features = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ seqARep.appendFeatures(tooltipText, pos, features,
+ this.ap.getSeqPanel().seqCanvas.fr);
+ }
+ if (tooltipText.length() == 6) //
+ {
+ setToolTipText(null);
+ lastTooltip = null;
+ }
+ else
+ {
+ if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
+ {
+ tooltipText.setLength(MAX_TOOLTIP_LENGTH);
+ tooltipText.append("...");
+ }
+ String textString = tooltipText.toString();
+ if (lastTooltip == null || !lastTooltip.equals(textString))
+ {
+ String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+ textString);
+ setToolTipText(formattedTooltipText);
+ lastTooltip = textString;
+ }
+ }
+ }
+
+ /**
+ * When the view is in wrapped mode, and the mouse is over an annotation row,
+ * shows the corresponding tooltip and status message (if any)
+ *
+ * @param pos
+ * @param column
+ */
+ protected void mouseMovedOverAnnotation(MousePos pos)
+ {
+ final int column = pos.column;
+ final int rowIndex = pos.annotationIndex;
+
+ if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation()
+ || rowIndex < 0)
+ {
+ return;
+ }
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+
+ String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
+ anns);
+ setToolTipText(tooltip);
+ lastTooltip = tooltip;
+
+ String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
+ anns[rowIndex]);
+ ap.alignFrame.setStatus(msg);
+ }
+
+ private Point lastp = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent event)
+ {
+ if (tooltipText == null || tooltipText.length() <= 6)
+ {
+ lastp = null;
+ return null;
+ }
+
+ int x = event.getX();
+ int w = getWidth();
+ // switch sides when tooltip is too close to edge
+ int wdth = (w - x < 200) ? -(w / 2) : 5;
+ Point p = lastp;
+ if (!event.isShiftDown() || p == null)
+ {
+ p = new Point(event.getX() + wdth, event.getY() - 20);
+ lastp = p;
+ }
+ /*
+ * TODO: try to set position so region is not obscured by tooltip
+ */
+ return p;
+ }
+
+ String lastTooltip;
+
+ /**
+ * set when the current UI interaction has resulted in a change that requires
+ * shading in overviews and structures to be recalculated. this could be
+ * changed to a something more expressive that indicates what actually has
+ * changed, so selective redraws can be applied (ie. only structures, only
+ * overview, etc)
+ */
+ private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
+
+ /**
+ * set if av.getSelectionGroup() refers to a group that is defined on the
+ * alignment view, rather than a transient selection
+ */
+ // private boolean editingDefinedGroup = false; // TODO: refactor to
+ // avcontroller or viewModel
+
+ /**
+ * Sets the status message in alignment panel, showing the sequence number
+ * (index) and id, and residue and residue position if not at a gap, for the
+ * given sequence and column position. Returns the residue position returned
+ * by Sequence.findPosition. Note this may be for the nearest adjacent residue
+ * if at a gapped position.
+ *
+ * @param sequence
+ * aligned sequence object
+ * @param column
+ * alignment column
+ * @param seqIndex
+ * index of sequence in alignment
+ * @return sequence position of residue at column, or adjacent residue if at a
+ * gap
+ */
+ int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
+ {
+ char sequenceChar = sequence.getCharAt(column);
+ int pos = sequence.findPosition(column);
+ setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+
+ return pos;
+ }
+
+ /**
+ * Builds the status message for the current cursor location and writes it to
+ * the status bar, for example
+ *
+ *
+ * Sequence 3 ID: FER1_SOLLC
+ * Sequence 5 ID: FER1_PEA Residue: THR (4)
+ * Sequence 5 ID: FER1_PEA Residue: B (3)
+ * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+ *
+ *
+ * @param sequence
+ * @param seqIndex
+ * sequence position in the alignment (1..)
+ * @param sequenceChar
+ * the character under the cursor
+ * @param residuePos
+ * the sequence residue position (if not over a gap)
+ */
+ protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ char sequenceChar, int residuePos)
+ {
+ StringBuilder text = new StringBuilder(32);
+
+ /*
+ * Sequence number (if known), and sequence name.
