+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
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 jalview.datamodel.*;\r
+\r
import java.util.*;\r
-import java.net.*;\r
-import java.io.*;\r
\r
-public class AAFrequency {\r
\r
+public class AAFrequency {\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
+ public static Vector calculate(Vector sequences, int start, int end) {\r
+ Vector result = new Vector();\r
+\r
+ for (int i = start; i <= end; i++) {\r
+ Hashtable residueHash = new Hashtable();\r
+ int maxCount = 0;\r
+ String maxResidue = "-";\r
+ int nongap = 0;\r
+\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ if (sequences.elementAt(j) instanceof Sequence) {\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
+\r
+ if (s.getSequence().length() > i) {\r
+ String res = s.getSequence().charAt(i) + "";\r
+\r
+ if (!jalview.util.Comparison.isGap(res.charAt(0))) {\r
+ nongap++;\r
+ } else {\r
+ res = "-"; // we always use this for gaps in the property vectors\r
+ }\r
+\r
+ if (residueHash.containsKey(res)) {\r
+ int count = ((Integer) residueHash.get(res)).intValue();\r
+ count++;\r
+\r
+ if (!jalview.util.Comparison.isGap(res.charAt(0)) &&\r
+ (count >= maxCount)) {\r
+ if (count > maxCount) {\r
+ maxResidue = res;\r
+ } else if (maxResidue.indexOf(res) == -1) {\r
+ maxResidue += res;\r
+ }\r
+\r
+ maxCount = count;\r
+ }\r
+\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
- 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
+ residueHash.put("maxCount", new Integer(maxCount));\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
+ if (maxCount < 0) {\r
+ System.out.println("asasa " + maxCount);\r
}\r
- else\r
- residueHash.put("-",new Integer(1));\r
\r
- }\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
- 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
+ return result;\r
+ }\r
\r
- Vector prev = null;\r
-\r
- for (int i = start;i <= end; i++) {\r
- Vector values = new Vector();\r
+ public static Vector calculatePID(SequenceI refseq, Vector sequences,\r
+ int window, int start, int end) {\r
+ Vector result = new Vector();\r
\r
- result.addElement(values);\r
+ boolean init = true;\r
\r
- // If start < window/2 then set value to zero.\r
+ Vector prev = null;\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
+ for (int i = start; i <= end; i++) {\r
+ Vector values = new Vector();\r
\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
+ result.addElement(values);\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
+ // If start < window/2 then set value to zero.\r
+ if ((i < (window / 2)) ||\r
+ (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
- for (int k = winstart; k <= winend; k++) {\r
- String refchar = refseq.getSequence().substring(k,k+1);\r
+ int winstart = i - (window / 2);\r
+ int winend = i + (window / 2);\r
\r
- for (int j = 0; j < sequences.size(); j++) {\r
+ if ((window % 2) != 0) {\r
+ winend++;\r
+ }\r
\r
- if (refchar.equals("-") == false) {\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ values.addElement(new Integer(0));\r
+ }\r
\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
+ for (int k = winstart; k <= winend; k++) {\r
+ String refchar = refseq.getSequence().substring(k, k + 1);\r
+\r
+ if (jalview.util.Comparison.isGap(refchar.charAt(0))) {\r
+ refchar = "-";\r
+ } else {\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
+\r
+ if (s.getSequence().length() > k) {\r
+ String res = s.getSequence().substring(k, k +\r
+ 1); // no gapchar test needed\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
\r
- if (s.getSequence().length() > k) {\r
+ prev = values;\r
+ } else {\r
+ int winstart = i - (window / 2);\r
+ int winend = i + (window / 2);\r
\r
- String res = s.getSequence().substring(k,k+1);\r
+ if ((window % 2) != 0) {\r
