-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
-package jalview.analysis;\r
-\r
-\r
-import java.util.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-\r
-\r
-public class Conservation {\r
- Vector sequences;\r
- int start;\r
- int end;\r
-\r
- Vector total = new Vector();\r
-\r
- String consString = "";\r
-\r
- DrawableSequence consSequence;\r
- Hashtable propHash;\r
- int threshold;\r
-\r
- String name = "";\r
-\r
- public Conservation(String name,Hashtable propHash, int threshold, Vector sequences, int start, int end) {\r
- this.name = name;\r
- this.propHash = propHash;\r
- this.threshold = threshold;\r
- this.sequences = sequences;\r
- this.start = start;\r
- this.end = end;\r
- }\r
-\r
-\r
- public void calculate() {\r
-\r
- for (int i = start;i <= end; i++) {\r
- Hashtable resultHash = null;\r
- Hashtable residueHash = null;\r
-\r
- resultHash = new Hashtable();\r
- residueHash = new Hashtable();\r
-\r
- for (int j=0; j < sequences.size(); j++) {\r
-\r
- if (sequences.elementAt(j) instanceof Sequence) {\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- if (s.getLength() > i) {\r
- String res = s.getSequence().substring(i,i+1);\r
-\r
- if (residueHash.containsKey(res)) {\r
- int count = ((Integer)residueHash.get(res)).intValue() ;\r
- count++;\r
- residueHash.put(res,new Integer(count));\r
- } else {\r
- residueHash.put(res,new Integer(1));\r
- }\r
- } else {\r
- if (residueHash.containsKey("-")) {\r
- int count = ((Integer)residueHash.get("-")).intValue() ;\r
- count++;\r
- residueHash.put("-",new Integer(count));\r
- } else {\r
- residueHash.put("-",new Integer(1));\r
- }\r
- }\r
- }\r
- }\r
-\r
- //What is the count threshold to count the residues in residueHash()\r
- int thresh = threshold*(sequences.size())/100;\r
-\r
- //loop over all the found residues\r
- Enumeration e = residueHash.keys();\r
-\r
- while (e.hasMoreElements()) {\r
-\r
- String res = (String)e.nextElement();\r
- if (((Integer)residueHash.get(res)).intValue() > thresh) {\r
-\r
- //Now loop over the properties\r
- Enumeration e2 = propHash.keys();\r
-\r
- while (e2.hasMoreElements()) {\r
- String type = (String)e2.nextElement();\r
- Hashtable ht = (Hashtable)propHash.get(type);\r
-\r
- //Have we ticked this before?\r
- if (! resultHash.containsKey(type)) {\r
- if (ht.containsKey(res)) {\r
- resultHash.put(type,ht.get(res));\r
- } else {\r
- resultHash.put(type,ht.get("-"));\r
- }\r
- } else if ( ((Integer)resultHash.get(type)).equals((Integer)ht.get(res)) == false) {\r
- resultHash.put(type,new Integer(-1));\r
- }\r
- }\r
- }\r
- }\r
- total.addElement(resultHash);\r
- }\r
- }\r
-\r
- public int countGaps(int j) {\r
- int count = 0;\r
-\r
- for (int i = 0; i < sequences.size();i++) {\r
- if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
- { count++; continue;}\r
-\r
- String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);\r
- if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {\r
- count++;\r
- }\r
- }\r
- return count;\r
- }\r
-\r
- public void verdict(boolean consflag, float percentageGaps) {\r
- String consString = "";\r
-\r
- for (int i=start; i <= end; i++) {\r
- int totGaps = countGaps(i);\r
- float pgaps = (float)totGaps*100/(float)sequences.size();\r
-\r
- if (percentageGaps > pgaps)\r
- {\r
- Hashtable resultHash = (Hashtable)total.elementAt(i-start);\r
-\r
- //Now find the verdict\r
- int count = 0;\r
- Enumeration e3 = resultHash.keys();\r
-\r
- while (e3.hasMoreElements())\r
- {\r
- String type = (String)e3.nextElement();\r
- Integer result = (Integer)resultHash.get(type);\r
-\r
- //Do we want to count +ve conservation or +ve and -ve cons.?\r
-\r
- if (consflag)\r
- {\r
- if (result.intValue() == 1)\r
- count++;\r
- }\r
- else\r
- {\r
- if (result.intValue() != -1)\r
- count++;\r
- }\r
- }\r
-\r
- if (count < 10)\r
- consString = consString + String.valueOf(count);\r
- else\r
- consString = consString + "*";\r
-\r
- }\r
- else\r
- {\r
- consString = consString + "-";\r
- }\r
- }\r
-\r
- consSequence = new DrawableSequence(name,consString,start,end);\r
- }\r
-\r
- public jalview.gui.DrawableSequence getConsSequence() {\r
- return consSequence;\r
- }\r
-\r
-}\r
+/*
+* 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
+*/
+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
+{
+ 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++)
+ {
+ 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;
+
+ 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[132];
+
+ 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 = '-';
+
+ if ('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(
+ (Integer) ht.get(res)) == false)
+ {
+ 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)
+ {
+ 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('-');
+
+
+ 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())
+ {
+ 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()
+ {
+ 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);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff