- public boolean getIgnoreGapsConsensus()
- {
- return ignoreGapsInConsensusCalculation;
- }
-
- public void setDataset(boolean b)
- {
- isDataset = b;
- }
-
- public boolean isDataset()
- {
- return isDataset;
- }
-
-
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
-
-
- public void hideColumns(int start, int end)
- {
- if(start==end)
- {
- colSel.hideColumns(start);
- }
- else
- {
- colSel.hideColumns(start, end);
- }
-
- hasHiddenColumns = true;
- }
-
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
- {
- int sSize = sg.getSize();
- if(sSize < 2)
- {
- return;
- }
-
- if(hiddenRepSequences==null)
- {
- hiddenRepSequences = new Hashtable();
- }
-
- hiddenRepSequences.put(repSequence, sg);
-
- //Hide all sequences except the repSequence
- SequenceI [] seqs = new SequenceI[sSize-1];
- int index = 0;
- for(int i=0; i<sSize; i++)
- {
- if(sg.getSequenceAt(i)!=repSequence)
- {
- if(index==sSize-1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
- }
- }
-
- hideSequence(seqs);
-
- }
-
- public void hideAllSelectedSeqs()
- {
- if (selectionGroup == null || selectionGroup.getSize()<1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
- }
-
- public void hideSequence(SequenceI [] seq)
- {
- if(seq!=null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seq[i]);
- }
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
- }
-
- public void showSequence(int index)
- {
- Vector tmp = alignment.getHiddenSequences().showSequence(index
- , hiddenRepSequences);
- if(tmp.size()>0)
- {
- if(selectionGroup==null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
- }
-
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence(
- (SequenceI) tmp.elementAt(t), false
- );
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- }
-
- if(alignment.getHiddenSequences().getSize()<1)
- {
- hasHiddenRows = false;
- }
- }
-
- public void showColumn(int col)
- {
- colSel.revealHiddenColumns(col);
- if(colSel.getHiddenColumns()==null)
- {
- hasHiddenColumns = false;
- }
- }
-
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if(alignment.getHiddenSequences().getSize()>0)
- {
- if(selectionGroup==null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
- }
- Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
- for(int t=0; t<tmp.size(); t++)
- {
- selectionGroup.addSequence(
- (SequenceI)tmp.elementAt(t), false
- );
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
- }
-
-
-
- public void invertColumnSelection()
- {
- for(int i=0; i<alignment.getWidth(); i++)
- {
- if(colSel.contains(i))
- {
- colSel.removeElement(i);
- }
- else
- {
- if (!hasHiddenColumns || colSel.isVisible(i))
- {
- colSel.addElement(i);
- }
- }
- }
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
- }
-
- /**
- * This method returns an array of new SequenceI objects
- * derived from the whole alignment or just the current
- * selection with start and end points adjusted
- * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
- * @return String[]
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
- for (int i=0; i<sequences.length; i++)
- {
- sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
- }
- }
- else
- {
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
- }
-
- return sequences;
- }
- /**
- * get the currently selected sequence objects or all the sequences in the alignment.
- * @return array of references to sequence objects
- */
- public SequenceI[] getSequenceSelection()
- {
- SequenceI[] sequences;
- if (selectionGroup==null)
- {
- sequences = alignment.getSequencesArray();
- }
- else
- {
- sequences = selectionGroup.getSequencesInOrder(alignment);
- }
- return sequences;
- }
- /**
- * This method returns the visible alignment as text, as
- * seen on the GUI, ie if columns are hidden they will not
- * be returned in the result.
- * Use this for calculating trees, PCA, redundancy etc on views
- * which contain hidden columns.
- * @return String[]
- */
- public jalview.datamodel.CigarArray getViewAsCigars(boolean
- selectedRegionOnly)
- {
- CigarArray selection=null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth()-1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for(i=0; i<iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection=new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns)
- {
- Vector regions = colSel.getHiddenColumns();
- int [] region;
- int hideStart, hideEnd;
- int last=start;
- for (int j = 0; last<end & j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
- // edit hidden regions to selection range
- if (hideStart < last)
- {
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
-
- if (hideStart>end)
- {
- break;
- }
-
- if (hideEnd>end)
- {
- hideEnd=end;
- }
-
- if (hideStart>hideEnd)
- {
- break;
- }
- /**
- * form operations...
- */
- if (last<hideStart)
- {
- selection.addOperation(CigarArray.M, hideStart-last);
- }
- selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
- last = hideEnd+1;
- }
- // Final match if necessary.
- if (last<end)
- {
- selection.addOperation(CigarArray.M, end-last+1);
- }
- }
- else
- {
- selection.addOperation(CigarArray.M, end-start+1);
- }
- return selection;
- }
- /**
- * return a compact representation of the current alignment selection to
- * pass to an analysis function
- * @param selectedOnly boolean true to just return the selected view
- * @return AlignmentView
- */
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)