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JAL-736 relocate group associated conservation symbols to alignment column position
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
1aa29e0
..
b8f1d92
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-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
@@
-108,7
+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();
@@
-274,7
+280,7
@@
public class Conservation
resultHash.put(type, ht.get("-"));
}
}
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals((Integer) ht
+ else if (((Integer) resultHash.get(type)).equals(ht
.get(res)) == false)
{
resultHash.put(type, new Integer(-1));
.get(res)) == false)
{
resultHash.put(type, new Integer(-1));
@@
-373,7
+379,7
@@
public class Conservation
{
gapcons = countConsNGaps(i);
totGaps = gapcons[1];
{
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)
consSymbs[i-start]=new String();
if (percentageGaps > pgaps)
@@
-679,7
+685,7
@@
public class Conservation
if (Character.isDigit(c))
{
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
}
else if (c == '*')
{
@@
-692,8
+698,11
@@
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),
- consSymbs[i-start], ' ', value, new Color(minR
+ conssym, ' ', value, new Color(minR
+ (maxR * vprop), minG + (maxG * vprop), minB
+ (maxB * vprop)));
+ (maxR * vprop), minG + (maxG * vprop), minB
+ (maxB * vprop)));