+ */
+ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
+
+ String residue = null;
+
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ boolean isGapped = Comparison.isGap(sequenceChar);
+
+ if (!isGapped)
+ {
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ String displayChar = String.valueOf(sequenceChar);
+ if (nucleotide)
+ {
+ residue = ResidueProperties.nucleotideName.get(displayChar);
+ }
+ else
+ {
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ("*".equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
+ }
+ text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
+ .append(": ").append(residue == null ? displayChar : residue);
+
+ text.append(" (").append(Integer.toString(residuePos)).append(")");
+ }
+ ap.alignFrame.setStatus(text.toString());
+ }
+
+ /**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResultsI results)
+ {
+ AlignmentI al = this.av.getAlignment();
+ int sequenceIndex = al.findIndex(results);
+ if (sequenceIndex == -1)
+ {
+ return;
+ }
+ SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ for (SearchResultMatchI m : results.getResults())
+ {
+ SequenceI seq = m.getSequence();
+ if (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+
+ if (seq == ds)
+ {
+ int start = m.getStart();
+ setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+ start);
+ return;
+ }
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.column == -1)
+ {
+ return;
+ }
+
+ if (mouseWheelPressed)
+ {
+ boolean inSplitFrame = ap.av.getCodingComplement() != null;
+ boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
+
+ int oldWidth = av.getCharWidth();
+
+ // Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
+ .abs(evt.getX() - lastMousePress.getX()))
+ {
+ /*
+ * on drag up or down, decrement or increment font size
+ */
+ int fontSize = av.font.getSize();
+ boolean fontChanged = false;
+
+ if (evt.getY() < lastMousePress.getY())
+ {
+ fontChanged = true;
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.getY())
+ {
+ fontChanged = true;
+ fontSize++;
+ }
+
+ if (fontSize < 1)
+ {
+ fontSize = 1;
+ }
+
+ if (fontChanged)
+ {
+ Font newFont = new Font(av.font.getName(), av.font.getStyle(),
+ fontSize);
+ av.setFont(newFont, true);
+ av.setCharWidth(oldWidth);
+ ap.fontChanged();
+ if (copyChanges)
+ {
+ ap.av.getCodingComplement().setFont(newFont, true);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
+ }
+ }
+ else
+ {
+ /*
+ * on drag left or right, decrement or increment character width
+ */
+ int newWidth = 0;
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
+ {
+ newWidth = av.getCharWidth() - 1;
+ av.setCharWidth(newWidth);
+ }
+ else if (evt.getX() > lastMousePress.getX())
+ {
+ newWidth = av.getCharWidth() + 1;
+ av.setCharWidth(newWidth);
+ }
+ if (newWidth > 0)
+ {
+ ap.paintAlignment(false, false);
+ if (copyChanges)
+ {
+ /*
+ * need to ensure newWidth is set on cdna, regardless of which
+ * panel the mouse drag happened in; protein will compute its
+ * character width as 1:1 or 3:1
+ */
+ av.getCodingComplement().setCharWidth(newWidth);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
+ }
+ }
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
+
+ lastMousePress = evt.getPoint();
+
+ return;
+ }
+
+ if (!editingSeqs)
+ {
+ dragStretchGroup(evt);
+ return;
+ }
+
+ int res = pos.column;
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if ((editLastRes == -1) || (editLastRes == res))
+ {
+ return;
+ }
+
+ if ((res < av.getAlignment().getWidth()) && (res < editLastRes))
+ {
+ // dragLeft, delete gap
+ editSequence(false, false, res);
+ }
+ else
+ {
+ editSequence(true, false, res);
+ }
+
+ mouseDragging = true;
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.setEvent(evt);
+ }
+ }
+
+ /**
+ * Edits the sequence to insert or delete one or more gaps, in response to a
+ * mouse drag or cursor mode command. The number of inserts/deletes may be
+ * specified with the cursor command, or else depends on the mouse event
+ * (normally one column, but potentially more for a fast mouse drag).
+ *
+ * Delete gaps is limited to the number of gaps left of the cursor position
+ * (mouse drag), or at or right of the cursor position (cursor mode).
+ *
+ * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in
+ * the current selection group.
+ *
+ * In locked editing mode (with a selection group present), inserts/deletions
+ * within the selection group are limited to its boundaries (and edits outside
+ * the group stop at its border).
