*/\r
package jalview.analysis;\r
\r
-import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
\r
import java.util.*;\r
\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
+/**\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
+ * @author $author$\r
+ * @version $Revision$\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
+ public static final Vector calculate(Vector sequences, int start, int end)\r
+ {\r
+ Vector result = new Vector();\r
+ Hashtable residueHash;\r
+ int count, maxCount, nongap, i, j, jSize = sequences.size();\r
+ String maxResidue, sequence, res;\r
+ float percentage;\r
+\r
+ for (i = start; i <= end; i++)\r
+ {\r
+ residueHash = new Hashtable();\r
+ maxCount = 0;\r
+ maxResidue = "-";\r
+ nongap = 0;\r
+\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ if (sequences.elementAt(j) instanceof Sequence)\r
+ {\r
+ sequence = ((Sequence) sequences.elementAt(j)).getSequence();\r
+\r
+ if (sequence.length() > i)\r
+ {\r
+ res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));\r
+\r
+ if (jalview.util.Comparison.isGap(res.charAt(0)))\r
+ {\r
res = "-"; // we always use this for gaps in the property vectors\r
}\r
+ else\r
+ { nongap++; }\r
\r
- if (residueHash.containsKey(res)) {\r
- int count = ((Integer) residueHash.get(res)).intValue();\r
+ if (residueHash.containsKey(res))\r
+ {\r
+ 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
+ (count >= maxCount))\r
+ {\r
+ if (count > maxCount)\r
+ {\r
maxResidue = res;\r
- } else if (maxResidue.indexOf(res) == -1) {\r
+ }\r
+ else if (maxResidue.indexOf(res) == -1)\r
+ {\r
maxResidue += res;\r
}\r
\r
}\r
\r
residueHash.put(res, new Integer(count));\r
- } else {\r
+ }\r
+ else\r
+ {\r
residueHash.put(res, new Integer(1));\r
}\r
- } else {\r
- if (residueHash.containsKey("-")) {\r
- int count = ((Integer) residueHash.get("-")).intValue();\r
+ }\r
+ else\r
+ {\r
+ if (residueHash.containsKey("-"))\r
+ {\r
+ count = ((Integer) residueHash.get("-")).intValue();\r
count++;\r
residueHash.put("-", new Integer(count));\r
- } else {\r
+ }\r
+ else\r
+ {\r
residueHash.put("-", new Integer(1));\r
}\r
}\r
}\r
\r
residueHash.put("maxCount", new Integer(maxCount));\r
-\r
- if (maxCount < 0) {\r
- System.out.println("asasa " + maxCount);\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
- return result;\r
- }\r
-\r
- public static Vector calculatePID(SequenceI refseq, Vector sequences,\r
- int window, int start, int end) {\r
- Vector result = new Vector();\r
-\r
- boolean init = true;\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
- 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
- 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
- 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
- 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
-\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 (refseq.getSequence().length() > winend) {\r
- pos_refchar = refseq.getSequence().substring(winend,\r
- winend + 1);\r
- }\r
-\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
- Sequence s = (Sequence) sequences.elementAt(j);\r
-\r
- String pre_char = s.getSequence().substring(winstart - 1,\r
- winstart);\r
-\r
- String pos_char = "-";\r
-\r
- if (s.getSequence().length() > winend) {\r
- pos_char = s.getSequence().substring(winend, winend +\r
- 1);\r
- }\r
-\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
- if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&\r
- pos_char.equals(pos_refchar)) {\r
- val++;\r
- }\r
-\r
- values.addElement(new Integer(val));\r
- }\r
-\r
- prev = values;\r
- }\r
- }\r
-\r
- return result;\r
- }\r
-\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
- 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
- SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
- char cc = jseq.getCharAt(i);\r
-\r
- if (cc != c) {\r
- found = false;\r
- }\r
- }\r
-\r
- j++;\r
- }\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
- //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
- bstart = -1;\r
- }\r
-\r
- prev = found;\r
- }\r
-\r
- if (bstart != -1) {\r
- int blockstart = bstart - start;\r
- int blocklen = end - bstart;\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
- 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
- int count = 0;\r
\r
- //System.out.println("Str " + tmpstr);\r
- for (int ii = 0; ii < kmers.size(); ii++) {\r
- String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();\r
+ //Size is redundant at present if we calculate percentage here\r
+ //residueHash.put("size", new Integer(jSize));\r
+ //residueHash.put("nogaps", new Integer(nongap));\r
\r
- int i = -1;\r
+ percentage = ((float)maxCount*100) / (float)jSize;\r
+ residueHash.put("pid_gaps", new Float(percentage) );\r
\r
- while (tmpstr.indexOf(kmer, i) != -1) {\r
- i = tmpstr.indexOf(kmer, i);\r
-\r
- i++;\r
- count++;\r
- }\r
-\r
- ii++;\r
- }\r
-\r
- vals.put(new Integer(tmpstart), new Integer(count));\r
- tmpstart += step;\r
- }\r
-\r
- return vals;\r
- }\r
-\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
- 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
- SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
- char cc = jseq.getCharAt(i);\r
-\r
- if (cc != c) {\r
- found = false;\r
- }\r
- }\r
-\r
- j++;\r
- }\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
- // 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
- bstart = -1;\r
- }\r
-\r
- prev = found;\r
+ percentage = ((float)maxCount*100) / (float)nongap;\r
+ residueHash.put("pid_nogaps", new Float(percentage) );\r
+ result.addElement(residueHash);\r
}\r
\r
- if (bstart != -1) {\r
- int blockstart = bstart - start;\r
- int blocklen = end - bstart;\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 result;\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff