharAt(i);
-
- // No need to check if its a '-'
- if (c == '.' || c == ' ')
- c = '-';
+ //Now loop over the properties
+ enumeration2 = propHash.keys();
- if ('a' <= c && c <= 'z')
- {
- c -= (32);// 32 = 'a' - 'A'
- }
+ while (enumeration2.hasMoreElements())
+ {
+ type = (String) enumeration2.nextElement();
+ ht = (Hashtable) propHash.get(type);
- values[c]++;
+ //Have we ticked this before?
+ if (!resultHash.containsKey(type))
+ {
+ if (ht.containsKey(res))
+ {
+ resultHash.put(type, ht.get(res));
}
else
{
- values['-']++;
+ resultHash.put(type, ht.get("-"));
}
}
-
- //What is the count threshold to count the residues in residueHash()
- thresh = (threshold * (jSize)) / 100;
-
- //loop over all the found residues
- resultHash = new Hashtable();
- for (char v = '-'; v < 'Z'; v++)
+ else if ( ( (Integer) resultHash.get(type)).equals(
+ (Integer) ht.get(res)) == false)
{
-
- if (values[v] > thresh)
- {
- res = String.valueOf( v );
-
- //Now loop over the properties
- enumeration2 = propHash.keys();
-
- while (enumeration2.hasMoreElements())
- {
- type = (String) enumeration2.nextElement();
- ht = (Hashtable) propHash.get(type);
-
- //Have we ticked this before?
- if (!resultHash.containsKey(type))
- {
- if (ht.containsKey(res))
- {
- resultHash.put(type, ht.get(res));
- }
- else
- {
- resultHash.put(type, ht.get("-"));
- }
- }
- else if (((Integer) resultHash.get(type)).equals(
- (Integer) ht.get(res)) == false)
- {
- resultHash.put(type, new Integer(-1));
- }
- }
- }
+ resultHash.put(type, new Integer( -1));
}
-
- total[i-start] = resultHash;
+ }
}
- }
-
+ }
- /***
- * countConsNGaps
- * returns gap count in int[0], and conserved residue count in int[1]
- */
- public int[] countConsNGaps(int j)
+ total[i - start] = resultHash;
+ }
+ }
+
+ /***
+ * countConsNGaps
+ * returns gap count in int[0], and conserved residue count in int[1]
+ */
+ public int[] countConsNGaps(int j)
+ {
+ int count = 0;
+ int cons = 0;
+ int nres = 0;
+ int[] r = new int[2];
+ char f = '$';
+ int i, iSize = sequences.length;
+ char c;
+
+ for (i = 0; i < iSize; i++)
{
- int count = 0;
- int cons = 0;
- int nres = 0;
- int[] r = new int[2];
- char f = '$';
- int i, iSize = sequences.length;
- char c;
-
- for (i = 0; i < iSize; i++)
- {
- if (j >= sequences[i].getLength())
- {
- count++;
- continue;
- }
+ if (j >= sequences[i].getLength())
+ {
+ count++;
+ continue;
+ }
- c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
+ c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
- if (jalview.util.Comparison.isGap((c)))
- {
- count++;
- }
- else
- {
- nres++;
-
- if (nres == 1)
- {
- f = c;
- cons++;
- }
- else if (f == c)
- {
- cons++;
- }
- }
- }
+ if (jalview.util.Comparison.isGap( (c)))
+ {
+ count++;
+ }
+ else
+ {
+ nres++;
- r[0] = (nres == cons) ? 1 : 0;
- r[1] = count;
+ if (nres == 1)
+ {
+ f = c;
+ cons++;
+ }
+ else if (f == c)
+ {
+ cons++;
+ }
+ }
+ }
- return r;
+ r[0] = (nres == cons) ? 1 : 0;
+ r[1] = count;
+
+ return r;
+ }
+
+ /**
+ * Calculates the conservation sequence
+ *
+ * @param consflag if true, poitiveve conservation; false calculates negative conservation
+ * @param percentageGaps commonly used value is 25
+ */
+ public void verdict(boolean consflag, float percentageGaps)
+ {
+ StringBuffer consString = new StringBuffer();
+ String type;
+ Integer result;
+ int[] gapcons;
+ int totGaps, count;
+ float pgaps;
+ Hashtable resultHash;
+ Enumeration enumeration;
+
+ //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
+ //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
+ //DOES NOT EXIST IN JALVIEW 2.1.2
+ for (int i = 0; i < start; i++)
+ {
+ consString.append('-');
}
- /**
- * Calculates the conservation sequence
- *
- * @param consflag if true, poitiveve conservation; false calculates negative conservation
- * @param percentageGaps commonly used value is 25
- */
- public void verdict(boolean consflag, float percentageGaps)
+ for (int i = start; i <= end; i++)
{
- StringBuffer consString = new StringBuffer();
- String type;
- Integer result;
- int[] gapcons;
- int totGaps, count;
- float pgaps;
- Hashtable resultHash ;
- Enumeration enumeration;
-
- //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
- //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
- //DOES NOT EXIST IN JALVIEW 2.1.2
- for(int i=0; i<start; i++)
- consString.append('-');
-
-
- for (int i = start; i <= end; i++)
+ gapcons = countConsNGaps(i);
+ totGaps = gapcons[1];
+ pgaps = ( (float) totGaps * 100) / (float) sequences.length;
+
+ if (percentageGaps > pgaps)
+ {
+ resultHash = total[i - start];
+
+ //Now find the verdict
+ count = 0;
+ enumeration = resultHash.keys();
+
+ while (enumeration.hasMoreElements())
{
- gapcons = countConsNGaps(i);
- totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.length;
+ type = (String) enumeration.nextElement();
+ result = (Integer) resultHash.get(type);
- if (percentageGaps > pgaps)
+ //Do we want to count +ve conservation or +ve and -ve cons.?
+ if (consflag)
+ {
+ if (result.intValue() == 1)
{
- resultHash = total[i - start];
-
- //Now find the verdict
- count = 0;
- enumeration = resultHash.keys();
-
- while (enumeration.hasMoreElements())
- {
- type = (String) enumeration.nextElement();
- result = (Integer) resultHash.get(type);
-
- //Do we want to count +ve conservation or +ve and -ve cons.?
- if (consflag)
- {
- if (result.intValue() == 1)
- {
- count++;
- }
- }
- else
- {
- if (result.intValue() != -1)
- {
- count++;
- }
- }
- }
-
- if (count < 10)
- {
- consString.append(count); // Conserved props!=Identity
- }
- else
- {
- consString.append((gapcons[0] == 1) ? "*" : "+");
- }
+ count++;
}
- else
+ }
+ else
+ {
+ if (result.intValue() != -1)
{
- consString.append('-');
+ count++;
}
+ }
}
- consSequence = new Sequence(name, consString.toString(), start, end);
+ if (count < 10)
+ {
+ consString.append(count); // Conserved props!=Identity
+ }
+ else
+ {
+ consString.append( (gapcons[0] == 1) ? "*" : "+");
+ }
+ }
+ else
+ {
+ consString.append('-');
+ }
}
- /**
- *
- *
- * @return Conservation sequence
- */
- public Sequence getConsSequence()
+ consSequence = new Sequence(name, consString.toString(), start, end);
+ }
+
+ /**
+ *
+ *
+ * @return Conservation sequence
+ */
+ public Sequence getConsSequence()
+ {
+ return consSequence;
+ }
+
+ // From Alignment.java in jalview118
+ public void findQuality()
+ {
+ findQuality(0, maxLength - 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ private void percentIdentity2()
+ {
+ seqNums = new Vector();
+ // calcSeqNum(s);
+ int i = 0, iSize = sequences.length;
+ //Do we need to calculate this again?
