X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=5b9a2a4be5eee5d0d5fa7134b5a312d19e37bfa1;hb=ae83cc59079dc5374a41402889b6f4192f66e9e2;hp=c8e6388ab31b34836969cea706c957da0d4bcc30;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index c8e6388..5b9a2a4 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,383 +1,150 @@ +/* +* 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.jbgui.*; import jalview.datamodel.*; -import jalview.io.*; -import jalview.analysis.*; -import java.awt.*; -import java.applet.Applet; import java.util.*; -import java.net.*; -import java.io.*; -public class AAFrequency { - // Takes in a vector of sequences and column start and column end - // and returns a vector of size (end-start+1). Each element of the - // vector contains a hashtable with the keys being residues and - // the values being the count of each residue in that column. - // This class is used extensively in calculating alignment colourschemes - // that depend on the amount of conservation in each alignment column. - - public static Vector calculate(Vector sequences,int start,int end) { - - Vector result = new Vector(); - - for (int i = start;i <= end; i++) +/** + * Takes in a vector or array of sequences and column start and column end + * and returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied. + * This class is used extensively in calculating alignment colourschemes + * that depend on the amount of conservation in each alignment column. + * @author $author$ + * @version $Revision$ + */ +public class AAFrequency +{ + //No need to store 1000s of strings which are not + //visible to the user. + public static final String MAXCOUNT = "C"; + public static final String MAXRESIDUE="R"; + public static final String PID_GAPS = "G"; + public static final String PID_NOGAPS="N"; + + public static final Hashtable [] calculate(Vector sequences, int start, int end) + { + SequenceI [] seqs = new SequenceI[sequences.size()]; + int width = 0; + for(int i=0; iwidth) + width = seqs[i].getLength(); + } + + Hashtable [] reply = new Hashtable[width]; + + if(end>=width) + { + end = width-1; + } + + calculate(seqs, start, end, reply); + + return reply; + } + +public static final void calculate(SequenceI[] sequences, + int start, int end, + Hashtable [] result) +{ + Hashtable residueHash; + int maxCount, nongap, i, j, v, jSize = sequences.length; + String maxResidue; + char c; + float percentage; + + int[] values = new int[132]; + + String seq; + + for (i = start; i < end; i++) + { + residueHash = new Hashtable(); + maxCount = 0; + maxResidue = ""; + nongap = 0; + values = new int[132]; + + for (j = 0; j < jSize; j++) { - - Hashtable residueHash = new Hashtable(); - int maxCount = -1; - String maxResidue = "-"; - int nongap = 0; - for (int j=0; j < sequences.size(); j++) + seq = sequences[j].getSequence(); + if (seq.length() > i) { + c = seq.charAt(i); - if (sequences.elementAt(j) instanceof Sequence) - { - Sequence s = (Sequence)sequences.elementAt(j); - - if (s.getSequence().length() > i) - { - - String res = s.getSequence().substring(i,i+1); - - if (!res.equals("-")) - nongap++; - - if (residueHash.containsKey(res)) - { - - int count = ((Integer)residueHash.get(res)).intValue() ; - count++; - - if (!res.equals("-") && count >= maxCount) - { - - if(count>maxCount) - maxResidue = res; - else if(maxResidue.indexOf(res)==-1) - maxResidue += res; - - maxCount = count; - } - - residueHash.put(res,new Integer(count)); - } - else - residueHash.put(res,new Integer(1)); - - - } - else - { - if (residueHash.containsKey("-")) - { - int count = ((Integer)residueHash.get("-")).intValue() ; - count++; - residueHash.put("-",new Integer(count)); - } - else - residueHash.put("-",new Integer(1)); + if(c == '.' || c==' ') + c = '-'; - } + if(c=='-') + { + values['-']++; + continue; + } + else if ('a' <= c && c <= 'z') + { + c -= 32 ;//('a' - 'A'); } - } - residueHash.put("maxCount",new Integer(maxCount)); - residueHash.put("maxResidue", maxResidue); - residueHash.put("size", new Integer(sequences.size())); - residueHash.put("nongap", new Integer(nongap)); - result.addElement(residueHash); - } - - return result; - } - - public static Vector calculatePID(SequenceI refseq,Vector sequences,int window,int start,int end) { - - Vector result = new Vector(); - - boolean init = true; - - - Vector prev = null; - - for (int i = start;i <= end; i++) { - Vector values = new Vector(); - - result.addElement(values); - - // If start < window/2 then set value to zero. - - if (i< window/2 || i >= refseq.getSequence().length()-window/2) { - for (int j = 0; j < sequences.size(); j++) { - values.addElement(new Integer(0)); - } - } else if (init == true) { - init = false; - - int winstart = i-window/2; - int winend = i+window/2; - - if (window%2 != 0) { - winend++; - } - - for (int j = 0; j < sequences.size(); j++) { - values.addElement(new Integer(0)); - } - - for (int k = winstart; k <= winend; k++) { - String refchar = refseq.getSequence().substring(k,k+1); - - for (int j = 0; j < sequences.size(); j++) { - - if (refchar.equals("-") == false) { - - Sequence s = (Sequence)sequences.elementAt(j); - - if (s.getSequence().length() > k) { - - String res = s.getSequence().substring(k,k+1); - - if (res.equals(refchar)) { - int val = ((Integer)values.elementAt(j)).intValue(); - val++; - values.setElementAt(new Integer(val),j); - } - } - } - } - } - prev = values; - } else { - int winstart = i-window/2; - int