X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=f12d8016905fbc9dd990d62f340624d2d2c91593;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=b914108dbeb4428eb7eebf2f9d6263feaba02b17;hpb=db8b5a2bbc50c28300729664f5a586b08748bb55;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b914108..f12d801 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,575 +1,780 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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.*;
-
-
-/**
- * Calculates conservation values for a given set of sequences
- *
- * @author $author$
- * @version $Revision$
- */
-public class Conservation
-{
- Vector 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;
- Vector total = new Vector();
-
- /** 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.sequences = sequences;
- this.start = start;
- this.end = end;
- seqNums = new Vector(sequences.size());
- calcSeqNums();
- }
-
- /**
- * DOCUMENT ME!
- */
- private void calcSeqNums()
- {
- int i=0, iSize=sequences.size();
- for (i=0; i < iSize; i++)
- {
- calcSeqNum(i);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- private void calcSeqNum(int i)
- {
- String sq = null; // for dumb jbuilder not-inited exception warning
- int[] sqnum = null;
-
- if ((i > -1) && (i < sequences.size()))
- {
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();
-
- if (seqNums.size() <= i)
- {
- seqNums.addElement(new int[sq.length() + 1]);
- }
-
- if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
- {
- int j;
- int len;
- seqNumsChanged = true;
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();
- len = sq.length();
-
- if (maxLength < len)
- {
- maxLength = len;
- }
-
- sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
- sqnum[0] = sq.hashCode();
-
- for (j = 1; j <= len; j++)
- {
- sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(String.valueOf(
- sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash
- }
-
- seqNums.setElementAt(sqnum, i);
- }
- }
- 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, residueHash, ht;
- int count, thresh, j, jSize = sequences.size();
- String type, res=null;
- SequenceI sequence;
- char c;
- Enumeration enumeration, enumeration2;
-
- for (int i = start; i <= end; i++)
- {
- resultHash = new Hashtable();
- residueHash = new Hashtable();
-
- for (j = 0; j < jSize; j++)
- {
- // JBPNote - have to make sure elements of the sequences vector
- // are tested like this everywhere...
- sequence = (Sequence) sequences.elementAt(j);
-
- if (sequence.getLength() > i)
- {
- c = sequence.getCharAt(i);
-
- if(jalview.util.Comparison.isGap(c))
- c = '-';
-
- if ('a' <= c && c <= 'z')
- {
- // TO UPPERCASE !!!
- //Faster than toUpperCase
- c -= ('a' - 'A') ;
- }
-
- res = String.valueOf( c );
-
-
- if (residueHash.containsKey(res))
- {
- count = ((Integer) residueHash.get(res)).intValue();
- count++;
- residueHash.put(res, new Integer(count));
- }
- else
- {
- residueHash.put(res, new Integer(1));
- }
- }
- else
- {
- if (residueHash.containsKey("-"))
- {
- count = ((Integer) residueHash.get("-")).intValue();
- count++;
- residueHash.put("-", new Integer(count));
- }
- else
- {
- residueHash.put("-", new Integer(1));
- }
- }
- }
-
- //What is the count threshold to count the residues in residueHash()
- thresh = (threshold * (sequences.size())) / 100;
-
- //loop over all the found residues
- enumeration = residueHash.keys();
-
- while (enumeration.hasMoreElements())
- {
- res = (String) enumeration.nextElement();
-
- if (((Integer) residueHash.get(res)).intValue() > thresh)
- {
- //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));
- }
- }
- }
- }
-
- total.addElement(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.size();
- char c;
-
- for (i = 0; i < iSize; i++)
- {
- if (j >= ((Sequence) sequences.elementAt(i)).getLength())
- {
- count++;
- continue;
- }
-
- c = ((Sequence) sequences.elementAt(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++;
- }
- }
- }
-
- 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;
-
-
- for (int i = start; i <= end; i++)
- {
- gapcons = countConsNGaps(i);
- totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.size();
-
- if (percentageGaps > pgaps)
- {
- resultHash = (Hashtable) total.elementAt(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) ? "*" : "+");
- }
- }
- else
- {
- consString.append("-");
- }
- }
-
- 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()
- {
- calcSeqNums(); // updates maxLength, too.
