import java.io.PrintStream;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
/**
* Transient object compactly representing a 'view' of an alignment - with
*/
private class ScGroup
{
- public Vector seqs;
+ public List<SeqCigar> seqs;
public SequenceGroup sg;
ScGroup()
{
- seqs = new Vector();
+ seqs = new ArrayList<SeqCigar>();
+ }
+
+ /**
+ * @param seq
+ * @return true if seq was not a member before and was added to group
+ */
+ public boolean add(SeqCigar seq)
+ {
+ if (!seq.isMemberOf(this))
+ {
+ seqs.add(seq);
+ seq.setGroupMembership(this);
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ /**
+ *
+ * @param seq
+ * @return true if seq was a member and was removed from group
+ */
+ public boolean remove(SeqCigar seq)
+ {
+ if (seq.removeGroupMembership(this))
+ {
+ seqs.remove(seq);
+ return true;
+ }
+ return false;
+ }
+
+ public int size()
+ {
+ return seqs.size();
}
}
* vector of selected seqCigars. This vector is also referenced by each
* seqCigar contained in it.
*/
- private Vector selected;
+ private ScGroup selected;
/**
* Construct an alignmentView from a live jalview alignment view. Note -
* the view
*/
public AlignmentView(AlignmentI alignment,
- ColumnSelection columnSelection, SequenceGroup selection,
+ HiddenColumns hidden,
+ SequenceGroup selection,
boolean hasHiddenColumns, boolean selectedRegionOnly,
boolean recordGroups)
{
// refactored from AlignViewport.getAlignmentView(selectedOnly);
this(new jalview.datamodel.CigarArray(alignment,
- (hasHiddenColumns ? columnSelection : null),
+ (hasHiddenColumns ? hidden : null),
(selectedRegionOnly ? selection : null)),
(selectedRegionOnly && selection != null) ? selection
.getStartRes() : 0);
if (selection != null && selection.getSize() > 0)
{
List<SequenceI> sel = selection.getSequences(null);
- this.selected = new Vector();
+ this.selected = new ScGroup();
selseqs = selection
.getSequencesInOrder(alignment, selectedRegionOnly);
}
if (selection != null && selection.getSize() > 0
&& !selectedRegionOnly)
{
- sequences[csi].setGroupMembership(selected);
- selected.addElement(sequences[csi]);
+ selected.add(sequences[csi]);
}
if (seqsets != null)
{
{
if ((seqsets.get(sg)).contains(selseqs[i]))
{
- sequences[csi].setGroupMembership(sgrps[sg]);
sgrps[sg].sg.deleteSequence(selseqs[i], false);
- sgrps[sg].seqs.addElement(sequences[csi]);
+ sgrps[sg].add(sequences[csi]);
if (!addedgps[sg])
{
if (scGroups == null)
if (!seqcigararray.isSeqCigarArray())
{
throw new Error(
- MessageManager
- .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+ "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
}
// contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
* char
* @return Object[] { SequenceI[], ColumnSelection}
*/
- public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+ public Object[] getAlignmentAndHiddenColumns(char gapCharacter)
{
- ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
return new Object[] {
- SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
- contigs), colsel };
+ SeqCigar.createAlignmentSequences(sequences, gapCharacter, hidden,
+ contigs), hidden };
}
/**
if (contigs != null && contigs.length > 0)
{
SequenceI[] alignment = new SequenceI[sequences.length];
- ColumnSelection columnselection = new ColumnSelection();
+ // ColumnSelection columnselection = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
if (contigs != null && contigs.length > 0)
{
int start = 0;
}
}
// mark hidden segment as hidden in the new alignment
- columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]
+ hidden.hideColumns(nwidth, nwidth + contigs[contig + 2]
- 1);
nwidth += contigs[contig + 2];
}
}
}
}
- return new Object[] { alignment, columnselection };
+ return new Object[] { alignment, hidden };
}
else
{
}
if (nvismsa[0] != null)
{
- return new Object[] { nvismsa[0], new ColumnSelection() };
+ return new Object[] { nvismsa[0], new HiddenColumns() };
}
else
{
- return getAlignmentAndColumnSelection(gapCharacter);
+ return getAlignmentAndHiddenColumns(gapCharacter);
}
}
}
if (start < fwidth)
{
viscontigs[nvis] = start;
- viscontigs[nvis + 1] = fwidth; // end is inclusive
+ viscontigs[nvis + 1] = fwidth - 1; // end is inclusive
nvis += 2;
}
return viscontigs;
}
else
{
- return new int[] { 0, width };
+ return new int[] { 0, width - 1 };
}
}
+ sgr.sg.getEndRes());
for (int s = 0; s < sgr.seqs.size(); s++)
{
- if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr))
+ // JBPnote this should be a unit test for ScGroup
+ if (!sgr.seqs.get(s).isMemberOf(sgr))
{
- os.println("** WARNING: sequence "
- + ((SeqCigar) sgr.seqs.elementAt(s)).toString()
+ os.println("** WARNING: sequence " + sgr.seqs.get(s).toString()
+ " is not marked as member of group.");
}
}
}
public static void testSelectionViews(AlignmentI alignment,
- ColumnSelection csel, SequenceGroup selection)
+ HiddenColumns hidden, SequenceGroup selection)
{
System.out.println("Testing standard view creation:\n");
AlignmentView view = null;
{
System.out
.println("View with no hidden columns, no limit to selection, no groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, false, false,
+ view = new AlignmentView(alignment, hidden, selection, false, false,
false);
summariseAlignmentView(view, System.out);
{
System.out
.println("View with no hidden columns, no limit to selection, and all groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, false, false,
+ view = new AlignmentView(alignment, hidden, selection, false, false,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
System.out
.println("View with no hidden columns, limited to selection and no groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, false, true,
+ view = new AlignmentView(alignment, hidden, selection, false, true,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
System.out
.println("View with no hidden columns, limited to selection, and all groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, false, true,
+ view = new AlignmentView(alignment, hidden, selection, false, true,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
System.out
.println("View *with* hidden columns, no limit to selection, no groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, true, false,
+ view = new AlignmentView(alignment, hidden, selection, true, false,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
System.out
.println("View *with* hidden columns, no limit to selection, and all groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, true, false,
+ view = new AlignmentView(alignment, hidden, selection, true, false,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
System.out
.println("View *with* hidden columns, limited to selection and no groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, true, true,
+ view = new AlignmentView(alignment, hidden, selection, true, true,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
System.out
.println("View *with* hidden columns, limited to selection, and all groups to be collected:");
- view = new AlignmentView(alignment, csel, selection, true, true, true);
+ view = new AlignmentView(alignment, hidden, selection, true, true,
+ true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
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