winend = i+window/2; - - if (window%2 != 0) { - winend++; - } - // We need to take the previous set of values - // subtract the pid at winstart-1 - // and add the pid at winend; - - String pre_refchar = refseq.getSequence().substring(winstart-1,winstart); - String pos_refchar = "-"; - - if (refseq.getSequence().length() > winend) { - pos_refchar = refseq.getSequence().substring(winend,winend+1); - } - - for (int j = 0; j < sequences.size(); j++) { - // First copy the pid value from i-1 - - int val = ((Integer)prev.elementAt(j)).intValue(); - - Sequence s = (Sequence)sequences.elementAt(j); - - String pre_char = s.getSequence().substring(winstart-1,winstart); - - String pos_char = "-"; - - if (s.getSequence().length() > winend) { - pos_char = s.getSequence().substring(winend,winend+1); - } - - // Now substract 1 if the chars at winstart-1 match - - if (pre_refchar.equals("-") == false && pre_char.equals(pre_refchar)) { - val--; - } - - if (pos_refchar.equals("-") == false && pos_char.equals(pos_refchar)) { - val++; - } - - values.addElement(new Integer(val)); - - - } - prev = values; - } - } - - return result; - } - - public static Hashtable findBlocks(Vector seqs, int start, int end,Vector exc) { - - // start and end are in real (not relative coords); - - // The coords in the hashtable that is returned are in relative coords - // i.e. start from 0 - - Hashtable blocks = new Hashtable(); - - boolean prev = false; - int bstart = -1; - - for (int i = start; i <= end ; i++) { - SequenceI seq = (SequenceI)seqs.elementAt(0); - - char c = seq.getCharAt(i); - - boolean found = true; - - int j = 1; - - while (j < seqs.size() && found == true) { - - SequenceI jseq = (SequenceI)seqs.elementAt(j); - - if (!exc.contains(jseq)) { - - char cc = jseq.getCharAt(i); - - if ( cc != c) { - found = false; - } - } - j++; - } - - - if (prev == false && found == true) { - bstart = i; - } else if (prev == true && found == false && bstart != -1) { - - int blockstart = bstart-start; - int blocklen = i-bstart; - - //System.out.println("Start len " + blockstart + " " + blocklen); - - for (int jj = blockstart; jj < blockstart + blocklen;jj++) { - blocks.put(new Integer(jj),new Integer(blocklen)); - } - - bstart = -1; - } - prev = found; - } - - if (bstart != -1) { - - int blockstart = bstart-start; - int blocklen = end-bstart; - - // System.out.println("Start len " + blockstart + " " + blocklen); - for (int jj = blockstart; jj < blockstart + blocklen;jj++) { - blocks.put(new Integer(blockstart),new Integer(blocklen)); - } + nongap++; + values[c]++; - } - return blocks; + } + else + { + values['-']++; + } } + for (v = 'A'; v < 'Z'; v++) + { + if (values[v] < 2 || values[v] < maxCount) + continue; - - public static Hashtable findKmerCount(SequenceI seq, int start, int end,int window, int step,Vector kmers) { - - int tmpstart = start; - Hashtable vals = new Hashtable(); - - while (tmpstart <= end) { - - String tmpstr = seq.getSequence().substring(tmpstart-window/2,tmpstart+window/2); - - int count = 0; - - //System.out.println("Str " + tmpstr); - - for (int ii = 0; ii < kmers.size(); ii++) { - String kmer = ((SequenceI)kmers.elementAt(ii)).getSequence(); - - int i = -1; - - while (tmpstr.indexOf(kmer,i) != -1) { - i = tmpstr.indexOf(kmer,i); - - i++; - count++; - } - ii++; - } - vals.put(new Integer(tmpstart),new Integer(count)); - tmpstart += step; - } - return vals; + if (values[v] > maxCount) + { + maxResidue = String.valueOf( (char) v); + } + else if (values[v] == maxCount) + { + maxResidue += String.valueOf( (char) v); + } + maxCount = values[v]; } - public static Hashtable findBlockStarts(Vector seqs, int start, int end,Vector exc) { - - // start and end are in real (not relative coords); - - // The coords in the hashtable that is returned are in relative coords - // i.e. start from 0 - - Hashtable blocks = new Hashtable(); - - boolean prev = false; - int bstart = -1; - - for (int i = start; i <= end ; i++) { - SequenceI seq = (SequenceI)seqs.elementAt(0); - - char c = seq.getCharAt(i); - - boolean found = true; - - int j = 1; - - while (j < seqs.size() && found == true) { - - SequenceI jseq = (SequenceI)seqs.elementAt(j); - - if (!exc.contains(jseq)) { + if(maxResidue.length()==0) + maxResidue = "-"; - char cc = jseq.getCharAt(i); + residueHash.put(MAXCOUNT, new Integer(maxCount)); + residueHash.put(MAXRESIDUE, maxResidue); - if ( cc != c) { - found = false; - } - } - j++; - } - - - if (prev == false && found == true) { - bstart = i; - } else if (prev == true && found == false && bstart != -1) { - - int blockstart = bstart-start; - int blocklen = i-bstart; - - // System.out.println("Start len " + blockstart + " " + blocklen); - - //for (int jj = blockstart; jj < blockstart + blocklen;jj++) { - blocks.put(new Integer(blockstart),new Integer(blocklen)); - // } - - bstart = -1; - } - prev = found; - } - - if (bstart != -1) { - - int blockstart = bstart-start; - int blocklen = end-bstart; - - // System.out.println("Start len " + blockstart + " " + blocklen); - - //for (int jj = blockstart; jj < blockstart + blocklen;jj++) { - blocks.put(new Integer(blockstart),new Integer(blocklen)); - // } - - } - return blocks; - } + percentage = ( (float) maxCount * 100) / (float) jSize; + residueHash.put(PID_GAPS, new Float(percentage)); + percentage = ( (float) maxCount * 100) / (float) nongap; + residueHash.put(PID_NOGAPS, new Float(percentage)); + result[i] = residueHash; + } +} } +