*/
package jalview.io;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
*/
public class FormatAdapter extends AppletFormatAdapter
{
- public FormatAdapter(AlignViewportI viewport)
+ public FormatAdapter(AlignmentViewPanel viewpanel)
{
- super(viewport);
+ super(viewpanel);
init();
}
init();
}
+ public FormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ super(alignPanel, settings);
+ }
+
private void init()
{
if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
return this.formatSequences(format, alignment, suffix);
}
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
- Alignment al = super.readFile(inFile, type, format);
+ AlignmentI al = super.readFile(inFile, type, format);
return al;
}
public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
- Alignment al = (Alignment) super.readFromFile(source, format);
+ AlignmentI al = super.readFromFile(source, format);
return al;
}
}
/**
- * Create a flat file representation of a given view or selected region of a view
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
* @param format
- * @param av
+ * @param ap
+ * alignment panel originating the view
* @return String containing flat file
*/
- public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(String format, AlignmentViewPanel ap,
+ boolean selectedOnly)
{
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
}