*/
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.datamodel.SequenceI;
import jalview.util.Comparison;
+import java.io.File;
import java.io.IOException;
-import java.util.Locale;
/**
* Additional formatting methods used by the application in a number of places.
}
public FormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
super(alignPanel, settings);
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
- true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
- true);
- serviceSecondaryStruct = jalview.bin.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,
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