*/
package jalview.io;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
import java.util.Locale;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqDistanceContactMatrix;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
import jalview.util.Platform;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-
/**
* A low level class for alignment and feature IO with alignment formatting
* methods used by both applet and application for generating flat alignment
DataSourceType sourceType, FileFormatI fileFormat)
throws IOException
{
+ return readFile(selectedFile, file, sourceType, fileFormat, null);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat,
+ AlignmentAnnotation.TFType tempfacType) throws IOException
+ {
this.selectedFile = selectedFile;
if (selectedFile != null)
{
// needs a File option
alignFile = new JmolParser(
- selectedFile == null ? inFile : selectedFile, sourceType);
+ selectedFile == null ? inFile : selectedFile, sourceType,
+ tempfacType);
}
else
{