/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 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
*/\r
public class Conservation\r
{\r
- Vector sequences;\r
+ SequenceI [] sequences;\r
int start;\r
int end;\r
Vector seqNums; // vector of int vectors where first is sequence checksum\r
int maxLength = 0; // used by quality calcs\r
boolean seqNumsChanged = false; // updated after any change via calcSeqNum;\r
- Vector total = new Vector();\r
+ Hashtable [] total;\r
\r
/** Stores calculated quality values */\r
public Vector quality;\r
public Conservation(String name, Hashtable propHash, int threshold,\r
Vector sequences, int start, int end)\r
{\r
+\r
this.name = name;\r
this.propHash = propHash;\r
this.threshold = threshold;\r
- this.sequences = sequences;\r
this.start = start;\r
this.end = end;\r
- seqNums = new Vector(sequences.size());\r
- calcSeqNums();\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- private void calcSeqNums()\r
- {\r
- for (int i = 0; i < sequences.size(); i++)\r
+\r
+ int s, sSize = sequences.size();\r
+ SequenceI[] sarray = new SequenceI[sSize];\r
+ this.sequences = sarray;\r
+\r
+ for (s = 0; s < sSize; s++)\r
{\r
- calcSeqNum(i);\r
+ sarray[s] = (SequenceI) sequences.elementAt(s);\r
+ if(sarray[s].getLength()>maxLength)\r
+ maxLength = sarray[s].getLength();\r
}\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
String sq = null; // for dumb jbuilder not-inited exception warning\r
int[] sqnum = null;\r
\r
- if ((i > -1) && (i < sequences.size()))\r
+ int sSize = sequences.length;\r
+\r
+ if ((i > -1) && (i < sSize))\r
{\r
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();\r
+ sq = sequences[i].getSequence();\r
\r
if (seqNums.size() <= i)\r
{\r
int j;\r
int len;\r
seqNumsChanged = true;\r
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();\r
len = sq.length();\r
\r
if (maxLength < len)\r
\r
for (j = 1; j <= len; j++)\r
{\r
- sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(\r
- sq.substring(j - 1, j)))).intValue(); // yuk\r
+ sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charAt(j-1)];\r
}\r
\r
+\r
seqNums.setElementAt(sqnum, i);\r
}\r
+ else\r
+ System.out.println("NEVER THE EXCEPTION");\r
}\r
else\r
{\r
*/\r
public void calculate()\r
{\r
- for (int i = start; i <= end; i++)\r
- {\r
- Hashtable resultHash = null;\r
- Hashtable residueHash = null;\r
+ Hashtable resultHash, ht;\r
+ int thresh, j, jSize = sequences.length;\r
+ int[] values; // Replaces residueHash\r
+ String type, res=null;\r
+ char c;\r
+ Enumeration enumeration2;\r
\r
- resultHash = new Hashtable();\r
- residueHash = new Hashtable();\r
+ total = new Hashtable[maxLength];\r
+\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ values = new int[132];\r
\r
- for (int j = 0; j < sequences.size(); j++)\r
+ for (j = 0; j < jSize; j++)\r
{\r
- // JBPNote - have to make sure elements of the sequences vector\r
- // are tested like this everywhere...\r
- if (sequences.elementAt(j) instanceof Sequence)\r
- {\r
- Sequence s = (Sequence) sequences.elementAt(j);\r
+ if (sequences[j].getLength() > i)\r
+ {\r
+ c = sequences[j].getCharAt(i);\r
\r
- if (s.getLength() > i)\r
- {\r
- String res = s.getSequence().substring(i, i + 1);\r
+ // No need to check if its a '-'\r
+ if (c == '.' || c == ' ')\r
+ c = '-';\r
\r
- if (residueHash.containsKey(res))\r
- {\r
- int count = ((Integer) residueHash.get(res)).intValue();\r
- count++;\r
- residueHash.put(res, new Integer(count));\r
- }\r
- else\r
- {\r
- residueHash.put(res, new Integer(1));\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
- {\r
- residueHash.put("-", new Integer(1));\r
- }\r
- }\r