+ for (i = 0; i < iSize; i++)
{
- return consSequence;
+ calcSeqNum(i);
}
- // From Alignment.java in jalview118
- public void findQuality()
+ if ( (cons2 == null) || seqNumsChanged)
{
- findQuality(0, maxLength - 1);
- }
+ cons2 = new int[maxLength][24];
- /**
- * DOCUMENT ME!
- */
- private void percentIdentity2()
- {
- seqNums = new Vector();
- // calcSeqNum(s);
- int i = 0, iSize = sequences.length;
- //Do we need to calculate this again?
- for (i = 0; i < iSize; i++)
+ // Initialize the array
+ for (int j = 0; j < 24; j++)
{
- calcSeqNum(i);
- }
-
-
- if ((cons2 == null) || seqNumsChanged)
+ for (i = 0; i < maxLength; i++)
{
- cons2 = new int[maxLength][24];
-
- // Initialize the array
- for (int j = 0; j < 24; j++)
- {
- for (i = 0; i < maxLength; i++)
- {
- cons2[i][j] = 0;
- }
- }
+ cons2[i][j] = 0;
+ }
+ }
- int[] sqnum;
- int j = 0;
+ int[] sqnum;
+ int j = 0;
- while (j < sequences.length)
- {
- sqnum = (int[]) seqNums.elementAt(j);
+ while (j < sequences.length)
+ {
+ sqnum = (int[]) seqNums.elementAt(j);
- for (i = 1; i < sqnum.length; i++)
- {
- cons2[i - 1][sqnum[i]]++;
- }
+ for (i = 1; i < sqnum.length; i++)
+ {
+ cons2[i - 1][sqnum[i]]++;
+ }
- for (i = sqnum.length - 1; i < maxLength; i++)
- {
- cons2[i][23]++; // gap count
- }
+ for (i = sqnum.length - 1; i < maxLength; i++)
+ {
+ cons2[i][23]++; // gap count
+ }
- j++;
- }
+ j++;
+ }
- // unnecessary ?
+ // unnecessary ?
- /* for (int i=start; i <= end; i++) {
- int max = -1000;
- int maxi = -1;
- int maxj = -1;
+ /* for (int i=start; i <= end; i++) {
+ int max = -1000;
+ int maxi = -1;
+ int maxj = -1;
- for (int j=0;j<24;j++) {
- if (cons2[i][j] > max) {
- max = cons2[i][j];
- maxi = i;
- maxj = j;
- }
+ for (int j=0;j<24;j++) {
+ if (cons2[i][j] > max) {
+ max = cons2[i][j];
+ maxi = i;
+ maxj = j;
+ }
- }
- } */
- }
+ }
+ } */
}
-
- /**
- * Calculates the quality of the set of sequences
- *
- * @param start Start residue
- * @param end End residue
- */
- public void findQuality(int start, int end)
+ }
+
+ /**
+ * Calculates the quality of the set of sequences
+ *
+ * @param start Start residue
+ * @param end End residue
+ */
+ public void findQuality(int start, int end)
+ {
+ quality = new Vector();
+
+ double max = -10000;
+ int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+
+ //Loop over columns // JBPNote Profiling info
+ //long ts = System.currentTimeMillis();
+ //long te = System.currentTimeMillis();
+ percentIdentity2();
+
+ int size = seqNums.size();
+ int[] lengths = new int[size];
+ double tot, bigtot, sr, tmp;
+ double[] x, xx;
+ int l, j, i, ii, i2, k, seqNum;
+
+ for (l = 0; l < size; l++)
{
- quality = new Vector();
-
- double max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+ lengths[l] = ( (int[]) seqNums.elementAt(l)).length - 1;
+ }
- //Loop over columns // JBPNote Profiling info
- //long ts = System.currentTimeMillis();
- //long te = System.currentTimeMillis();
- percentIdentity2();
+ for (j = start; j <= end; j++)
+ {
+ bigtot = 0;
