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JAL-98 minor fixes to / tests for annotation derivation
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
569b036
..
61e11c4
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-47,18
+47,8
@@
import java.util.List;
*/
public class AAFrequency
{
*/
public class AAFrequency
{
- public static final String MAXCOUNT = "C";
-
- public static final String MAXRESIDUE = "R";
-
- public static final String PID_GAPS = "G";
-
- public static final String PID_NOGAPS = "N";
-
public static final String PROFILE = "P";
public static final String PROFILE = "P";
- public static final String ENCODED_CHARS = "E";
-
/*
* Quick look-up of String value of char 'A' to 'Z'
*/
/*
* Quick look-up of String value of char 'A' to 'Z'
*/
@@
-275,7
+265,16
@@
public class AAFrequency
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
- consensus.annotations[i] = new Annotation(profile.getModalResidue(),
+ String modalResidue = profile.getModalResidue();
+ if ("".equals(modalResidue))
+ {
+ modalResidue = "-";
+ }
+ else if (modalResidue.length() > 1)
+ {
+ modalResidue = "+";
+ }
+ consensus.annotations[i] = new Annotation(modalResidue,
description, ' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
description, ' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
@@
-318,15
+317,18
@@
public class AAFrequency
String maxRes = profile.getModalResidue();
if (maxRes.length() > 1)
{
String maxRes = profile.getModalResidue();
if (maxRes.length() > 1)
{
- sb.append("[").append(maxRes).append("] ");
- maxRes = "+";
+ sb.append("[").append(maxRes).append("]");
}
else
{
}
else
{
- sb.append(maxRes).append(" ");
+ sb.append(maxRes);
+ }
+ if (maxRes.length() > 0)
+ {
+ sb.append(" ");
+ Format.appendPercentage(sb, pid, dp);
+ sb.append("%");
}
}
- Format.appendPercentage(sb, pid, dp);
- sb.append("%");
description = sb.toString();
}
return description;
description = sb.toString();
}
return description;