+ *
+ * @param insertGap
+ * true to insert gaps, false to delete gaps
+ * @param editSeq
+ * (unused parameter)
+ * @param startres
+ * the column at which to perform the action; the number of columns
+ * affected depends on this.editLastRes
(cursor column
+ * position)
+ */
+ synchronized void editSequence(boolean insertGap, boolean editSeq,
+ final int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
+
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
+
+ // No group, but the sequence may represent a group
+ if (!groupEditing && av.hasHiddenRows())
+ {
+ if (av.isHiddenRepSequence(seq))
+ {
+ sg = av.getRepresentedSequences(seq);
+ groupEditing = true;
+ }
+ }
+
+ StringBuilder message = new StringBuilder(64); // for status bar
+
+ /*
+ * make a name for the edit action, for
+ * status bar message and Undo/Redo menu
+ */
+ String label = null;
+ if (groupEditing)
+ {
+ message.append("Edit group:");
+ label = MessageManager.getString("action.edit_group");
+ }
+ else
+ {
+ message.append("Edit sequence: " + seq.getName());
+ label = seq.getName();
+ if (label.length() > 10)
+ {
+ label = label.substring(0, 10);
+ }
+ label = MessageManager.formatMessage("label.edit_params",
+ new String[]
+ { label });
+ }
+
+ /*
+ * initialise the edit command if there is not
+ * already one being extended
+ */
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand(label);
+ }
+
+ if (insertGap)
+ {
+ message.append(" insert ");
+ }
+ else
+ {
+ message.append(" delete ");
+ }
+
+ message.append(Math.abs(startres - editLastRes) + " gaps.");
+ ap.alignFrame.setStatus(message.toString());
+
+ /*
+ * is there a selection group containing the sequence being edited?
+ * if so the boundary of the group is the limit of the edit
+ * (but the edit may be inside or outside the selection group)
+ */
+ boolean inSelectionGroup = sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq);
+ if (groupEditing || inSelectionGroup)
+ {
+ fixedColumns = true;
+
+ // sg might be null as the user may only see 1 sequence,
+ // but the sequence represents a group
+ if (sg == null)
+ {
+ if (!av.isHiddenRepSequence(seq))
+ {
+ endEditing();
+ return;
+ }
+ sg = av.getRepresentedSequences(seq);
+ }
+
+ fixedLeft = sg.getStartRes();
+ fixedRight = sg.getEndRes();
+
+ if ((startres < fixedLeft && editLastRes >= fixedLeft)
+ || (startres >= fixedLeft && editLastRes < fixedLeft)
+ || (startres > fixedRight && editLastRes <= fixedRight)
+ || (startres <= fixedRight && editLastRes > fixedRight))
+ {
+ endEditing();
+ return;
+ }
+
+ if (fixedLeft > startres)
+ {
+ fixedRight = fixedLeft - 1;
+ fixedLeft = 0;
+ }
+ else if (fixedRight < startres)
+ {
+ fixedLeft = fixedRight;
+ fixedRight = -1;
+ }
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ fixedColumns = true;
+ int y1 = av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(true, startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(false, startres);
+
+ if ((insertGap && startres > y1 && editLastRes < y1)
+ || (!insertGap && startres < y2 && editLastRes > y2))
+ {
+ endEditing();
+ return;
+ }
+
+ // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ // Selection spans a hidden region
+ if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+ {
+ if (startres >= y2)
+ {
+ fixedLeft = y2;
+ }
+ else
+ {
+ fixedRight = y2 - 1;
+ }
+ }
+ }
+
+ boolean success = doEditSequence(insertGap, editSeq, startres,
+ fixedRight, fixedColumns, sg);
+
+ /*
+ * report what actually happened (might be less than
+ * what was requested), by inspecting the edit commands added
+ */
+ String msg = getEditStatusMessage(editCommand);
+ ap.alignFrame.setStatus(msg == null ? " " : msg);
+ if (!success)
+ {
+ endEditing();
+ }
+
+ editLastRes = startres;
+ seqCanvas.repaint();
+ }
+
+ /**
+ * A helper method that performs the requested editing to insert or delete
+ * gaps (if possible). Answers true if the edit was successful, false if could
+ * only be performed in part or not at all. Failure may occur in 'locked edit'
+ * mode, when an insertion requires a matching gapped position (or column) to
+ * delete, and deletion requires an adjacent gapped position (or column) to
+ * remove.
+ *
+ * @param insertGap
+ * true if inserting gap(s), false if deleting
+ * @param editSeq
+ * (unused parameter, currently always false)
+ * @param startres
+ * the column at which to perform the edit
+ * @param fixedRight
+ * fixed right boundary column of a locked edit (within or to the
+ * left of a selection group)
+ * @param fixedColumns
+ * true if this is a locked edit
+ * @param sg
+ * the sequence group (if group edit is being performed)
+ * @return
+ */
+ protected boolean doEditSequence(final boolean insertGap,
+ final boolean editSeq, final int startres, int fixedRight,
+ final boolean fixedColumns, final SequenceGroup sg)
+ {
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
+ SequenceI[] seqs = new SequenceI[] { seq };
+
+ if (groupEditing)
+ {
+ List vseqs = sg.getSequences(av.getHiddenRepSequences());
+ int g, groupSize = vseqs.size();
+ SequenceI[] groupSeqs = new SequenceI[groupSize];
+ for (g = 0; g < groupSeqs.length; g++)
+ {
+ groupSeqs[g] = vseqs.get(g);
+ }
+
+ // drag to right
+ if (insertGap)
+ {
+ // If the user has selected the whole sequence, and is dragging to
+ // the right, we can still extend the alignment and selectionGroup
+ if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)
+ {
+ sg.setEndRes(
+ av.getAlignment().getWidth() + startres - editLastRes);
+ fixedRight = sg.getEndRes();
+ }
+
+ // Is it valid with fixed columns??
