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JAL-1894 update year/version in copyright
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
4d64685
..
d868959
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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,10
+20,16
@@
*/
package jalview.analysis;
*/
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
/**
* Calculates conservation values for a given set of sequences
@@
-71,6
+77,8
@@
public class Conservation
int[][] cons2;
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
/**
* Creates a new Conservation object.
*
@@
-106,7
+114,7
@@
public class Conservation
{
for (s = 0; s < sSize; s++)
{
{
for (s = 0; s < sSize; s++)
{
- sarray[s] = (SequenceI) sequences.get(s);
+ sarray[s] = sequences.get(s);
if (sarray[s].getLength() > maxLength)
{
maxLength = sarray[s].getLength();
if (sarray[s].getLength() > maxLength)
{
maxLength = sarray[s].getLength();
@@
-272,8
+280,7
@@
public class Conservation
resultHash.put(type, ht.get("-"));
}
}
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));
}
{
resultHash.put(type, new Integer(-1));
}
@@
-366,17
+373,17
@@
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];
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];
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
+392,12
@@
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
+405,17
@@
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++;
}
}
@@
-669,7
+687,7
@@
public class Conservation
if (Character.isDigit(c))
{
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
}
else if (c == '*')
{
@@
-682,10
+700,12
@@
public class Conservation
float vprop = value - min;
vprop /= max;
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),
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)
// Quality calc
if (quality2 != null)