X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=ded1eb65293ebaf3433de2533cc3f1c4e5d7ad17;hb=6e514532a128c47d099985375d6126111ef548cb;hp=f7ad5f6db537420408f4ce683b0c95a6c972d6bf;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index f7ad5f6..ded1eb6 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,25 +1,32 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
+import java.util.Hashtable;
+import java.util.List;
/**
* Takes in a vector or array of sequences and column start and column end and
@@ -32,8 +39,8 @@ import jalview.datamodel.*;
*/
public class AAFrequency
{
- // No need to store 1000s of strings which are not
- // visible to the user.
+ private static final int TO_UPPER_CASE = 'A' - 'a'; // -32
+
public static final String MAXCOUNT = "C";
public static final String MAXRESIDUE = "R";
@@ -44,6 +51,19 @@ public class AAFrequency
public static final String PROFILE = "P";
+ /*
+ * Quick look-up of String value of char 'A' to 'Z'
+ */
+ private static final String[] CHARS = new String['Z' - 'A' + 1];
+
+ static
+ {
+ for (char c = 'A'; c <= 'Z'; c++)
+ {
+ CHARS[c - 'A'] = String.valueOf(c);
+ }
+ }
+
public static final Hashtable[] calculate(List list,
int start, int end)
{
@@ -79,18 +99,13 @@ public class AAFrequency
}
public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result)
- {
- calculate(sequences, start, end, result, false);
- }
-
- public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result, boolean profile)
{
Hashtable residueHash;
- int maxCount, nongap, i, j, v, jSize = sequences.length;
+ int maxCount, nongap, i, j, v;
+ int jSize = sequences.length;
String maxResidue;
- char c;
+ char c = '-';
float percentage;
int[] values = new int[255];
@@ -130,7 +145,7 @@ public class AAFrequency
}
else if ('a' <= c && c <= 'z')
{
- c -= 32; // ('a' - 'A');
+ c += TO_UPPER_CASE;
}
nongap++;
@@ -142,25 +157,31 @@ 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 = CHARS[v - 'A'];
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += CHARS[v - 'A'];
+ }
+ maxCount = values[v];
}
- maxCount = values[v];
}
-
if (maxResidue.length() == 0)
{
maxResidue = "-";
@@ -177,8 +198,13 @@ 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 +220,22 @@ 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[]
- // { 'A', 'C', 'G', 'T', 'U' });
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq);
}
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 +245,26 @@ 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 +275,6 @@ public class AAFrequency
consensus.annotations[i] = null;
continue;
}
-
value = 0;
Float fv;
if (ignoreGapsInConsensusCalculation)
@@ -265,7 +310,7 @@ 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 +333,9 @@ 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 +345,8 @@ public class AAFrequency
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
+ + "%";
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
@@ -317,8 +365,10 @@ public class AAFrequency
int[] rtnval = new int[64];
int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
if (profile == null)
+ {
return null;
- Object[] ca = new Object[profile[0].length];
+ }
+ char[][] ca = new char[profile[0].length][];
float[] vl = new float[profile[0].length];
for (int c = 0; c < ca.length; c++)
{
@@ -326,16 +376,15 @@ public class AAFrequency
{ (char) c };
vl[c] = profile[0][c];
}
- ;
jalview.util.QuickSort.sort(vl, ca);
rtnval[0] = 2;
rtnval[1] = 0;
- for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ for (int c = ca.length - 1; profile[0][ca[c][0]] > 0; c--)
{
- if (((char[]) ca[c])[0] != '-')
+ if (ca[c][0] != '-')
{
- rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
- rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[rtnval[0]++] = ca[c][0];
+ rtnval[rtnval[0]] = (int) (profile[0][ca[c][0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
rtnval[1] += rtnval[rtnval[0]++];
}