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JAL-1683 replace year/version strings with tokens in source
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
0625a9a
..
1aa29e0
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
*
*
* This file is part of Jalview.
*
@@
-71,6
+71,8
@@
public class Conservation
int[][] cons2;
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
/**
* Creates a new Conservation object.
*
@@
-366,17
+368,17
@@
public class Conservation
{
consString.append('-');
}
{
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;
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];
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
-
// Now find the verdict
count = 0;
enumeration = resultHash.keys();
// Now find the verdict
count = 0;
enumeration = resultHash.keys();
@@
-385,12
+387,12
@@
public class Conservation
{
type = (String) enumeration.nextElement();
result = (Integer) resultHash.get(type);
{
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)
{
// 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++;
}
}
count++;
}
}
@@
-398,6
+400,14
@@
public class Conservation
{
if (result.intValue() != -1)
{
{
if (result.intValue() != -1)
{
+ {
+ if (result.intValue()==0) {
+ consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
+ } else {
+ consSymbs[i-start] = type+" "+consSymbs[i-start];
+ }
+ }
+
count++;
}
}
count++;
}
}
@@
-683,7
+693,7
@@
public class Conservation
float vprop = value - min;
vprop /= max;
conservation.annotations[i] = new Annotation(String.valueOf(c),
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)));
+ (maxR * vprop), minG + (maxG * vprop), minB
+ (maxB * vprop)));