*/\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
- int i=0, iSize=sequences.size();\r
- for (i=0; i < iSize; 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(String.valueOf(\r
- sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash\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
- Hashtable resultHash, residueHash, ht;\r
- int count, thresh, j, jSize = sequences.size();\r
+ Hashtable resultHash, ht;\r
+ int thresh, j, jSize = sequences.length;\r
+ int[] values; // Replaces residueHash\r
String type, res=null;\r
- SequenceI sequence;\r
char c;\r
- Enumeration enumeration, enumeration2;\r
+ Enumeration enumeration2;\r
+\r
+ total = new Hashtable[maxLength];\r
\r
for (int i = start; i <= end; i++)\r
{\r
- resultHash = new Hashtable();\r
- residueHash = new Hashtable();\r
+ values = new int[132];\r
\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
- sequence = (Sequence) sequences.elementAt(j);\r
-\r
- if (sequence.getLength() > i)\r
- {\r
- c = sequence.getCharAt(i);\r
-\r
- // No need to check if its a '-'\r
- if(c == '.' || c==' ')\r
- c = '-';\r
-\r
- if ('a' <= c && c <= 'z')\r
- {\r
- // TO UPPERCASE !!!\r
- //Faster than toUpperCase\r
- c -= ('a' - 'A') ;\r
- }\r
+ if (sequences[j].getLength() > i)\r
+ {\r
+ c = sequences[j].getCharAt(i);\r
\r
- res = String.valueOf( c );\r
+ // No need to check if its a '-'\r
+ if (c == '.' || c == ' ')\r
+ c = '-';\r
\r
+ if ('a' <= c && c <= 'z')\r
+ {\r
+ c -= (32);// 32 = 'a' - 'A'\r
+ }\r
\r
- if (residueHash.containsKey(res))\r
- {\r
- 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
- 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
+ values[c]++;\r
+ }\r
+ else\r
+ {\r
+ values['-']++;\r
+ }\r
}\r
\r
//What is the count threshold to count the residues in residueHash()\r
- thresh = (threshold * (sequences.size())) / 100;\r
+ thresh = (threshold * (jSize)) / 100;\r
\r
//loop over all the found residues\r
- enumeration = residueHash.keys();\r
-\r
- while (enumeration.hasMoreElements())\r
+ resultHash = new Hashtable();\r
+ for (int v = '-'; v < 'Z'; v++)\r
{\r
- res = (String) enumeration.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
enumeration2 = propHash.keys();\r
\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.size();\r
+ int i, iSize = sequences.length;\r
char c;\r
\r
for (i = 0; i < iSize; i++)\r
{\r
- if (j >= ((Sequence) sequences.elementAt(i)).getLength())\r
+ if (j >= sequences[i].getLength())\r
{\r
count++;\r
continue;\r
}\r
\r
- c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case\r
+ c = sequences[i].getCharAt(j); // gaps do not have upper/lower case\r
\r
if (jalview.util.Comparison.isGap((c)))\r
{\r
{\r
gapcons = countConsNGaps(i);\r
totGaps = gapcons[1];\r
- pgaps = ((float) totGaps * 100) / (float) sequences.size();\r
+ pgaps = ((float) totGaps * 100) / (float) sequences.length;\r
\r
if (percentageGaps > pgaps)\r
{\r
- resultHash = (Hashtable) total.elementAt(i - start);\r
+ resultHash = total[i - start];\r
\r
//Now find the verdict\r
count = 0;\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
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[] lengths = new int[size];\r
double tot, bigtot, sr, tmp;\r
double [] x, xx;\r
- int l, j, i, ii, seqNum;\r
+ int l, j, i, ii, i2, k, seqNum;\r
\r
for (l = 0; l < size; l++)\r
lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;\r
\r
-\r
for (j = start; j <= end; j++)\r
{\r
bigtot = 0;\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
tot = 0;\r
xx = new double[24];\r
{\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
-\r
// Need to normalize by gaps\r
}\r
\r
git://source.jalview.org / jalview.git / commitdiff