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Transparency available again
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueColourScheme.java
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
a993802
..
64fd62e
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-41,7
+41,7
@@
public class ResidueColourScheme implements ColourSchemeI
int threshold = 0;
\r
\r
/* Set when threshold colouring to either pid_gaps or pid_nogaps*/
\r
int threshold = 0;
\r
\r
/* Set when threshold colouring to either pid_gaps or pid_nogaps*/
\r
- protected String ignoreGaps = "pid_gaps";
\r
+ protected String ignoreGaps = AAFrequency.PID_GAPS;
\r
\r
/** Consenus as a hashtable array */
\r
Hashtable [] consensus;
\r
\r
/** Consenus as a hashtable array */
\r
Hashtable [] consensus;
\r
@@
-83,7
+83,7
@@
public class ResidueColourScheme implements ColourSchemeI
*/
\r
public Color findColour(String aa)
\r
{
\r
*/
\r
public Color findColour(String aa)
\r
{
\r
- return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
\r
+ return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
\r
}
\r
\r
\r
}
\r
\r
\r
@@
-91,7
+91,7
@@
public class ResidueColourScheme implements ColourSchemeI
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
\r
- int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
\r
+ int index = ResidueProperties.aaIndex[s.charAt(0)];
\r
\r
if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
\r
{
\r
\r
if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
\r
{
\r
@@
-129,9
+129,9
@@
public class ResidueColourScheme implements ColourSchemeI
{
\r
threshold = ct;
\r
if(ignoreGaps)
\r
{
\r
threshold = ct;
\r
if(ignoreGaps)
\r
- this.ignoreGaps = "pid_nogaps";
\r
+ this.ignoreGaps = AAFrequency.PID_NOGAPS;
\r
else
\r
else
\r
- this.ignoreGaps = "pid_gaps";
\r
+ this.ignoreGaps = AAFrequency.PID_GAPS;
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-153,14
+153,16
@@
public class ResidueColourScheme implements ColourSchemeI
s = String.valueOf(c);
\r
}
\r
\r
s = String.valueOf(c);
\r
}
\r
\r
+ if (consensus == null || consensus[j] == null)
\r
+ return false;
\r
\r
\r
- if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
\r
- consensus[j].contains(s))
\r
+ if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
\r
+ consensus[j].contains(s))
\r
{
\r
{
\r
- if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
\r
- {
\r
- return true;
\r
- }
\r
+ if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
\r
+ {
\r
+ return true;
\r
+ }
\r
}
\r
\r
return false;
\r
}
\r
\r
return false;
\r