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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
3027ab1
..
31751f5
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-20,7
+20,9
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
@@
-32,6
+34,7
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
+import java.io.File;
import java.io.IOException;
/**
import java.io.IOException;
/**
@@
-55,7
+58,7
@@
public class FormatAdapter extends AppletFormatAdapter
}
public FormatAdapter(AlignmentViewPanel alignPanel,
}
public FormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
super(alignPanel, settings);
}
{
super(alignPanel, settings);
}
@@
-161,7
+164,8
@@
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(Locale.ROOT) + "_JVSUFFIX",
+ true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
@@
-211,12
+215,12
@@
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);
}
@@
-234,6
+238,13
@@
public class FormatAdapter extends AppletFormatAdapter
return al;
}
return al;
}
+ public AlignmentI readFile(File file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+ return al;
+ }
+
@Override
public AlignmentI readFromFile(FileParse source, FileFormatI format)
throws IOException
@Override
public AlignmentI readFromFile(FileParse source, FileFormatI format)
throws IOException