+ // Find the next gap before the end
+ // of the visible region boundary
+ boolean blank = false;
+ for (; fixedRight > editLastRes; fixedRight--)
+ {
+ blank = true;
+
+ for (g = 0; g < groupSize; g++)
+ {
+ for (int j = 0; j < startres - editLastRes; j++)
+ {
+ if (!Comparison
+ .isGap(groupSeqs[g].getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ {
+ break;
+ }
+ }
+
+ if (!blank)
+ {
+ if (sg.getSize() == av.getAlignment().getHeight())
+ {
+ if ((av.hasHiddenColumns()
+ && startres < av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(false, startres)))
+ {
+ return false;
+ }
+
+ int alWidth = av.getAlignment().getWidth();
+ if (av.hasHiddenRows())
+ {
+ int hwidth = av.getAlignment().getHiddenSequences()
+ .getWidth();
+ if (hwidth > alWidth)
+ {
+ alWidth = hwidth;
+ }
+ }
+ // We can still insert gaps if the selectionGroup
+ // contains all the sequences
+ sg.setEndRes(sg.getEndRes() + startres - editLastRes);
+ fixedRight = alWidth + startres - editLastRes;
+ }
+ else
+ {
+ return false;
+ }
+ }
+ }
+
+ // drag to left
+ else if (!insertGap)
+ {
+ // / Are we able to delete?
+ // ie are all columns blank?
+
+ for (g = 0; g < groupSize; g++)
+ {
+ for (int j = startres; j < editLastRes; j++)
+ {
+ if (groupSeqs[g].getLength() <= j)
+ {
+ continue;
+ }
+
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ {
+ // Not a gap, block edit not valid
+ return false;
+ }
+ }
+ }
+ }
+
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = editLastRes; j < startres; j++)
+ {
+ insertGap(j, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - editLastRes, false);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = editLastRes; j > startres; j--)
+ {
+ deleteChar(startres, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ editLastRes - startres, false);
+ }
+ }
+ }
+ else
+ {
+ /*
+ * editing a single sequence
+ */
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = editLastRes; j < startres; j++)
+ {
+ if (!insertGap(j, seqs, fixedRight))
+ {
+ /*
+ * e.g. cursor mode command specified
+ * more inserts than are possible
+ */
+ return false;
+ }
+ }
+ }
+ else
+ {
+ appendEdit(Action.INSERT_GAP, seqs, editLastRes,
+ startres - editLastRes, false);
+ }
+ }
+ else
+ {
+ if (!editSeq)
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = editLastRes; j > startres; j--)
+ {
+ if (!Comparison.isGap(seq.getCharAt(startres)))
+ {
+ return false;
+ }
+ deleteChar(startres, seqs, fixedRight);
+ }
+ }
+ else
+ {
+ // could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < editLastRes; m++)
+ {
+ if (!Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+ if (max > 0)
+ {
+ appendEdit(Action.DELETE_GAP, seqs, startres, max, false);
+ }
+ }
+ }
+ else
+ {// insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = editLastRes; j < startres; j++)
+ {
+ insertGap(j, seqs, fixedRight);
+ }
+ }
+ else
+ {
+ appendEdit(Action.INSERT_NUC, seqs, editLastRes,
+ startres - editLastRes, false);
+ }
+ }
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * Constructs an informative status bar message while dragging to insert or
+ * delete gaps. Answers null if inserts and deletes cancel out.
