+ private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+ '}', '<', '>' };
+
+ private AppVarnaBinding vab;
+
+ private AlignmentPanel ap;
+
+ private String viewId;
+
+ private StructureSelectionManager ssm;
+
+ /*
+ * Lookup for sequence and annotation mapped to each RNA in the viewer. Using
+ * a linked hashmap means that order is preserved when saved to the project.
+ */
+ private Map<RNA, RnaModel> models = new LinkedHashMap<RNA, RnaModel>();
+
+ private Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>();
+
+ private Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>();
+
+ private JSplitPane split;
+
+ private VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter();
+
+ private VarnaHighlighter selectionHighlighter = new VarnaHighlighter();
+
+ private class VarnaHighlighter
+ {
+ private HighlightRegionAnnotation _lastHighlight;
+
+ private RNA _lastRNAhighlighted = null;
+
+ public VarnaHighlighter()
+ {
+
+ }
+
+ /**
+ * Constructor when restoring from Varna session, including any highlight
+ * state
+ *
+ * @param rna
+ */
+ public VarnaHighlighter(RNA rna)
+ {
+ // TODO nice try but doesn't work; do we need a highlighter per model?
+ _lastRNAhighlighted = rna;
+ List<HighlightRegionAnnotation> highlights = rna.getHighlightRegion();
+ if (highlights != null && !highlights.isEmpty())
+ {
+ _lastHighlight = highlights.get(0);
+ }
+ }
+
+ public void highlightRegion(RNA rna, int start, int end)
+ {
+ clearLastSelection();
+ HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(
+ rna.getBasesBetween(start, end));
+ rna.addHighlightRegion(highlight);
+ _lastHighlight = highlight;
+ _lastRNAhighlighted = rna;
+ }
+
+ public HighlightRegionAnnotation getLastHighlight()
+ {
+ return _lastHighlight;
+ }
+
+ /**
+ * Clears all structure selection and refreshes the display
+ */
+ public void clearSelection()
+ {
+ if (_lastRNAhighlighted != null)
+ {
+ _lastRNAhighlighted.getHighlightRegion().clear();
+ vab.updateSelectedRNA(_lastRNAhighlighted);
+ _lastRNAhighlighted = null;
+ _lastHighlight = null;
+ }
+ }
+
+ /**
+ * Clear the last structure selection
+ */
+ public void clearLastSelection()
+ {
+ if (_lastRNAhighlighted != null)
+ {
+ _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
+ _lastRNAhighlighted = null;
+ _lastHighlight = null;
+ }
+ }
+ }
+
+ /**
+ * Constructor
+ *
+ * @param seq
+ * the RNA sequence
+ * @param aa
+ * the annotation with the secondary structure string
+ * @param ap
+ * the AlignmentPanel creating this object
+ */
+ public AppVarna(SequenceI seq, AlignmentAnnotation aa, AlignmentPanel ap)
+ {
+ this(ap);
+
+ String sname = aa.sequenceRef == null ? "secondary structure (alignment)"
+ : seq.getName() + " structure";
+ String theTitle = sname
+ + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
+ theTitle = MessageManager.formatMessage("label.varna_params",
+ new String[] { theTitle });
+ setTitle(theTitle);
+
+ String gappedTitle = sname + " (with gaps)";
+ RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true);
+ addModel(gappedModel, gappedTitle);
+
+ String trimmedTitle = "trimmed " + sname;
+ RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false);
+ addModel(trimmedModel, trimmedTitle);
+ vab.setSelectedIndex(0);
+ }
+
+ /**
+ * Constructor that links the viewer to a parent panel (but has no structures
+ * yet - use addModel to add them)
+ *
+ * @param ap
+ */
+ protected AppVarna(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.viewId = System.currentTimeMillis() + "." + this.hashCode();
+ vab = new AppVarnaBinding();
+ initVarna();
+
+ this.ssm = ap.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
+ close();
+ }
+ });
+ }
+
+ /**
+ * Constructor given viewer data read from a saved project file
+ *
+ * @param model
+ * @param ap
+ * the (or a) parent alignment panel
+ */
+ public AppVarna(RnaViewerModel model, AlignmentPanel ap)
+ {
+ this(ap);
+ setTitle(model.title);
+ this.viewId = model.viewId;
+ setBounds(model.x, model.y, model.width, model.height);
+ this.split.setDividerLocation(model.dividerLocation);
+ }
+
+ /**
+ * Constructs a split pane with an empty selection list and display panel, and
+ * adds it to the desktop
+ */
+ public void initVarna()
+ {
+ VARNAPanel varnaPanel = vab.get_varnaPanel();
+ setBackground(Color.white);
+ split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true,
+ vab.getListPanel(), varnaPanel);
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(split, BorderLayout.CENTER);
+
+ varnaPanel.addSelectionListener(this);
+ jalview.gui.Desktop.addInternalFrame(this, "", getBounds().width,
+ getBounds().height);
+ this.pack();
+ showPanel(true);
+ }
+
+ /**
+ * Constructs a new RNA model from the given one, without gaps. Also
+ * calculates and saves a 'shift list'
+ *
+ * @param rna
+ * @param name
+ * @return
+ */
+ public RNA trimRNA(RNA rna, String name)
+ {
+ ShiftList offset = new ShiftList();
+
+ RNA rnaTrim = new RNA(name);
+ try
+ {
+ String structDBN = rna.getStructDBN(true);
+ rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(structDBN));
+ } catch (ExceptionUnmatchedClosingParentheses e2)
+ {
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3)
+ {
+ e3.printStackTrace();
+ }
+
+ String seq = rnaTrim.getSeq();
+ StringBuilder struc = new StringBuilder(256);
+ struc.append(rnaTrim.getStructDBN(true));
+ int ofstart = -1;
+ int sleng = seq.length();
+
+ for (int i = 0; i < sleng; i++)
+ {
+ if (Comparison.isGap(seq.charAt(i)))
+ {
+ if (ofstart == -1)
+ {
+ ofstart = i;
+ }
+ /*
+ * mark base or base & pair in the structure with *
+ */
+ if (!rnaTrim.findPair(i).isEmpty())
+ {
+ int m = rnaTrim.findPair(i).get(1);
+ int l = rnaTrim.findPair(i).get(0);
+
+ struc.replace(m, m + 1, "*");
+ struc.replace(l, l + 1, "*");
+ }
+ else
+ {
+ struc.replace(i, i + 1, "*");
+ }
+ }
+ else
+ {
+ if (ofstart > -1)
+ {
+ offset.addShift(offset.shift(ofstart), ofstart - i);
+ ofstart = -1;
+ }
+ }
+ }
+ // final gap
+ if (ofstart > -1)
+ {
+ offset.addShift(offset.shift(ofstart), ofstart - sleng);
+ ofstart = -1;
+ }
+
+ /*
+ * remove the marked gaps from the structure
+ */
+ String newStruc = struc.toString().replace("*", "");
+
+ /*
+ * remove gaps from the sequence
+ */
+ String newSeq = AlignSeq.extractGaps(Comparison.GapChars, seq);
+
+ try
+ {
+ rnaTrim.setRNA(newSeq, newStruc);
+ registerOffset(rnaTrim, offset);
+ } catch (ExceptionUnmatchedClosingParentheses e)
+ {
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e)
+ {
+ e.printStackTrace();
+ }
+ return rnaTrim;
+ }
+
+ /**
+ * Save the sequence to structure mapping, and also its inverse.
+ *
+ * @param rnaTrim
+ * @param offset
+ */
+ private void registerOffset(RNA rnaTrim, ShiftList offset)
+ {
+ offsets.put(rnaTrim, offset);
+ offsetsInv.put(rnaTrim, offset.getInverse());
+ }
+
+ public void showPanel(boolean show)
+ {
+ this.setVisible(show);
+ }
+
+ /**
+ * If a mouseOver event from the AlignmentPanel is noticed the currently
+ * selected RNA in the VARNA window is highlighted at the specific position.
+ * To be able to remove it before the next highlight it is saved in
+ * _lastHighlight
+ *
+ * @param sequence
+ * @param index
+ * the aligned sequence position (base 0)
+ * @param position
+ * the dataset sequence position (base 1)
+ */
+ @Override
+ public void mouseOverSequence(SequenceI sequence, final int index,
+ final int position)
+ {
+ RNA rna = vab.getSelectedRNA();
+ if (rna == null)
+ {
+ return;
+ }
+ RnaModel rnaModel = models.get(rna);
+ if (rnaModel.seq == sequence)
+ {
+ int highlightPos = rnaModel.gapped ? index : position - 1;
+ mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
+ vab.updateSelectedRNA(rna);
+ }
+ }
+
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
+ {
+ if (source != ap.av)
+ {
+ // ignore events from anything but our parent alignpanel
+ // TODO - reuse many-one panel-view system in jmol viewer
+ return;
+ }
+ RNA rna = vab.getSelectedRNA();
+ if (rna == null)
+ {
+ return;
+ }
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ int start = seqsel.getStartRes(), end = seqsel.getEndRes();
+ ShiftList shift = offsets.get(rna);
+ if (shift != null)
+ {
+ start = shift.shift(start);
+ end = shift.shift(end);
+ }
+ selectionHighlighter.highlightRegion(rna, start, end);
+ selectionHighlighter.getLastHighlight().setOutlineColor(
+ seqsel.getOutlineColour());
+ // TODO - translate column markings to positions on structure if present.
+ vab.updateSelectedRNA(rna);
+ }
+ else
+ {
+ selectionHighlighter.clearSelection();
+ }
+ }
+
+ /**
+ * Respond to a change of the base hovered over in the Varna viewer
+ */
+ @Override
+ public void onHoverChanged(ModeleBase previousBase, ModeleBase newBase)
+ {
+ RNA rna = vab.getSelectedRNA();
+ ShiftList shift = offsetsInv.get(rna);
+ SequenceI seq = models.get(rna).seq;
+ if (newBase != null && seq != null)
+ {
+ if (shift != null)
+ {
+ int i = shift.shift(newBase.getIndex());
+ // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+ ssm.mouseOverVamsasSequence(seq, i, this);
+ }
+ else
+ {
+ ssm.mouseOverVamsasSequence(seq, newBase.getIndex(), this);
+ }
+ }
+ }
+
+ @Override
+ public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
+ {
+ // TODO translate selected regions in VARNA to a selection on the
+ // alignpanel.
+
+ }
+
+ /**
+ * Returns the path to a temporary file containing a representation of the
+ * state of one Varna display
+ *
+ * @param rna
+ *
+ * @return
+ */
+ public String getStateInfo(RNA rna)
+ {
+ return vab.getStateInfo(rna);
+ }
+
+ public AlignmentPanel getAlignmentPanel()
+ {
+ return ap;
+ }
+
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Returns true if any of the viewer's models (not necessarily the one
+ * currently displayed) is for the given sequence
+ *
+ * @param seq
+ * @return
+ */
+ public boolean isListeningFor(SequenceI seq)
+ {
+ for (RnaModel model : models.values())
+ {
+ if (model.seq == seq)
+ {
+ return true;
+ }
+ }
+ return false;
+ }