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JAL-1517 source formatting
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
0f53882
..
69d32cb
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-94,7
+94,7
@@
public class AAFrequency
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
- char c='-';
+ char c = '-';
float percentage;
int[] values = new int[255];
float percentage;
int[] values = new int[255];
@@
-108,7
+108,7
@@
public class AAFrequency
maxResidue = "";
nongap = 0;
values = new int[255];
maxResidue = "";
nongap = 0;
values = new int[255];
-
+
for (j = 0; j < jSize; j++)
{
if (sequences[j] == null)
for (j = 0; j < jSize; j++)
{
if (sequences[j] == null)
@@
-146,27
+146,30
@@
public class AAFrequency
values['-']++;
}
}
values['-']++;
}
}
- if (jSize==1)
+ if (jSize == 1)
{
maxResidue = String.valueOf(c);
{
maxResidue = String.valueOf(c);
- maxCount=1;
- } else {for (v = 'A'; v < 'Z'; v++)
+ maxCount = 1;
+ }
+ else
{
{
- if (values[v] < 2 || values[v] < maxCount)
+ for (v = 'A'; v < 'Z'; v++)
{
{
- continue;
- }
+ if (values[v] < 2 || values[v] < maxCount)
+ {
+ continue;
+ }
- if (values[v] > maxCount)
- {
- maxResidue = String.valueOf((char) v);
- }
- else if (values[v] == maxCount)
- {
- maxResidue += String.valueOf((char) v);
+ if (values[v] > maxCount)
+ {
+ maxResidue = String.valueOf((char) v);
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += String.valueOf((char) v);
+ }
+ maxCount = values[v];
}
}
- maxCount = values[v];
- }
}
if (maxResidue.length() == 0)
{
}
if (maxResidue.length() == 0)
{
@@
-184,12
+187,13
@@
public class AAFrequency
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- if (nongap>0) {
+ if (nongap > 0)
+ {
// calculate for non-gapped too
percentage = ((float) maxCount * 100) / nongap;
}
residueHash.put(PID_NOGAPS, new Float(percentage));
// calculate for non-gapped too
percentage = ((float) maxCount * 100) / nongap;
}
residueHash.put(PID_NOGAPS, new Float(percentage));
-
+
result[i] = residueHash;
}
}
result[i] = residueHash;
}
}
@@
-205,7
+209,7
@@
public class AAFrequency
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
- * @param nseq
+ * @param nseq
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
@@
-213,8
+217,9
@@
public class AAFrequency
boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
- // char[]
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq); // new
+ // char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
// { 'A', 'C', 'G', 'T', 'U' });
}
@@
-231,21
+236,24
@@
public class AAFrequency
// initialised properly
return;
}
// initialised properly
return;
}
- String fmtstr="%3.1f";
- int precision=0;
- while (nseq>=10) {
+ String fmtstr = "%3.1f";
+ int precision = 0;
+ while (nseq >= 10)
+ {
precision++;
precision++;
- nseq/=10;
+ nseq /= 10;
}
final Format fmt;
}
final Format fmt;
- if (precision>1)
+ if (precision > 1)
{
{
- //if (precision>2)
+ // if (precision>2)
{
{
- fmtstr = "%"+(2+precision)+"."+(precision)+"f";
+ fmtstr = "%" + (2 + precision) + "." + (precision) + "f";
}
fmt = new Format(fmtstr);
}
fmt = new Format(fmtstr);
- } else {
+ }
+ else
+ {
fmt = null;
}
for (int i = iStart; i < width; i++)
fmt = null;
}
for (int i = iStart; i < width; i++)
@@
-293,7
+301,7
@@
public class AAFrequency
tval = profile[0][alphabet[c]] * 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
tval = profile[0][alphabet[c]] * 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval)) + "%";
}
}
else
}
}
else
@@
-316,7
+324,9
@@
public class AAFrequency
* 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
* 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
+ + " "
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval))
+ + "%";
p++;
}
p++;
}
@@
-326,7
+336,8
@@
public class AAFrequency
}
else
{
}
else
{
- mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
+ mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
+ + "%";
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);