String refSeqId = null;
+ public boolean annotateAlignmentView(AlignViewportI viewport,
+ String file, String protocol)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+ file, protocol);
+ if (rslt
+ && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ {
+ viewport.setColumnSelection(colSel);
+ }
+
+ return rslt;
+ }
public boolean readAnnotationFile(AlignmentI al, String file,
String protocol)
{
+ return readAnnotationFile(al, null, file, protocol);
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+ String file, String protocol)
+ {
BufferedReader in = null;
try
{
modified = true;
continue;
}
+ else if (token.equalsIgnoreCase("VIEW_SETREF"))
+ {
+ if (refSeq != null)
+ {
+ al.setSeqrep(refSeq);
+ }
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
+ {
+ SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
+ if (sr == null)
+ {
+ sr = al.getSequenceAt(0);
+ }
+ if (sr != null)
+ {
+ if (colSel == null)
+ {
+ System.err
+ .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ + line);
+ }
+ else
+ {
+ // consider deferring this till after the file has been parsed ?
+ colSel.hideInsertionsFor(sr);
+ }
+ }
+ modified = true;
+ continue;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);