X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=69d32cb3efd05661837c3472816d5c38fc4b2e69;hb=76139ef711627a3176736af47272ff55be62e720;hp=df5ca8da8131ed49e70b089da9c9674e4b96fe8d;hpb=14ffa72a74309f6d8e7a36d73c78bb4500fc32a2;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index df5ca8d..69d32cb 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
@@ -91,7 +94,7 @@ public class AAFrequency
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
- char c='-';
+ char c = '-';
float percentage;
int[] values = new int[255];
@@ -105,7 +108,7 @@ public class AAFrequency
maxResidue = "";
nongap = 0;
values = new int[255];
-
+
for (j = 0; j < jSize; j++)
{
if (sequences[j] == null)
@@ -143,27 +146,30 @@ public class AAFrequency
values['-']++;
}
}
- if (jSize==1)
+ if (jSize == 1)
{
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)
{
@@ -181,8 +187,13 @@ public class AAFrequency
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- percentage = ((float) maxCount * 100) / nongap;
+ if (nongap > 0)
+ {
+ // calculate for non-gapped too
+ percentage = ((float) maxCount * 100) / nongap;
+ }
residueHash.put(PID_NOGAPS, new Float(percentage));
+
result[i] = residueHash;
}
}
@@ -198,7 +209,7 @@ public class AAFrequency
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
- * @param nseq
+ * @param nseq
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
@@ -206,8 +217,9 @@ public class AAFrequency
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' });
}
@@ -224,21 +236,24 @@ public class AAFrequency
// initialised properly
return;
}
- String fmtstr="%3.1f";
- int precision=0;
- while (nseq>=10) {
+ String fmtstr = "%3.1f";
+ int precision = 0;
+ while (nseq >= 10)
+ {
precision++;
- nseq/=10;
+ nseq /= 10;
}
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);
- } else {
+ }
+ else
+ {
fmt = null;
}
for (int i = iStart; i < width; i++)
@@ -286,7 +301,7 @@ public class AAFrequency
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
@@ -309,7 +324,9 @@ public class AAFrequency
* 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++;
}
@@ -319,7 +336,8 @@ public class AAFrequency
}
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);