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Declare variables outside loops
author
amwaterhouse
<Andrew Waterhouse>
Mon, 15 Aug 2005 12:04:32 +0000
(12:04 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Mon, 15 Aug 2005 12:04:32 +0000
(12:04 +0000)
src/jalview/analysis/Conservation.java
patch
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diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
0fe4f5e
..
d814abb
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-79,7
+79,8
@@
public class Conservation
*/
\r
private void calcSeqNums()
\r
{
\r
*/
\r
private void calcSeqNums()
\r
{
\r
- for (int i = 0; i < sequences.size(); i++)
\r
+ int i=0, iSize=sequences.size();
\r
+ for (i=0; i < iSize; i++)
\r
{
\r
calcSeqNum(i);
\r
}
\r
{
\r
calcSeqNum(i);
\r
}
\r
@@
-142,29
+143,31
@@
public class Conservation
*/
\r
public void calculate()
\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, residueHash, ht;
\r
+ int count, thresh, j, jSize = sequences.size();
\r
+ String sequence, res, type;
\r
+ Enumeration enumeration, enumeration2;
\r
\r
\r
+ for (int i = start; i <= end; i++)
\r
+ {
\r
resultHash = new Hashtable();
\r
residueHash = new Hashtable();
\r
\r
resultHash = new Hashtable();
\r
residueHash = new Hashtable();
\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
{
\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
+ sequence = ((Sequence) sequences.elementAt(j)).getSequence();
\r
\r
\r
- if (s.getLength() > i)
\r
+ if (sequence.length() > i)
\r
{
\r
{
\r
- String res = s.getSequence().substring(i, i + 1);
\r
+ res = sequence.substring(i, i + 1);
\r
\r
if (residueHash.containsKey(res))
\r
{
\r
\r
if (residueHash.containsKey(res))
\r
{
\r
- int count = ((Integer) residueHash.get(res)).intValue();
\r
+ count = ((Integer) residueHash.get(res)).intValue();
\r
count++;
\r
residueHash.put(res, new Integer(count));
\r
}
\r
count++;
\r
residueHash.put(res, new Integer(count));
\r
}
\r
@@
-177,7
+180,7
@@
public class Conservation
{
\r
if (residueHash.containsKey("-"))
\r
{
\r
{
\r
if (residueHash.containsKey("-"))
\r
{
\r
- int count = ((Integer) residueHash.get("-")).intValue();
\r
+ count = ((Integer) residueHash.get("-")).intValue();
\r
count++;
\r
residueHash.put("-", new Integer(count));
\r
}
\r
count++;
\r
residueHash.put("-", new Integer(count));
\r
}
\r
@@
-190,24
+193,24
@@
public class Conservation
}
\r
\r
//What is the count threshold to count the residues in residueHash()
\r
}
\r
\r
//What is the count threshold to count the residues in residueHash()
\r
- int thresh = (threshold * (sequences.size())) / 100;
\r
+ thresh = (threshold * (sequences.size())) / 100;
\r
\r
//loop over all the found residues
\r
\r
//loop over all the found residues
\r
- Enumeration e = residueHash.keys();
\r
+ enumeration = residueHash.keys();
\r
\r
\r
- while (e.hasMoreElements())
\r
+ while (enumeration.hasMoreElements())
\r
{
\r
{
\r
- String res = (String) e.nextElement();
\r
+ res = (String) enumeration.nextElement();
\r
\r
if (((Integer) residueHash.get(res)).intValue() > thresh)
\r
{
\r
//Now loop over the properties
\r
\r
if (((Integer) residueHash.get(res)).intValue() > thresh)
\r
{
\r
//Now loop over the properties
\r
- Enumeration e2 = propHash.keys();
\r
+ enumeration2 = propHash.keys();
\r
\r
\r
- while (e2.hasMoreElements())
\r
+ while (enumeration2.hasMoreElements())
\r
{
\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
//Have we ticked this before?
