X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=7b3ce25ac1036120deb7cb3dc75d5b0f6fd5aa61;hb=f6cf71697dde4b4cdc4dcc8941e30fb5c71a5a41;hp=6957b5cb0e3f6ba119dc7c08e18a1a866fe0008d;hpb=3e51d4b043f8ac3e262f9b3660ec1f8561d1db93;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 6957b5c..7b3ce25 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,26 +1,35 @@
/*
- * 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.
- *
+ * 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.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* Calculates conservation values for a given set of sequences
@@ -68,6 +77,8 @@ public class Conservation
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
@@ -99,20 +110,22 @@ public class Conservation
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
this.sequences = sarray;
- try {
- for (s = 0; s < sSize; s++)
+ try
{
- sarray[s] = (SequenceI) sequences.get(s);
- if (sarray[s].getLength() > maxLength)
+ for (s = 0; s < sSize; s++)
{
- maxLength = sarray[s].getLength();
+ sarray[s] = sequences.get(s);
+ if (sarray[s].getLength() > maxLength)
+ {
+ maxLength = sarray[s].getLength();
+ }
}
- }
} catch (ArrayIndexOutOfBoundsException ex)
{
- // bail - another thread has modified the sequence array, so the current calculation is probably invalid.
- this.sequences=new SequenceI[0];
- maxLength=0;
+ // bail - another thread has modified the sequence array, so the current
+ // calculation is probably invalid.
+ this.sequences = new SequenceI[0];
+ maxLength = 0;
}
}
@@ -222,10 +235,7 @@ public class Conservation
c = '-';
}
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
+ c = toUpperCase(c);
}
values[c]++;
}
@@ -267,8 +277,7 @@ public class Conservation
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals((Integer) ht
- .get(res)) == false)
+ else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
{
resultHash.put(type, new Integer(-1));
}
@@ -276,7 +285,8 @@ public class Conservation
}
}
- if (total.length>0) {
+ if (total.length > 0)
+ {
total[i - start] = resultHash;
}
}
@@ -313,6 +323,7 @@ public class Conservation
}
else
{
+ c = toUpperCase(c);
nres++;
if (nres == 1)
@@ -334,6 +345,22 @@ public class Conservation
}
/**
+ * Returns the upper-cased character if between 'a' and 'z', else the
+ * unchanged value
+ *
+ * @param c
+ * @return
+ */
+ char toUpperCase(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
* @param consflag
@@ -360,17 +387,17 @@ public class Conservation
{
consString.append('-');
}
-
+ consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
gapcons = countConsNGaps(i);
totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.length;
+ pgaps = ((float) totGaps * 100) / sequences.length;
+ consSymbs[i - start] = new String();
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
-
// Now find the verdict
count = 0;
enumeration = resultHash.keys();
@@ -379,12 +406,12 @@ public class Conservation
{
type = (String) enumeration.nextElement();
result = (Integer) resultHash.get(type);
-
// Do we want to count +ve conservation or +ve and -ve cons.?
if (consflag)
{
if (result.intValue() == 1)
{
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
}
@@ -392,6 +419,17 @@ public class Conservation
{
if (result.intValue() != -1)
{
+ {
+ if (result.intValue() == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
+ }
+
count++;
}
}
@@ -663,7 +701,7 @@ public class Conservation
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
@@ -676,10 +714,12 @@ public class Conservation
float vprop = value - min;
vprop /= max;
+ int consp = i - start;
+ String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
conservation.annotations[i] = new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
// Quality calc
if (quality2 != null)
@@ -697,33 +737,52 @@ public class Conservation
/**
* construct and call the calculation methods on a new Conservation object
- * @param name - name of conservation
- * @param consHash - hash table of properties for each amino acid (normally ResidueProperties.propHash)
- * @param threshold - minimum number of conserved residues needed to indicate conservation (typically 3)
+ *
+ * @param name
+ * - name of conservation
+ * @param consHash
+ * - hash table of properties for each amino acid (normally
+ * ResidueProperties.propHash)
+ * @param threshold
+ * - minimum number of conserved residues needed to indicate
+ * conservation (typically 3)
* @param seqs
- * @param start first column in calculation window
- * @param end last column in calculation window
- * @param posOrNeg positive (true) or negative (false) conservation
- * @param consPercGaps percentage of gaps tolerated in column
- * @param calcQuality flag indicating if alignment quality should be calculated
+ * @param start
+ * first column in calculation window
+ * @param end
+ * last column in calculation window
+ * @param posOrNeg
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
* @return Conservation object ready for use in visualization
*/
public static Conservation calculateConservation(String name,
- Hashtable consHash, int threshold, List seqs, int start, int end, boolean posOrNeg, int consPercGaps, boolean calcQuality)
+ Hashtable consHash, int threshold, List seqs,
+ int start, int end, boolean posOrNeg, int consPercGaps,
+ boolean calcQuality)
{
- Conservation cons = new Conservation(name, consHash, threshold, seqs, start,end);
+ Conservation cons = new Conservation(name, consHash, threshold, seqs,
+ start, end);
return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
}
+
/**
- * @param b positive (true) or negative (false) conservation
- * @param consPercGaps percentage of gaps tolerated in column
- * @param calcQuality flag indicating if alignment quality should be calculated
- * @return Conservation object ready for use in visualization
- */
- public static Conservation calculateConservation(Conservation cons, boolean b, int consPercGaps, boolean calcQuality)
- {
- cons.calculate();
- cons.verdict(b, consPercGaps);
+ * @param b
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(Conservation cons,
+ boolean b, int consPercGaps, boolean calcQuality)
+ {
+ cons.calculate();
+ cons.verdict(b, consPercGaps);
if (calcQuality)
{