-
- if ((cons2 == null) || seqNumsChanged)
- {
- cons2 = new int[maxLength][24];
-
- // Initialize the array
- for (int j = 0; j < 24; j++)
- {
- for (int i = 0; i < maxLength; i++)
- {
- cons2[i][j] = 0;
- }
- }
-
- int[] sqnum;
- int j = 0;
-
- while (j < sequences.size())
- {
- sqnum = (int[]) seqNums.elementAt(j);
-
- for (int i = 1; i < sqnum.length; i++)
- {
- cons2[i - 1][sqnum[i]]++;
- }
-
- for (int i = sqnum.length - 1; i < maxLength; i++)
- {
- cons2[i][23]++; // gap count
- }
-
- j++;
- }
-
- // unnecessary ?
-
- /* 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;
- }
-
- }
- } */
- }
- }
-
- /**
- * 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, seqNum;
-
- for (l = 0; l < size; l++)
- lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
-
-
- for (j = start; j <= end; j++)
- {
- bigtot = 0;
-
- // First Xr = depends on column only
- x = new double[24];
-
- for (ii = 0; ii < 24; ii++)
- {
- x[ii] = 0;
-
- try
- {
- for (int i2 = 0; i2 < 24; i2++)
- {
- x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) +
- 4);
- }
- }
- catch (Exception e)
- {
- System.err.println("Exception during quality calculation.");
- e.printStackTrace();
- }
-
- //System.out.println("X " + ii + " " + x[ii]);
- x[ii] /= (size);
-
- //System.out.println("X " + ii + " " + x[ii]);
- }
-
- // Now calculate D for each position and sum
- for (int 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
-
- // This is a loop over r
- for (i = 0; i < 23; i++)
- {
- sr = 0;
-
- try
- {
- sr = (double) BLOSUM62[i][seqNum] + 4;
- }
- catch (Exception e)
- {
- System.out.println("Exception in sr: " + e);
- e.printStackTrace();
- }
-
- //Calculate X with another loop over residues
- // System.out.println("Xi " + i + " " + x[i] + " " + sr);
- xx[i] = x[i] - sr;
-
- tot += (xx[i] * xx[i]);
- }
-
- bigtot += Math.sqrt(tot);
- }
-
- // This is the quality for one column
- if (max < bigtot)
- {
- max = bigtot;
- }
-
- // bigtot = bigtot * (size-cons2[j][23])/size;
- quality.addElement(new Double(bigtot));
-
-
- // Need to normalize by gaps
- }
-
- double newmax = -10000;
-
- for (j = start; j <= end; j++)
- {
- tmp = ((Double) quality.elementAt(j)).doubleValue();
- tmp = ((max - tmp) * (size - cons2[j][23])) / size;
-
- // System.out.println(tmp+ " " + j);
- quality.setElementAt(new Double(tmp), j);
-
- if (tmp > newmax)
- {
- newmax = tmp;
- }
- }
-
- // System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+/**
+ * Calculates conservation values for a given set of sequences
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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;
+
+ boolean canonicaliseAa = true; // if true then conservation calculation will
+
+ // map all symbols to canonical aa numbering
+ // rather than consider conservation of that
+ // symbol
+
+ /** 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;
+
+ private String[] consSymbs;
+
+ /**
+ * Creates a new Conservation object.
+ *
+ * @param name
+ * Name of conservation
+ * @param propHash
+ * hash of properties for each symbol
+ * @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,
+ List 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;
+ try
+ {
+ for (s = 0; s < sSize; s++)
+ {
+ sarray[s] = sequences.get(s);
+ if (sarray[s].getLength() > maxLength)
+ {
+ maxLength = sarray[s].getLength();
+ }
+ }
+ } catch (ArrayIndexOutOfBoundsException ex)
+ {
+ // bail - another thread has modified the sequence array, so the current
+ // calculation is probably invalid.
+ this.sequences = new SequenceI[0];
+ maxLength = 0;
+ }
+ }
+
+ /**
+ * Translate sequence i into a numerical representation and store it in the
+ * i'th position of the seqNums array.
