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JAL-3474 removed all .cvsignore files stored in the repo
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
f09e8a0
..
6d3c18a
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-116,8
+116,8
@@
public class FormatAdapter extends AppletFormatAdapter
startIndex = startEnd[0];
endIndex = startEnd[1];
// get first non-gaped residue start position
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++;
}
{
startIndex++;
}
@@
-161,7
+161,8
@@
public class FormatAdapter extends AppletFormatAdapter
public boolean getCacheSuffixDefault(FileFormatI format)
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+ return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+ true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
@@
-211,12
+212,12
@@
public class FormatAdapter extends AppletFormatAdapter
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
- hidden.makeVisibleAnnotation(selgp.getStartRes(),
- selgp.getEndRes(), na);
+ na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+ hidden);
}
else
{
}
else
{
- hidden.makeVisibleAnnotation(na);
+ na.makeVisibleAnnotation(hidden);
}
alv.addAnnotation(na);
}
}
alv.addAnnotation(na);
}