X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=0f538825c0f9d05b182577295c0137b6a192d3d7;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=656cdcbf634ddb0daad93bb6af156b50ae04f082;hpb=948228d480dcd77e194de69b393dfe5f29f51bb3;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 656cdcb..0f53882 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)
@@ -143,8 +146,11 @@ public class AAFrequency
values['-']++;
}
}
-
- for (v = 'A'; v < 'Z'; v++)
+ if (jSize==1)
+ {
+ maxResidue = String.valueOf(c);
+ maxCount=1;
+ } else {for (v = 'A'; v < 'Z'; v++)
{
if (values[v] < 2 || values[v] < maxCount)
{
@@ -161,7 +167,7 @@ public class AAFrequency
}
maxCount = values[v];
}
-
+ }
if (maxResidue.length() == 0)
{
maxResidue = "-";
@@ -178,8 +184,12 @@ 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;
}
}
@@ -222,16 +232,22 @@ public class AAFrequency
return;
}
String fmtstr="%3.1f";
- int precision=2;
- while (nseq>100) {
+ int precision=0;
+ while (nseq>=10) {
precision++;
nseq/=10;
}
- if (precision>2)
+ final Format fmt;
+ if (precision>1)
{
- fmtstr = "%"+(2+precision)+"."+precision+"f";
+ //if (precision>2)
+ {
+ fmtstr = "%"+(2+precision)+"."+(precision)+"f";
+ }
+ fmt = new Format(fmtstr);
+ } else {
+ fmt = null;
}
- Format fmt = new Format(fmtstr);
for (int i = iStart; i < width; i++)
{
Hashtable hci;
@@ -277,7 +293,7 @@ public class AAFrequency
tval = profile[0][alphabet[c]] * 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + fmt.form(tval) + "%";
+ + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
}
}
else
@@ -300,7 +316,7 @@ public class AAFrequency
* 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + fmt.form(tval) + "%";
+ + " " + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
p++;
}
@@ -310,7 +326,7 @@ public class AAFrequency
}
else
{
- mouseOver += (fmt.form(value) + "%");
+ mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);