git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Percentage precalculated in aafrequency
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
cfc9f94
..
8cea507
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-18,8
+18,6
@@
*/
\r
package jalview.schemes;
\r
\r
*/
\r
package jalview.schemes;
\r
\r
-import java.util.*;
\r
-
\r
import java.awt.*;
\r
\r
import jalview.datamodel.*;
\r
import java.awt.*;
\r
\r
import jalview.datamodel.*;
\r
@@
-45,18
+43,14
@@
public class PIDColourScheme
}
\r
\r
Color c = Color.white;
\r
}
\r
\r
Color c = Color.white;
\r
- Hashtable hash = (Hashtable) consensus.elementAt(j);
\r
\r
double sc = 0;
\r
\r
\r
double sc = 0;
\r
\r
- if ( (Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
\r
- hash.contains(s))
\r
+ if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
\r
+ consensus[j].contains(s))
\r
{
\r
{
\r
- sc = ( ( (Integer) hash.get(s)).intValue() * 100.0) /
\r
- ( (Integer) hash.get(
\r
- "size")).intValue();
\r
+ sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
\r
\r
\r
- // MC Should be isGap
\r
if (!jalview.util.Comparison.isGap( (s.charAt(0))))
\r
{
\r
for (int i = 0; i < thresholds.length; i++)
\r
if (!jalview.util.Comparison.isGap( (s.charAt(0))))
\r
{
\r
for (int i = 0; i < thresholds.length; i++)
\r