X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=66a6d78987d69047947255cf4a669935442612c5;hb=b29fc6b24c97d0817a116c0241781a0410f6d8c7;hp=910279fea5c6441f575c83423f23732b88ecc874;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 910279f..66a6d78 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.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;
@@ -68,6 +71,8 @@ public class Conservation
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
@@ -363,17 +368,17 @@ 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;
-
+ consSymbs[i-start]=new String();
+
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
-
// Now find the verdict
count = 0;
enumeration = resultHash.keys();
@@ -382,12 +387,12 @@ 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++;
}
}
@@ -395,6 +400,14 @@ 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++;
}
}
@@ -680,7 +693,7 @@ public class Conservation
float vprop = value - min;
vprop /= max;
conservation.annotations[i] = new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value, new Color(minR
+ consSymbs[i-start], ' ', value, new Color(minR
+ (maxR * vprop), minG + (maxG * vprop), minB
+ (maxB * vprop)));