- int size = seqNums.size();
- int[] lengths = new int[size];
- double tot, bigtot, sr, tmp;
- double [] x, xx;
- int l, j, i, ii, i2, k, seqNum;
+ // First Xr = depends on column only
+ x = new double[24];
- for (l = 0; l < size; l++)
- lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+ for (ii = 0; ii < 24; ii++)
+ {
+ x[ii] = 0;
- for (j = start; j <= end; j++)
+ for (i2 = 0; i2 < 24; i2++)
{
- bigtot = 0;
-
- // First Xr = depends on column only
- x = new double[24];
-
- for (ii = 0; ii < 24; ii++)
- {
- x[ii] = 0;
-
- for (i2 = 0; i2 < 24; i2++)
- {
- x[ii] += ( ( (double) cons2[j][i2] * BLOSUM62[ii][i2]) +
- 4);
- }
-
- x[ii] /= size;
- }
+ x[ii] += ( ( (double) cons2[j][i2] * BLOSUM62[ii][i2]) +
+ 4);
+ }
- // Now calculate D for each position and sum
- for (k = 0; k < size; k++)
- {
- tot = 0;
- xx = new double[24];
- seqNum = (j < lengths[k])
- ? ((int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end
+ x[ii] /= size;
+ }
- // This is a loop over r
- for (i = 0; i < 23; i++)
- {
- sr = 0;
+ // Now calculate D for each position and sum
+ for (k = 0; k < size; k++)
+ {
+ tot = 0;
+ xx = new double[24];
+ seqNum = (j < lengths[k])
+ ? ( (int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end
- sr = (double) BLOSUM62[i][seqNum] + 4;
+ // This is a loop over r
+ for (i = 0; i < 23; i++)
+ {
+ sr = 0;
- //Calculate X with another loop over residues
- // System.out.println("Xi " + i + " " + x[i] + " " + sr);
- xx[i] = x[i] - sr;
+ sr = (double) BLOSUM62[i][seqNum] + 4;
- tot += (xx[i] * xx[i]);
- }
+ //Calculate X with another loop over residues
+ // System.out.println("Xi " + i + " " + x[i] + " " + sr);
+ xx[i] = x[i] - sr;
- bigtot += Math.sqrt(tot);
- }
+ tot += (xx[i] * xx[i]);
+ }
- // This is the quality for one column
- if (max < bigtot)
- {
- max = bigtot;
- }
+ bigtot += Math.sqrt(tot);
+ }
- // bigtot = bigtot * (size-cons2[j][23])/size;
- quality.addElement(new Double(bigtot));
+ // This is the quality for one column
+ if (max < bigtot)
+ {
+ max = bigtot;
+ }
- // Need to normalize by gaps
- }
+ // bigtot = bigtot * (size-cons2[j][23])/size;
+ quality.addElement(new Double(bigtot));
- double newmax = -10000;
+ // Need to normalize by gaps
+ }
- for (j = start; j <= end; j++)
- {
- tmp = ((Double) quality.elementAt(j)).doubleValue();
- tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+ double newmax = -10000;
- // System.out.println(tmp+ " " + j);
- quality.setElementAt(new Double(tmp), j);
+ for (j = start; j <= end; j++)
+ {
+ tmp = ( (Double) quality.elementAt(j)).doubleValue();
+ tmp = ( (max - tmp) * (size - cons2[j][23])) / size;
- if (tmp > newmax)
- {
- newmax = tmp;
- }
- }
+ // System.out.println(tmp+ " " + j);
+ quality.setElementAt(new Double(tmp), j);
- // System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
+ if (tmp > newmax)
+ {
+ newmax = tmp;
+ }
}
+
+ // System.out.println("Quality " + s);
+ qualityRange[0] = new Double(0);
+ qualityRange[1] = new Double(newmax);
+ }
}