X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=ded1eb65293ebaf3433de2533cc3f1c4e5d7ad17;hb=6e514532a128c47d099985375d6126111ef548cb;hp=08a3f52c87492c3cc86d9424edc9ffb674fdc7ba;hpb=416f6e172aa77e3b0f2c2bd2b7a5655a6194d936;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 08a3f52..ded1eb6 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,26 +1,32 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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.
+ * 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
@@ -33,8 +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";
@@ -45,6 +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)
{
@@ -80,18 +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];
@@ -105,7 +119,7 @@ public class AAFrequency
maxResidue = "";
nongap = 0;
values = new int[255];
-
+
for (j = 0; j < jSize; j++)
{
if (sequences[j] == null)
@@ -131,7 +145,7 @@ public class AAFrequency
}
else if ('a' <= c && c <= 'z')
{
- c -= 32; // ('a' - 'A');
+ c += TO_UPPER_CASE;
}
nongap++;
@@ -143,27 +157,30 @@ 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 = CHARS[v - 'A'];
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += CHARS[v - 'A'];
+ }
+ maxCount = values[v];
}
- maxCount = values[v];
- }
}
if (maxResidue.length() == 0)
{
@@ -181,10 +198,13 @@ public class AAFrequency
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));
}
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
result[i] = residueHash;
}
}
@@ -200,7 +220,7 @@ 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,
@@ -208,9 +228,8 @@ public class AAFrequency
boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
- // char[]
- // { 'A', 'C', 'G', 'T', 'U' });
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq);
}
public static void completeConsensus(AlignmentAnnotation consensus,
@@ -226,21 +245,24 @@ 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++)
@@ -288,7 +310,7 @@ 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
@@ -311,7 +333,9 @@ 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++;
}
@@ -321,7 +345,8 @@ 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);
@@ -340,8 +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++)
{
@@ -349,16 +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]++];
}