+ winend++;\r
+ }\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
+ // We need to take the previous set of values\r
+ // subtract the pid at winstart-1\r
+ // and add the pid at winend;\r
+ String pre_refchar = refseq.getSequence().substring(winstart -\r
+ 1, winstart);\r
+ String pos_refchar = "-";\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
+ if (refseq.getSequence().length() > winend) {\r
+ pos_refchar = refseq.getSequence().substring(winend,\r
+ winend + 1);\r
+ }\r
\r
- String pre_refchar = refseq.getSequence().substring(winstart-1,winstart);\r
- String pos_refchar = "-";\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ // First copy the pid value from i-1\r
+ int val = ((Integer) prev.elementAt(j)).intValue();\r
\r
- if (refseq.getSequence().length() > winend) {\r
- pos_refchar = refseq.getSequence().substring(winend,winend+1);\r
- }\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
\r
- for (int j = 0; j < sequences.size(); j++) {\r
- // First copy the pid value from i-1\r
+ String pre_char = s.getSequence().substring(winstart - 1,\r
+ winstart);\r
\r
- int val = ((Integer)prev.elementAt(j)).intValue();\r
+ String pos_char = "-";\r
\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
+ if (s.getSequence().length() > winend) {\r
+ pos_char = s.getSequence().substring(winend, winend +\r
+ 1);\r
+ }\r
\r
- String pre_char = s.getSequence().substring(winstart-1,winstart);\r
+ // Now substract 1 if the chars at winstart-1 match\r
+ if ((jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false) &&\r
+ pre_char.equals(pre_refchar)) {\r
+ val--;\r
+ }\r
\r
- String pos_char = "-";\r
+ if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&\r
+ pos_char.equals(pos_refchar)) {\r
+ val++;\r
+ }\r
\r
- if (s.getSequence().length() > winend) {\r
- pos_char = s.getSequence().substring(winend,winend+1);\r
+ values.addElement(new Integer(val));\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
+ prev = values;\r
+ }\r
+ }\r
\r
- return result;\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
+ public static Hashtable findBlocks(Vector seqs, int start, int end,\r
+ Vector exc) {\r
+ // start and end are in real (not relative coords);\r
+ // The coords in the hashtable that is returned are in relative coords\r
+ // i.e. start from 0\r
+ Hashtable blocks = new Hashtable();\r
\r
- char c = seq.getCharAt(i);\r
+ boolean prev = false;\r
+ int bstart = -1;\r
\r
- boolean found = true;\r
+ for (int i = start; i <= end; i++) {\r
+ SequenceI seq = (SequenceI) seqs.elementAt(0);\r
\r
- int j = 1;\r
+ char c = seq.getCharAt(i);\r
\r
- while (j < seqs.size() && found == true) {\r
+ boolean found = true;\r
\r
- SequenceI jseq = (SequenceI)seqs.elementAt(j);\r
+ int j = 1;\r
\r
- if (!exc.contains(jseq)) {\r
+ while ((j < seqs.size()) && (found == true)) {\r
+ SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
\r
- char cc = jseq.getCharAt(i);\r
+ if (!exc.contains(jseq)) {\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
+ if (cc != c) {\r
+ found = false;\r
+ }\r
+ }\r
\r
- //System.out.println("Start len " + blockstart + " " + blocklen);\r
+ j++;\r
+ }\r
\r
- for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(jj),new Integer(blocklen));\r
- }\r
+ if ((prev == false) && (found == true)) {\r
+ bstart = i;\r
+ } else if ((prev == true) && (found == false) && (bstart != -1)) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = i - bstart;\r
\r
- bstart = -1;\r
- }\r
- prev = found;\r
- }\r
+ //System.out.println("Start len " + blockstart + " " + blocklen);\r
+ for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {\r
+ blocks.put(new Integer(jj), new Integer(blocklen));\r
+ }\r
\r
- if (bstart != -1) {\r
+ bstart = -1;\r
+ }\r
\r
- int blockstart = bstart-start;\r
- int blocklen = end-bstart;\r
