/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
{
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();
{
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++;
}
}
{
if (result.intValue() != -1)
{
+ {
+ if (result.intValue()==0) {
+ consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
+ } else {
+ consSymbs[i-start] = type+" "+consSymbs[i-start];
+ }
+ }
+
count++;
}
}
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)));