/**
* This Method is used to return all the HiddenColumn regions
+ *
* @return empty list or List of hidden column intervals
*/
public List<int[]> getHiddenColumns()
}
else if (end < region[0] && start < region[0])
{
- hiddenColumns.insertElementAt(new int[]
- { start, end }, i);
+ hiddenColumns.insertElementAt(new int[] { start, end }, i);
added = true;
break;
}
}
else if (!added)
{
- hiddenColumns.addElement(new int[]
- { start, end });
+ hiddenColumns.addElement(new int[] { start, end });
}
}
}
if (hideStart > vstart)
{
- visiblecontigs.add(new int[]
- { vstart, hideStart - 1 });
+ visiblecontigs.add(new int[] { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
- visiblecontigs.add(new int[]
- { vstart, end - 1 });
+ visiblecontigs.add(new int[] { vstart, end - 1 });
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
}
else
{
- return new int[]
- { start, end - 1 };
+ return new int[] { start, end - 1 };
}
}
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector<Annotation []> annels = new Vector<Annotation []>();
+ Vector<Annotation[]> annels = new Vector<Annotation[]>();
Annotation[] els = null;
List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
- for (Annotation [] chnk : annels)
+ for (Annotation[] chnk : annels)
{
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
* profileseq marked as hidden.
*/
public static ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
+ AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
{
return hiddenColumns != null && hiddenColumns.size() > 0;
}
-
+
/**
*
* @return true if there are more than one set of columns hidden
hideColumns(r[0], r[1]);
}
}
-
+
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{