+ *
+ * @param i
+ */
+ private void calcSeqNum(int i)
+ {
+ String sq = null; // for dumb jbuilder not-inited exception warning
+ int[] sqnum = null;
+
+ int sSize = sequences.length;
+
+ if ((i > -1) && (i < sSize))
+ {
+ sq = sequences[i].getSequenceAsString();
+
+ if (seqNums.size() <= i)
+ {
+ seqNums.addElement(new int[sq.length() + 1]);
+ }
+
+ if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+ {
+ int j;
+ int len;
+ seqNumsChanged = true;
+ len = sq.length();
+
+ if (maxLength < len)
+ {
+ maxLength = len;
+ }
+
+ sqnum = new int[len + 1]; // better to always make a new array -
+ // sequence can change its length
+ sqnum[0] = sq.hashCode();
+
+ for (j = 1; j <= len; j++)
+ {
+ sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq
+ .charAt(j - 1)];
+ }
+
+ 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];
+
+ for (j = 0; j < jSize; j++)
+ {
+ if (sequences[j].getLength() > i)
+ {
+ c = sequences[j].getCharAt(i);
+
+ if (canonicaliseAa)
+ { // lookup the base aa code symbol
+ c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
+ .getCharAt(i)];
+ if (c > 20)
+ {
+ c = '-';
+ }
+ else
+ {
+ // recover canonical aa symbol
+ c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
+ }
+ }
+ else
+ {
+ // original behaviour - operate on ascii symbols directly
+ // No need to check if its a '-'
+ if (c == '.' || c == ' ')
+ {
+ c = '-';
+ }
+
+ if (!canonicaliseAa && 'a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
+ }
+ values[c]++;
+ }
+ else
+ {
+ values['-']++;
+ }
+ }
+
+ // 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++)
+ {
+
+ 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(ht.get(res)) == false)
+ {
+ resultHash.put(type, new Integer(-1));
+ }
+ }
+ }
+ }
+
+ if (total.length > 0)
+ {
+ total[i - start] = resultHash;
+ }
+ }
+ }
+
+ /*****************************************************************************
+ * count conservation for the j'th column of the alignment
+ *
+ * @return { gap count, conserved residue count}
+ */
+ 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++)
+ {
+ if (j >= sequences[i].getLength())
+ {
+ count++;
+ continue;
+ }
+
+ 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++;
+ }
+ }
+ }
+
+ 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('-');
+ }
+ consSymbs = new String[end - start + 1];
+ for (int i = start; i <= end; i++)
+ {
+ gapcons = countConsNGaps(i);
+ totGaps = gapcons[1];
+ pgaps = ((float) totGaps * 100) / sequences.length;
+ consSymbs[i - start] = new String();
+
+ if (percentageGaps > pgaps)
+ {
+ 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)
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ count++;
+ }
+ }
+ else
+ {
+ if (result.intValue() != -1)
+ {
+ {
+ if (result.intValue() == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
+ }
+
+ count++;
+ }
+ }
+ }
+
+ if (count < 10)
+ {
+ consString.append(count); // Conserved props!=Identity
+ }
+ else
+ {
+ consString.append((gapcons[0] == 1) ? "*" : "+");
+ }
+ }
+ else
+ {
+ consString.append('-');
+ }
+ }
+
+ 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++)
+ {
+ calcSeqNum(i);
+ }
+
+ if ((cons2 == null) || seqNumsChanged)
+ {
+ 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;
+ }
+ }
+
+ int[] sqnum;
+ int j = 0;
+
+ while (j < sequences.length)
+ {
+ sqnum = (int[]) seqNums.elementAt(j);
+
+ 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
+ }
+
+ j++;
+ }
+
+ // unnecessary ?
