import jalview.util.Comparison;
import java.io.IOException;
+import java.util.Locale;
/**
* Additional formatting methods used by the application in a number of places.
startIndex = startEnd[0];
endIndex = startEnd[1];
// get first non-gaped residue start position
- while (Comparison.isGap(seqs[i]
- .getCharAt(startIndex)) && startIndex < endIndex)
+ while (Comparison.isGap(seqs[i].getCharAt(startIndex))
+ && startIndex < endIndex)
{
startIndex++;
}
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
+ true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
- hidden.makeVisibleAnnotation(selgp.getStartRes(),
- selgp.getEndRes(), na);
+ na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+ hidden);
}
else
{
- hidden.makeVisibleAnnotation(na);
+ na.makeVisibleAnnotation(hidden);
}
alv.addAnnotation(na);
}