X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=4ef250b2cf6b10d564fd938b9b85557144eae437;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=c61e7ef43b2da5375135442df1f7a9e651e7e191;hpb=bec86286aeecc7008a006e56efe3816a509cc593;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index c61e7ef..4ef250b 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,386 +1,134 @@ +/* +* 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.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. +import jalview.datamodel.*; - public static Vector calculate(Vector sequences,int start,int end) { +import java.util.*; - Vector result = new Vector(); - for (int i = start;i <= end; i++) +/** + * 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. + * @author $author$ + * @version $Revision$ + */ +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(); - Hashtable residueHash = new Hashtable(); - int maxCount = 0; - String maxResidue = "-"; - int nongap = 0; - for (int j=0; j < sequences.size(); j++) - { - - if (sequences.elementAt(j) instanceof Sequence) + for (int i = start; i <= end; i++) { - Sequence s = (Sequence)sequences.elementAt(j); - - if (s.getSequence().length() > i) - { + Hashtable residueHash = new Hashtable(); + int maxCount = 0; + String maxResidue = "-"; + int nongap = 0; - String res = s.getSequence().charAt(i)+""; - - if (!jalview.util.Comparison.isGap(res.charAt(0))) - nongap++; - - if (residueHash.containsKey(res)) + for (int j = 0; j < sequences.size(); j++) { - - int count = ((Integer)residueHash.get(res)).intValue() ; - count++; - - if (!jalview.util.Comparison.isGap(res.charAt(0)) && count >= maxCount) - { - - if(count>maxCount) - maxResidue = res; - else if(maxResidue.indexOf(res)==-1) - maxResidue += res; - - maxCount = count; - } - - residueHash.put(res,new Integer(count)); + if (sequences.elementAt(j) instanceof Sequence) + { + Sequence s = (Sequence) sequences.elementAt(j); + + if (s.getSequence().length() > i) + { + String res = s.getSequence().charAt(i) + ""; + + if (!jalview.util.Comparison.isGap(res.charAt(0))) + { + nongap++; + } + else + { + res = "-"; // we always use this for gaps in the property vectors + } + + if (residueHash.containsKey(res)) + { + int count = ((Integer) residueHash.get(res)).intValue(); + count++; + + if (!jalview.util.Comparison.isGap(res.charAt(0)) && + (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)); + } + } + } } - else - residueHash.put(res,new Integer(1)); + residueHash.put("maxCount", new Integer(maxCount)); - } - else - { - if (residueHash.containsKey("-")) + if (maxCount < 0) { - int count = ((Integer)residueHash.get("-")).intValue() ; - count++; - residueHash.put("-",new Integer(count)); + System.out.println("asasa " + maxCount); } - else - residueHash.put("-",new Integer(1)); - } + residueHash.put("maxResidue", maxResidue); + residueHash.put("size", new Integer(sequences.size())); + residueHash.put("nongap", new Integer(nongap)); + result.addElement(residueHash); } - } - residueHash.put("maxCount",new Integer(maxCount)); - if(maxCount<0) - System.out.println("asasa "+maxCount); - residueHash.put("maxResidue", maxResidue); - residueHash.put("size", new Integer(sequences.size())); - residueHash.put("nongap", new Integer(nongap)); - result.addElement(residueHash); + return result; } - - 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)); - } - - } - return blocks; - } - - - - 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; - } - - 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)) { - - 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(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; - } - } -