+ if ('a' <= c && c <= 'z')\r
+ {\r
+ c -= (32);// 32 = 'a' - 'A'\r
}\r
+\r
+ values[c]++;\r
+ }\r
+ else\r
+ {\r
+ values['-']++;\r
+ }\r
}\r
\r
//What is the count threshold to count the residues in residueHash()\r
- int thresh = (threshold * (sequences.size())) / 100;\r
+ thresh = (threshold * (jSize)) / 100;\r
\r
//loop over all the found residues\r
- Enumeration e = residueHash.keys();\r
-\r
- while (e.hasMoreElements())\r
+ resultHash = new Hashtable();\r
+ for (int v = '-'; v < 'Z'; v++)\r
{\r
- String res = (String) e.nextElement();\r
\r
- if (((Integer) residueHash.get(res)).intValue() > thresh)\r
+ if (values[v] > thresh)\r
{\r
+ res = String.valueOf( (char) v);\r
+\r
//Now loop over the properties\r
- Enumeration e2 = propHash.keys();\r
+ enumeration2 = propHash.keys();\r
\r
- while (e2.hasMoreElements())\r
+ while (enumeration2.hasMoreElements())\r
{\r
- String type = (String) e2.nextElement();\r
- Hashtable ht = (Hashtable) propHash.get(type);\r
+ type = (String) enumeration2.nextElement();\r
+ ht = (Hashtable) propHash.get(type);\r
\r
//Have we ticked this before?\r
if (!resultHash.containsKey(type))\r
}\r
}\r
\r
- total.addElement(resultHash);\r
+ total[i] = resultHash;\r
}\r
}\r
\r
int nres = 0;\r
int[] r = new int[2];\r
char f = '$';\r
+ int i, iSize = sequences.length;\r
+ char c;\r
\r
- for (int i = 0; i < sequences.size(); i++)\r
+ for (i = 0; i < iSize; i++)\r
{\r
- if (j >= ((Sequence) sequences.elementAt(i)).getSequence().length())\r
+ if (j >= sequences[i].getLength())\r
{\r
count++;\r
-\r
continue;\r
}\r
\r
- char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);\r
+ c = sequences[i].getCharAt(j); // gaps do not have upper/lower case\r
\r
if (jalview.util.Comparison.isGap((c)))\r
{\r
*/\r
public void verdict(boolean consflag, float percentageGaps)\r
{\r
- String consString = "";\r
+ StringBuffer consString = new StringBuffer();\r
+ String type;\r
+ Integer result;\r
+ int[] gapcons;\r
+ int totGaps, count;\r
+ float pgaps;\r
+ Hashtable resultHash ;\r
+ Enumeration enumeration;\r
+\r
\r
for (int i = start; i <= end; i++)\r
{\r
- int[] gapcons = countConsNGaps(i);\r
- int totGaps = gapcons[1];\r
- float pgaps = ((float) totGaps * 100) / (float) sequences.size();\r
+ gapcons = countConsNGaps(i);\r
+ totGaps = gapcons[1];\r
+ pgaps = ((float) totGaps * 100) / (float) sequences.length;\r
\r
- // System.out.println("percentage gaps = "+pgaps+"\n");\r
if (percentageGaps > pgaps)\r
{\r
- Hashtable resultHash = (Hashtable) total.elementAt(i - start);\r
+ resultHash = total[i - start];\r
\r
//Now find the verdict\r
- int count = 0;\r
- Enumeration e3 = resultHash.keys();\r
+ count = 0;\r
+ enumeration = resultHash.keys();\r
\r
- while (e3.hasMoreElements())\r
+ while (enumeration.hasMoreElements())\r
{\r
- String type = (String) e3.nextElement();\r
- Integer result = (Integer) resultHash.get(type);\r
+ type = (String) enumeration.nextElement();\r
+ result = (Integer) resultHash.get(type);\r
\r
//Do we want to count +ve conservation or +ve and -ve cons.?\r
if (consflag)\r
\r
if (count < 10)\r
{\r
- consString = consString + String.valueOf(count); // Conserved props!=Identity\r
+ consString.append(count); // Conserved props!=Identity\r
}\r
else\r
{\r
- consString = consString + ((gapcons[0] == 1) ? "*" : "+");\r
+ consString.append((gapcons[0] == 1) ? "*" : "+");\r
}\r
}\r
else\r
{\r
- consString = consString + "-";\r
+ consString.append("-");\r
}\r
}\r
\r
- consSequence = new Sequence(name, consString, start, end);\r
+ consSequence = new Sequence(name, consString.toString(), start, end);\r
}\r
\r
/**\r
*/\r
private void percentIdentity2()\r
{\r
