-package jalview.analysis;\r
-\r
-import jalview.jbgui.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.analysis.*;\r
-\r
-import java.awt.*;\r
-import java.applet.Applet;\r
-import java.util.*;\r
-import java.net.*;\r
-import java.io.*;\r
-\r
-public class AAFrequency {\r
-\r
- // Takes in a vector of sequences and column start and column end\r
- // and returns a vector of size (end-start+1). Each element of the\r
- // vector contains a hashtable with the keys being residues and\r
- // the values being the count of each residue in that column.\r
- // This class is used extensively in calculating alignment colourschemes\r
- // that depend on the amount of conservation in each alignment column.\r
-\r
- public static Vector calculate(Vector sequences,int start,int end) {\r
-\r
- Vector result = new Vector();\r
-\r
- for (int i = start;i <= end; i++)\r
- {\r
-\r
- Hashtable residueHash = new Hashtable();\r
- int maxCount = -1;\r
- String maxResidue = "-";\r
- int nongap = 0;\r
- for (int j=0; j < sequences.size(); j++)\r
- {\r
-\r
- if (sequences.elementAt(j) instanceof Sequence)\r
- {\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > i)\r
- {\r
-\r
- String res = s.getSequence().substring(i,i+1);\r
-\r
- if (!res.equals("-"))\r
- nongap++;\r
-\r
- if (residueHash.containsKey(res))\r
- {\r
-\r
- int count = ((Integer)residueHash.get(res)).intValue() ;\r
- count++;\r
-\r
- if (!res.equals("-") && count >= maxCount)\r
- {\r
-\r
- if(count>maxCount)\r
- maxResidue = res;\r
- else if(maxResidue.indexOf(res)==-1)\r
- maxResidue += res;\r
-\r
- maxCount = count;\r
- }\r
-\r
- residueHash.put(res,new Integer(count));\r
- }\r
- else\r
- residueHash.put(res,new Integer(1));\r
-\r
-\r
- }\r
- else\r
- {\r
- if (residueHash.containsKey("-"))\r
- {\r
- int count = ((Integer)residueHash.get("-")).intValue() ;\r
- count++;\r
- residueHash.put("-",new Integer(count));\r
- }\r
- else\r
- residueHash.put("-",new Integer(1));\r
-\r
- }\r
- }\r
- }\r
- residueHash.put("maxCount",new Integer(maxCount));\r
- residueHash.put("maxResidue", maxResidue);\r
- residueHash.put("size", new Integer(sequences.size()));\r
- residueHash.put("nongap", new Integer(nongap));\r
- result.addElement(residueHash);\r
- }\r
-\r
- return result;\r
- }\r
-\r
- public static Vector calculatePID(SequenceI refseq,Vector sequences,int window,int start,int end) {\r
-\r
- Vector result = new Vector();\r
-\r
- boolean init = true;\r
-\r
-\r
- Vector prev = null;\r
-\r
- for (int i = start;i <= end; i++) {\r
- Vector values = new Vector();\r
-\r
- result.addElement(values);\r
-\r
- // If start < window/2 then set value to zero.\r
-\r
- if (i< window/2 || i >= refseq.getSequence().length()-window/2) {\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
- } else if (init == true) {\r
- init = false;\r
-\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
-\r
- if (window%2 != 0) {\r
- winend++;\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
-\r
- for (int k = winstart; k <= winend; k++) {\r
- String refchar = refseq.getSequence().substring(k,k+1);\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
-\r
- if (refchar.equals("-") == false) {\r
-\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > k) {\r
-\r
- String res = s.getSequence().substring(k,k+1);\r
-\r
- if (res.equals(refchar)) {\r
- int val = ((Integer)values.elementAt(j)).intValue();\r
- val++;\r
- values.setElementAt(new Integer(val),j);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- prev = values;\r
- } else {\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
-\r
- if (window%2 != 0) {\r
- winend++;\r
- }\r
- // We need to take the previous set of values\r
- // subtract the pid at winstart-1\r
- // and add the pid at winend;\r
-\r
- String pre_refchar = refseq.getSequence().substring(winstart-1,winstart);\r
- String pos_refchar = "-";\r
-\r
- if (refseq.getSequence().length() > winend) {\r
- pos_refchar = refseq.getSequence().substring(winend,winend+1);\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- // First copy the pid value from i-1\r
-\r
- int val = ((Integer)prev.elementAt(j)).intValue();\r
-\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- String pre_char = s.getSequence().substring(winstart-1,winstart);\r
-\r
- String pos_char = "-";\r
-\r
- if (s.getSequence().length() > winend) {\r
- pos_char = s.getSequence().substring(winend,winend+1);\r
- }\r
-\r
- // Now substract 1 if the chars at winstart-1 match\r
-\r
- if (pre_refchar.equals("-") == false && pre_char.equals(pre_refchar)) {\r
- val--;\r
- }\r
-\r
- if (pos_refchar.equals("-") == false && pos_char.equals(pos_refchar)) {\r
- val++;\r
- }\r
-\r
- values.addElement(new Integer(val));\r
-\r
-\r
- }\r
- prev = values;\r
- }\r
- }\r
-\r
- return result;\r
- }\r
-\r
- public static Hashtable findBlocks(Vector seqs, int start, int end,Vector exc) {\r
-\r
- // start and end are in real (not relative coords);\r
-\r
- // The coords in the hashtable that is returned are in relative coords\r
- // i.e. start from 0\r
-\r
- Hashtable blocks = new Hashtable();\r
-\r
- boolean prev = false;\r
- int bstart = -1;\r
-\r
- for (int i = start; i <= end ; i++) {\r
- SequenceI seq = (SequenceI)seqs.elementAt(0);\r
-\r
- char c = seq.getCharAt(i);\r
-\r
- boolean found = true;\r
-\r
- int j = 1;\r
-\r
- while (j < seqs.size() && found == true) {\r
-\r
- SequenceI jseq = (SequenceI)seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
-\r
- char cc = jseq.getCharAt(i);\r
-\r
- if ( cc != c) {\r
- found = false;\r
- }\r
- }\r
- j++;\r
- }\r
-\r
-\r
- if (prev == false && found == true) {\r
- bstart = i;\r
- } else if (prev == true && found == false && bstart != -1) {\r
-\r
- int blockstart = bstart-start;\r
- int blocklen = i-bstart;\r
-\r
- //System.out.println("Start len " + blockstart + " " + blocklen);\r
-\r
- for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(jj),new Integer(blocklen));\r
- }\r
-\r
- bstart = -1;\r
- }\r
- prev = found;\r
- }\r
-\r
- if (bstart != -1) {\r
-\r
- int blockstart = bstart-start;\r
- int blocklen = end-bstart;\r
-\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
-\r
- for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- }\r
-\r
- }\r
- return blocks;\r
- }\r
-\r
-\r
-\r
- public static Hashtable findKmerCount(SequenceI seq, int start, int end,int window, int step,Vector kmers) {\r
-\r
- int tmpstart = start;\r
- Hashtable vals = new Hashtable();\r
-\r
- while (tmpstart <= end) {\r
-\r
- String tmpstr = seq.getSequence().substring(tmpstart-window/2,tmpstart+window/2);\r
-\r
- int count = 0;\r
-\r
- //System.out.println("Str " + tmpstr);\r
-\r
- for (int ii = 0; ii < kmers.size(); ii++) {\r
- String kmer = ((SequenceI)kmers.elementAt(ii)).getSequence();\r
-\r
- int i = -1;\r
-\r
- while (tmpstr.indexOf(kmer,i) != -1) {\r
- i = tmpstr.indexOf(kmer,i);\r
-\r
- i++;\r
- count++;\r
- }\r
- ii++;\r
- }\r
- vals.put(new Integer(tmpstart),new Integer(count));\r
- tmpstart += step;\r
- }\r
- return vals;\r
- }\r
-\r
- public static Hashtable findBlockStarts(Vector seqs, int start, int end,Vector exc) {\r
-\r
- // start and end are in real (not relative coords);\r
-\r
- // The coords in the hashtable that is returned are in relative coords\r
- // i.e. start from 0\r
-\r
- Hashtable blocks = new Hashtable();\r
-\r
- boolean prev = false;\r
- int bstart = -1;\r
-\r
- for (int i = start; i <= end ; i++) {\r
- SequenceI seq = (SequenceI)seqs.elementAt(0);\r
-\r
- char c = seq.getCharAt(i);\r
-\r
- boolean found = true;\r
-\r
- int j = 1;\r
-\r
- while (j < seqs.size() && found == true) {\r
-\r
- SequenceI jseq = (SequenceI)seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
-\r
- char cc = jseq.getCharAt(i);\r
-\r
- if ( cc != c) {\r
- found = false;\r
- }\r
- }\r
- j++;\r
- }\r
-\r
-\r
- if (prev == false && found == true) {\r
- bstart = i;\r
- } else if (prev == true && found == false && bstart != -1) {\r
-\r
- int blockstart = bstart-start;\r
- int blocklen = i-bstart;\r
-\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
-\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- // }\r
-\r
- bstart = -1;\r
- }\r
- prev = found;\r
- }\r
-\r
- if (bstart != -1) {\r
-\r
- int blockstart = bstart-start;\r
- int blocklen = end-bstart;\r
-\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
-\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- // }\r
-\r
- }\r
- return blocks;\r
- }\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.*;
+
+
+/**
+ * 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 final Vector calculate(Vector sequences, int start, int end)
+ {
+ Vector result = new Vector();
+ Hashtable residueHash;
+ int count, maxCount, nongap, i, j, jSize = sequences.size();
+ String maxResidue, sequence, res;
+ float percentage;
+
+ for (i = start; i <= end; i++)
+ {
+ residueHash = new Hashtable();
+ maxCount = 0;
+ maxResidue = "-";
+ nongap = 0;
+
+ for (j = 0; j < jSize; j++)
+ {
+ if (sequences.elementAt(j) instanceof Sequence)
+ {
+ sequence = ((Sequence) sequences.elementAt(j)).getSequence();
+
+ if (sequence.length() > i)
+ {
+ res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
+
+ if (jalview.util.Comparison.isGap(res.charAt(0)))
+ {
+ res = "-"; // we always use this for gaps in the property vectors
+ }
+ else
+ { nongap++; }
+
+ if (residueHash.containsKey(res))
+ {
+ 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("-"))
+ {
+ count = ((Integer) residueHash.get("-")).intValue();
+ count++;
+ residueHash.put("-", new Integer(count));
+ }
+ else
+ {
+ residueHash.put("-", new Integer(1));
+ }
+ }
+ }
+ }
+
+ residueHash.put("maxCount", new Integer(maxCount));
+ residueHash.put("maxResidue", maxResidue);
+
+
+ //Size is redundant at present if we calculate percentage here
+ //residueHash.put("size", new Integer(jSize));
+ //residueHash.put("nogaps", new Integer(nongap));
+
+ 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.addElement(residueHash);
+ }
+
+
+
+ return result;
+ }
+}