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JAL-3725 restrict mapped virtual feature location to mapped region
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
7647a16
..
4d8794f
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-33,6
+33,7
@@
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.io.IOException;
import jalview.util.Comparison;
import java.io.IOException;
+import java.util.Locale;
/**
* Additional formatting methods used by the application in a number of places.
/**
* Additional formatting methods used by the application in a number of places.
@@
-161,7
+162,7
@@
public class FormatAdapter extends AppletFormatAdapter
public boolean getCacheSuffixDefault(FileFormatI format)
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
true);
}
true);
}
@@
-212,12
+213,12
@@
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);
}