- calcSeqNums(); // updates maxLength, too.\r
+ seqNums = new Vector();\r
+ // calcSeqNum(s);\r
+ int i = 0, iSize = sequences.length;\r
+ //Do we need to calculate this again?\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ calcSeqNum(i);\r
+ }\r
+\r
\r
if ((cons2 == null) || seqNumsChanged)\r
{\r
// Initialize the array\r
for (int j = 0; j < 24; j++)\r
{\r
- for (int i = 0; i < maxLength; i++)\r
+ for (i = 0; i < maxLength; i++)\r
{\r
cons2[i][j] = 0;\r
}\r
int[] sqnum;\r
int j = 0;\r
\r
- while (j < sequences.size())\r
+ while (j < sequences.length)\r
{\r
sqnum = (int[]) seqNums.elementAt(j);\r
\r
- for (int i = 1; i < sqnum.length; i++)\r
+ for (i = 1; i < sqnum.length; i++)\r
{\r
cons2[i - 1][sqnum[i]]++;\r
}\r
\r
- for (int i = sqnum.length - 1; i < maxLength; i++)\r
+ for (i = sqnum.length - 1; i < maxLength; i++)\r
{\r
cons2[i][23]++; // gap count\r
}\r
quality = new Vector();\r
\r
double max = -10000;\r
- String s = "";\r
int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();\r
\r
//Loop over columns // JBPNote Profiling info\r
- // long ts = System.currentTimeMillis();\r
+ //long ts = System.currentTimeMillis();\r
//long te = System.currentTimeMillis();\r
percentIdentity2();\r
\r
int size = seqNums.size();\r
int[] lengths = new int[size];\r
+ double tot, bigtot, sr, tmp;\r
+ double [] x, xx;\r
+ int l, j, i, ii, i2, k, seqNum;\r
\r
- for (int l = 0; l < size; l++)\r
+ for (l = 0; l < size; l++)\r
lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;\r
\r
- for (int j = start; j <= end; j++)\r
+ for (j = start; j <= end; j++)\r
{\r
- double bigtot = 0;\r
+ bigtot = 0;\r
\r
// First Xr = depends on column only\r
- double[] x = new double[24];\r
+ x = new double[24];\r
\r
- for (int ii = 0; ii < 24; ii++)\r
+ for (ii = 0; ii < 24; ii++)\r
{\r
x[ii] = 0;\r
\r
- try\r
- {\r
- for (int i2 = 0; i2 < 24; i2++)\r
- {\r
- x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) +\r
- 4);\r
- }\r
- }\r
- catch (Exception e)\r
+ for (i2 = 0; i2 < 24; i2++)\r
{\r
- System.err.println("Exception during quality calculation.");\r
- e.printStackTrace();\r
+ x[ii] += ( ( (double) cons2[j][i2] * BLOSUM62[ii][i2]) +\r
+ 4);\r
}\r
\r
- //System.out.println("X " + ii + " " + x[ii]);\r
- x[ii] /= (size);\r
-\r
- //System.out.println("X " + ii + " " + x[ii]);\r
+ x[ii] /= size;\r
}\r
\r
// Now calculate D for each position and sum\r
- for (int k = 0; k < size; k++)\r
+ for (k = 0; k < size; k++)\r
{\r
- double tot = 0;\r
- double[] xx = new double[24];\r
- int seqNum = (j < lengths[k])\r
+ tot = 0;\r
+ xx = new double[24];\r
+ seqNum = (j < lengths[k])\r
? ((int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end\r
\r
// This is a loop over r\r
- for (int i = 0; i < 23; i++)\r
+ for (i = 0; i < 23; i++)\r
{\r
- double sr = 0;\r
+ sr = 0;\r
\r
- try\r
- {\r
- sr = (double) BLOSUM62[i][seqNum] + 4;\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("Exception in sr: " + e);\r
- e.printStackTrace();\r
- }\r
+ sr = (double) BLOSUM62[i][seqNum] + 4;\r
\r
//Calculate X with another loop over residues\r
// System.out.println("Xi " + i + " " + x[i] + " " + sr);\r
// bigtot = bigtot * (size-cons2[j][23])/size;\r
quality.addElement(new Double(bigtot));\r
\r
- s += "-";\r
-\r
// Need to normalize by gaps\r
}\r
\r
double newmax = -10000;\r
\r
- for (int j = start; j <= end; j++)\r
+ for (j = start; j <= end; j++)\r
{\r
- double tmp = ((Double) quality.elementAt(j)).doubleValue();\r
+ tmp = ((Double) quality.elementAt(j)).doubleValue();\r
tmp = ((max - tmp) * (size - cons2[j][23])) / size;\r
\r
// System.out.println(tmp+ " " + j);\r
git://source.jalview.org / jalview.git / blobdiff