\r
if (!resultHash.containsKey(type))
\r
@@
-246,17
+249,18
@@
public class Conservation
int nres = 0;
\r
int[] r = new int[2];
\r
char f = '$';
\r
int nres = 0;
\r
int[] r = new int[2];
\r
char f = '$';
\r
+ int i, iSize = sequences.size();
\r
+ char c;
\r
\r
\r
- for (int i = 0; i < sequences.size(); i++)
\r
+ for (i = 0; i < iSize; i++)
\r
{
\r
{
\r
- if (j >= ((Sequence) sequences.elementAt(i)).getSequence().length())
\r
+ if (j >= ((Sequence) sequences.elementAt(i)).getLength())
\r
{
\r
count++;
\r
{
\r
count++;
\r
-
\r
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
- char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);
\r
+ c = ((Sequence) sequences.elementAt(i)).getCharAt(j);
\r
\r
if (jalview.util.Comparison.isGap((c)))
\r
{
\r
\r
if (jalview.util.Comparison.isGap((c)))
\r
{
\r
@@
-292,27
+296,34
@@
public class Conservation
*/
\r
public void verdict(boolean consflag, float percentageGaps)
\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
\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.size();
\r
\r
\r
- // System.out.println("percentage gaps = "+pgaps+"\n");
\r
if (percentageGaps > pgaps)
\r
{
\r
if (percentageGaps > pgaps)
\r
{
\r
- Hashtable resultHash = (Hashtable) total.elementAt(i - start);
\r
+ resultHash = (Hashtable) total.elementAt(i - start);
\r
\r
//Now find the verdict
\r
\r
//Now find the verdict
\r
- int count = 0;
\r
- Enumeration e3 = resultHash.keys();
\r
+ count = 0;
\r
+ enumeration = resultHash.keys();
\r
\r
\r
- while (e3.hasMoreElements())
\r
+ while (enumeration.hasMoreElements())
\r
{
\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
//Do we want to count +ve conservation or +ve and -ve cons.?
\r
if (consflag)
\r
@@
-333,20
+344,20
@@
public class Conservation
\r
if (count < 10)
\r
{
\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
}
\r
else
\r
{
\r
- consString = consString + ((gapcons[0] == 1) ? "*" : "+");
\r
+ consString.append((gapcons[0] == 1) ? "*" : "+");
\r
}
\r
}
\r
else
\r
{
\r
}
\r
}
\r
else
\r
{
\r
- consString = consString + "-";
\r
+ consString.append("-");
\r
}
\r
}
\r
\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
\r
/**
\r
@@
-435,7
+446,6
@@
public class Conservation
quality = new Vector();
\r
\r
double max = -10000;
\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
int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
\r
\r
//Loop over columns // JBPNote Profiling info
\r
@@
-445,18
+455,22
@@
public class Conservation
\r
int size = seqNums.size();
\r
int[] lengths = new int[size];
\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, seqNum;
\r
\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
lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
\r
\r
- for (int j = start; j <= end; j++)
\r
+
\r
+ for (j = start; j <= end; j++)
\r
{
\r
{
\r
- double bigtot = 0;
\r
+ bigtot = 0;
\r
\r
// First Xr = depends on column only
\r
\r
// First Xr = depends on column only
\r
- double[] x = new double[24];
\r
+ x = new double[24];
\r
\r
\r
- for (int ii = 0; ii < 24; ii++)
\r
+ for (ii = 0; ii < 24; ii++)
\r
{
\r
x[ii] = 0;
\r
\r
{
\r
x[ii] = 0;
\r
\r
@@
-483,15
+497,15
@@
public class Conservation
// Now calculate D for each position and sum
\r
for (int k = 0; k < size; k++)
\r
{
\r
// Now calculate D for each position and sum
\r
for (int 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
? ((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
{
\r
- double sr = 0;
\r
+ sr = 0;
\r
\r
try
\r
{
\r
\r
try
\r
{
\r
@@
-522,16
+536,15
@@
public class Conservation
// bigtot = bigtot * (size-cons2[j][23])/size;
\r
quality.addElement(new Double(bigtot));
\r
\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
\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
{
\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
tmp = ((max - tmp) * (size - cons2[j][23])) / size;
\r
\r
// System.out.println(tmp+ " " + j);
\r