X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=69d32cb3efd05661837c3472816d5c38fc4b2e69;hb=e07fc11d5aaf4d1237d83e5f7ea0909dea09902e;hp=f7ad5f6db537420408f4ce683b0c95a6c972d6bf;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index f7ad5f6..69d32cb 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,24 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.
- *
- * 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
+ * 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.
+ *
+ * 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;
import java.util.*;
+import jalview.util.Format;
import jalview.datamodel.*;
/**
@@ -90,7 +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];
@@ -142,25 +146,31 @@ public class AAFrequency
values['-']++;
}
}
-
- for (v = 'A'; v < 'Z'; v++)
+ if (jSize == 1)
{
- if (values[v] < 2 || values[v] < maxCount)
+ maxResidue = String.valueOf(c);
+ maxCount = 1;
+ }
+ else
+ {
+ 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)
{
maxResidue = "-";
@@ -177,8 +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;
}
}
@@ -194,22 +209,24 @@ public class AAFrequency
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
+ * @param nseq
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols)
+ boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
- // char[]
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq); // new
+ // char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, char[] alphabet)
+ boolean includeAllConsSymbols, char[] alphabet, long nseq)
{
float tval, value;
if (consensus == null || consensus.annotations == null
@@ -219,6 +236,26 @@ public class AAFrequency
// initialised properly
return;
}
+ String fmtstr = "%3.1f";
+ int precision = 0;
+ while (nseq >= 10)
+ {
+ precision++;
+ nseq /= 10;
+ }
+ final Format fmt;
+ if (precision > 1)
+ {
+ // if (precision>2)
+ {
+ fmtstr = "%" + (2 + precision) + "." + (precision) + "f";
+ }
+ fmt = new Format(fmtstr);
+ }
+ else
+ {
+ fmt = null;
+ }
for (int i = iStart; i < width; i++)
{
Hashtable hci;
@@ -229,7 +266,6 @@ public class AAFrequency
consensus.annotations[i] = null;
continue;
}
-
value = 0;
Float fv;
if (ignoreGapsInConsensusCalculation)
@@ -265,7 +301,7 @@ public class AAFrequency
tval = profile[0][alphabet[c]] * 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((int) tval) + "%";
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval)) + "%";
}
}
else
@@ -288,7 +324,9 @@ public class AAFrequency
* 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + ((int) tval) + "%";
+ + " "
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval))
+ + "%";
p++;
}
@@ -298,7 +336,8 @@ public class AAFrequency
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
+ + "%";
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);