- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- /**
- * Property change listener for changes in alignment
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
-
- /**
- * Property change listener for changes in alignment
- *
- * @param prop
- * DOCUMENT ME!
- * @param oldvalue
- * DOCUMENT ME!
- * @param newvalue
- * DOCUMENT ME!
- */
- public void firePropertyChange(String prop, Object oldvalue,
- Object newvalue)
- {
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
- }
-
- public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(ap);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
- }
- }
-
- 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);
- }
- }
- sg.setSeqrep(repSequence);
- sg.setHidereps(true);
- 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());
- sendSelection();
- }
-
- 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());
- sendSelection();
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
- }
-
- public void invertColumnSelection()
- {
- colSel.invertColumnSelection(0, alignment.getWidth());
- }
-
- 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 selection as new sequenceI objects
- */
- 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=null;
- if (selectionGroup!=null)
- {
- sequences = selectionGroup.getSequencesInOrder(alignment);
- }
- if (sequences == null)
- {
- sequences = alignment.getSequencesArray();
- }
- 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)
- {
- // JBPNote:
- // this is here because the AlignmentView constructor modifies the
- // CigarArray
- // object. Refactoring of Cigar and alignment view representation should
- // be done to remove redundancy.
- CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview != null)
- {
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup != null) ? selectionGroup
- .getStartRes() : 0);
- }
- return null;
- }
-
- /**
- * 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 String[] getViewAsString(boolean selectedRegionOnly)
- {
- String[] 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() + 1;
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
- }
-
- selection = new String[iSize];
- if (hasHiddenColumns)
- {
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- }
- else
- {
- for (i = 0; i < iSize; i++)
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
-
- }
- return selection;
- }
-
- public int[][] getVisibleRegionBoundaries(int min, int max)
- {
- Vector regions = new Vector();
- int start = min;
- int end = max;
-
- do
- {
- if (hasHiddenColumns)
- {
- if (start == 0)
- {
- start = colSel.adjustForHiddenColumns(start);
- }
-
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
- {
- end = max;
- }
- }
-
- regions.addElement(new int[]
- { start, end });
-
- if (hasHiddenColumns)
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
-
- int[][] startEnd = new int[regions.size()][2];
-
- regions.copyInto(startEnd);
-
- return startEnd;
-
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
- }
- /**
- * unique viewId for synchronizing state with stored Jalview Project
- *
- */
- private String viewId=null;
-
-
- public String getViewId()
- {
- if (viewId==null)
- {
- viewId = this.getSequenceSetId()+"."+this.hashCode()+"";
- }
- return viewId;
- }
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConservation(ap);
- }
- if (autoCalculateConsensus)
- {
- updateConsensus(ap);
- }
-
- // Reset endRes of groups if beyond alignment width
- int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
- if (groups != null)
- {
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getEndRes() > alWidth)
- {
- sg.setEndRes(alWidth - 1);
- }
- }
- }
-
- if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
- {
- selectionGroup.setEndRes(alWidth - 1);
- }
-
- resetAllColourSchemes();
-
- // alignment.adjustSequenceAnnotations();
- }
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = globalColourScheme;
- if (cs != null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
-
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
- {
- Alignment al = (Alignment) alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
- c.calculate();
- c.verdict(false, ConsPercGaps);
-
- cs.setConservation(c);
- }
- }
-
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
- {
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
- }
- sg.recalcConservation();
- }
- }
-
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else