*/
package jalview.io;
+import java.io.File;
+import java.io.IOException;
import java.util.Locale;
import jalview.api.AlignExportSettingsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
import jalview.util.Comparison;
-import java.io.File;
-import java.io.IOException;
-
/**
* Additional formatting methods used by the application in a number of places.
*
{
if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
- annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
- true);
- localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
- true);
- serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
- true);
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN", true);
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN", true);
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW", true);
}
else
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
- true);
+ return Cache.getDefault(
+ format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX", true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
}
@Override
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat,
+ StructureImportSettings.TFType tempfacType) throws IOException
+ {
+ AlignmentI al = super.readFile(selectedFile, file, sourceType,
+ fileFormat, tempfacType);
+ return al;
+ }
+
+ @Override
public AlignmentI readFile(String file, DataSourceType sourceType,
FileFormatI fileFormat) throws IOException
{