+
+ /*
+ * 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; } } }
+ */
+ }
+ }
+
+ /**
+ * 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++)
+ {
+ lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+ }
+
+ for (j = start; j <= end; j++)
+ {
+ 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;
+ }
+
+ // 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
+
+ // This is a loop over r
+ for (i = 0; i < 23; i++)
+ {
+ sr = 0;
+
+ sr = (double) BLOSUM62[i][seqNum] + 4;
+
+ // Calculate X with another loop over residues
+ // System.out.println("Xi " + i + " " + x[i] + " " + sr);
+ xx[i] = x[i] - sr;
+
+ tot += (xx[i] * xx[i]);
+ }
+
+ bigtot += Math.sqrt(tot);
+ }
+
+ // This is the quality for one column
+ if (max < bigtot)
+ {
+ max = bigtot;
+ }
+
+ // bigtot = bigtot * (size-cons2[j][23])/size;
+ quality.addElement(new Double(bigtot));
+
+ // Need to normalize by gaps
+ }
+
+ double newmax = -10000;
+
+ for (j = start; j <= end; j++)
+ {
+ tmp = ((Double) quality.elementAt(j)).doubleValue();
+ tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+
+ // System.out.println(tmp+ " " + j);
+ quality.setElementAt(new Double(tmp), j);
+
+ if (tmp > newmax)
+ {
+ newmax = tmp;
+ }
+ }
+
+ // System.out.println("Quality " + s);
+ qualityRange[0] = new Double(0);
+ qualityRange[1] = new Double(newmax);
+ }
+
+ /**
+ * complete the given consensus and quuality annotation rows. Note: currently
+ * this method will enlarge the given annotation row if it is too small,
+ * otherwise will leave its length unchanged.
+ *
+ * @param conservation
+ * conservation annotation row
+ * @param quality2
+ * (optional - may be null)
+ * @param istart
+ * first column for conservation
+ * @param alWidth
+ * extent of conservation
+ */
+ public void completeAnnotations(AlignmentAnnotation conservation,
+ AlignmentAnnotation quality2, int istart, int alWidth)
+ {
+ char[] sequence = getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and
+ // Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ if (conservation.annotations != null
+ && conservation.annotations.length < alWidth)
+ {
+ conservation.annotations = new Annotation[alWidth];
+ }
+
+ if (quality2 != null)
+ {
+ quality2.graphMax = qualityRange[1].floatValue();
+ if (quality2.annotations != null
+ && quality2.annotations.length < alWidth)
+ {
+ quality2.annotations = new Annotation[alWidth];
+ }
+ qmin = qualityRange[0].floatValue();
+ qmax = qualityRange[1].floatValue();
+ }
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
+
+ if (Character.isDigit(c))
+ {
+ value = c - '0';
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ float vprop = value - min;
+ vprop /= max;
+ int consp = i - start;
+ String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
+ conservation.annotations[i] = new Annotation(String.valueOf(c),
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
+
+ // Quality calc
+ if (quality2 != null)
+ {
+ value = ((Double) quality.elementAt(i)).floatValue();
+ vprop = value - qmin;
+ vprop /= qmax;
+ quality2.annotations[i] = new Annotation(" ",
+ String.valueOf(value), ' ', value, new Color(minR
+ + (maxR * vprop), minG + (maxG * vprop), minB
+ + (maxB * vprop)));
+ }
+ }
+ }
+
+ /**
+ * construct and call the calculation methods on a new Conservation object
+ *
+ * @param name
+ * - name of conservation
+ * @param consHash
+ * - hash table of properties for each amino acid (normally
+ * ResidueProperties.propHash)
+ * @param threshold
+ * - minimum number of conserved residues needed to indicate
+ * conservation (typically 3)
+ * @param seqs
+ * @param start
+ * first column in calculation window
+ * @param end
+ * last column in calculation window
+ * @param posOrNeg
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(String name,
+ Hashtable consHash, int threshold, List seqs,
+ int start, int end, boolean posOrNeg, int consPercGaps,
+ boolean calcQuality)
+ {
+ Conservation cons = new Conservation(name, consHash, threshold, seqs,
+ start, end);
+ return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
+ }
+
+ /**
+ * @param b
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(Conservation cons,
+ boolean b, int consPercGaps, boolean calcQuality)
+ {
+ cons.calculate();
+ cons.verdict(b, consPercGaps);
+
+ if (calcQuality)
+ {
+ cons.findQuality();
+ }
+
+ return cons;
+ }
+}