*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
/**
* Additional formatting methods used by the application in a number of places.
public boolean getCacheSuffixDefault(String format)
{
if (isValidFormat(format))
+ {
return jalview.bin.Cache.getDefault(format.toUpperCase()
+ "_JVSUFFIX", true);
+ }
return false;
}
return this.formatSequences(format, alignment, suffix);
}
+ public Alignment readFile(String inFile, String type, String format)
+ throws java.io.IOException
+ {
+ Alignment al;
+ if (format.equals("HTML"))
+ {
+ afile = new HtmlFile(inFile, type);
+ al = new Alignment(afile.getSeqsAsArray());
+ afile.addAnnotations(al);
+ }
+ else
+ {
+ al = super.readFile(inFile, type, format);
+ }
+
+ return al;
+ }
+
+ public AlignmentI readFromFile(FileParse source, String format)
+ throws java.io.IOException
+ {
+ Alignment al;
+ if (format.equals("HTML"))
+ {
+ afile = new HtmlFile(source);
+ al = new Alignment(afile.getSeqsAsArray());
+ afile.addAnnotations(al);
+ }
+ else
+ {
+ al = (Alignment) super.readFromFile(source, format);
+ }
+ return al;
+ }
+
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for
}
return AppletFormatAdapter.isValidFormat(format, forwriting);
}
+
+ /**
+ * Create a flat file representation of a given view or selected region of a view
+ * @param format
+ * @param av
+ * @return String containing flat file
+ */
+ public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ {
+ return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ }
+
}