+ prev = found;\r
+ }\r
\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ if (bstart != -1) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = end - bstart;\r
\r
- for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- }\r
+ // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {\r
+ blocks.put(new Integer(blockstart), new Integer(blocklen));\r
+ }\r
+ }\r
\r
- }\r
- return blocks;\r
+ return blocks;\r
}\r
\r
+ public static Hashtable findKmerCount(SequenceI seq, int start, int end,\r
+ int window, int step, Vector kmers) {\r
+ int tmpstart = start;\r
+ Hashtable vals = new Hashtable();\r
\r
+ while (tmpstart <= end) {\r
+ String tmpstr = seq.getSequence().substring(tmpstart -\r
+ (window / 2), tmpstart + (window / 2));\r
\r
- public static Hashtable findKmerCount(SequenceI seq, int start, int end,int window, int step,Vector kmers) {\r
+ int count = 0;\r
\r
- int tmpstart = start;\r
- Hashtable vals = new Hashtable();\r
+ //System.out.println("Str " + tmpstr);\r
+ for (int ii = 0; ii < kmers.size(); ii++) {\r
+ String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();\r
\r
- while (tmpstart <= end) {\r
+ int i = -1;\r
\r
- String tmpstr = seq.getSequence().substring(tmpstart-window/2,tmpstart+window/2);\r
+ while (tmpstr.indexOf(kmer, i) != -1) {\r
+ i = tmpstr.indexOf(kmer, i);\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
+ i++;\r
+ count++;\r
+ }\r
\r
- int i = -1;\r
+ ii++;\r
+ }\r
\r
- while (tmpstr.indexOf(kmer,i) != -1) {\r
- i = tmpstr.indexOf(kmer,i);\r
+ vals.put(new Integer(tmpstart), new Integer(count));\r
+ tmpstart += step;\r
+ }\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
+ 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
+ public static Hashtable findBlockStarts(Vector seqs, int start, int end,\r
+ Vector exc) {\r
+ // start and end are in real (not relative coords);\r
+ // The coords in the hashtable that is returned are in relative coords\r
+ // i.e. start from 0\r
+ Hashtable blocks = new Hashtable();\r
\r
- char c = seq.getCharAt(i);\r
+ boolean prev = false;\r
+ int bstart = -1;\r
\r
- boolean found = true;\r
+ for (int i = start; i <= end; i++) {\r
+ SequenceI seq = (SequenceI) seqs.elementAt(0);\r
\r
- int j = 1;\r
+ char c = seq.getCharAt(i);\r
\r
- while (j < seqs.size() && found == true) {\r
+ boolean found = true;\r
\r
- SequenceI jseq = (SequenceI)seqs.elementAt(j);\r
+ int j = 1;\r
\r
- if (!exc.contains(jseq)) {\r
+ while ((j < seqs.size()) && (found == true)) {\r
+ SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
\r
- char cc = jseq.getCharAt(i);\r
+ if (!exc.contains(jseq)) {\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
+ if (cc != c) {\r
+ found = false;\r
+ }\r
+ }\r
\r
- int blockstart = bstart-start;\r
- int blocklen = i-bstart;\r
+ j++;\r
+ }\r
\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ if ((prev == false) && (found == true)) {\r
+ bstart = i;\r
+ } else if ((prev == true) && (found == false) && (bstart != -1)) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = i - bstart;\r
\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- // }\r
+ // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
+ blocks.put(new Integer(blockstart), new Integer(blocklen));\r
\r
- bstart = -1;\r
- }\r
- prev = found;\r
- }\r
+ // }\r
+ bstart = -1;\r
+ }\r
\r
- if (bstart != -1) {\r
+ prev = found;\r
+ }\r
\r
- int blockstart = bstart-start;\r
- int blocklen = end-bstart;\r
+ if (bstart != -1) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = end - bstart;\r
\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
+ blocks.put(new Integer(blockstart), new Integer(blocklen));\r
\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- // }\r
+ // }\r
+ }\r
\r
- }\r
- return blocks;\r
+ return blocks;\r
}\r
-\r
}\r
-\r