+ *
+ * @param editCommand
+ * a command containing the list of individual edits
+ * @return
+ */
+ protected static String getEditStatusMessage(EditCommand editCommand)
+ {
+ if (editCommand == null)
+ {
+ return null;
+ }
+
+ /*
+ * add any inserts, and subtract any deletes,
+ * not counting those auto-inserted when doing a 'locked edit'
+ * (so only counting edits 'under the cursor')
+ */
+ int count = 0;
+ for (Edit cmd : editCommand.getEdits())
+ {
+ if (!cmd.isSystemGenerated())
+ {
+ count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber()
+ : -cmd.getNumber();
+ }
+ }
+
+ if (count == 0)
+ {
+ /*
+ * inserts and deletes cancel out
+ */
+ return null;
+ }
+
+ String msgKey = count > 1 ? "label.insert_gaps"
+ : (count == 1 ? "label.insert_gap"
+ : (count == -1 ? "label.delete_gap"
+ : "label.delete_gaps"));
+ count = Math.abs(count);
+
+ return MessageManager.formatMessage(msgKey, String.valueOf(count));
+ }
+
+ /**
+ * Inserts one gap at column j, deleting the right-most gapped column up to
+ * (and including) fixedColumn. Returns true if the edit is successful, false
+ * if no blank column is available to allow the insertion to be balanced by a
+ * deletion.
+ *
+ * @param j
+ * @param seq
+ * @param fixedColumn
+ * @return
+ */
+ boolean insertGap(int j, SequenceI[] seq, int fixedColumn)
+ {
+ int blankColumn = fixedColumn;
+ for (int s = 0; s < seq.length; s++)
+ {
+ // Find the next gap before the end of the visible region boundary
+ // If lastCol > j, theres a boundary after the gap insertion
+
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ {
+ // Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return false;
+ }
+ }
+
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, true);
+
+ appendEdit(Action.INSERT_GAP, seq, j, 1, false);
+
+ return true;
+ }
+
+ /**
+ * Helper method to add and perform one edit action
+ *
+ * @param action
+ * @param seq
+ * @param pos
+ * @param count
+ * @param systemGenerated
+ * true if the edit is a 'balancing' delete (or insert) to match a
+ * user's insert (or delete) in a locked editing region
+ */
+ protected void appendEdit(Action action, SequenceI[] seq, int pos,
+ int count, boolean systemGenerated)
+ {
+
+ final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+ av.getAlignment().getGapCharacter());
+ edit.setSystemGenerated(systemGenerated);
+
+ editCommand.appendEdit(edit, av.getAlignment(), true, null);
+ }
+
+ /**
+ * Deletes the character at column j, and inserts a gap at fixedColumn, in
+ * each of the given sequences. The caller should ensure that all sequences
+ * are gapped in column j.
+ *
+ * @param j
+ * @param seqs
+ * @param fixedColumn
+ */
+ void deleteChar(int j, SequenceI[] seqs, int fixedColumn)
+ {
+ appendEdit(Action.DELETE_GAP, seqs, j, 1, false);
+
+ appendEdit(Action.INSERT_GAP, seqs, fixedColumn, 1, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
+ {
+ oldSeq = 0;
+ }
+
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.stopScrolling();
+ scrollThread = null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ ap.alignFrame.setStatus(" ");
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ /**
+ * Handler for double-click on a position with one or more sequence features.
+ * Opens the Amend Features dialog to allow feature details to be amended, or
+ * the feature deleted.
+ */
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ SequenceGroup sg = null;
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+ {
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ sg = av.getSelectionGroup();
+ if (sg != null && sg.getSize() == 1
+ && sg.getEndRes() - sg.getStartRes() < 2)
+ {
+ av.setSelectionGroup(null);
+ }
+
+ int column = pos.column;
+
+ /*
+ * find features at the position (if not gapped), or straddling
+ * the position (if at a gap)
+ */
+ SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex);
+ List features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+
+ if (!features.isEmpty())
+ {
+ /*
+ * highlight the first feature at the position on the alignment
+ */
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
+ seqCanvas.highlightSearchResults(highlight, false);
+
+ /*
+ * open the Amend Features dialog; clear highlighting afterwards,
+ * whether changes were made or not
+ */
+ List seqs = Collections.singletonList(sequence);
+ seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+ ap);
+ av.setSearchResults(null); // clear highlighting
+ seqCanvas.repaint(); // draw new/amended features
+ }
+ }
+ }
+
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ e.consume();
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(true);
+
+ }
+ else
+ {
+ av.getRanges().scrollUp(false);
+ }
+ }
+ else if (wheelRotation < 0)
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(false);
+ }
+ else
+ {
+ av.getRanges().scrollUp(true);
+ }
+ }
+
+ /*
+ * update status bar and tooltip for new position
+ * (need to synthesize a mouse movement to refresh tooltip)
+ */
+ mouseMoved(e);
+ ToolTipManager.sharedInstance().mouseMoved(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pos
+ * DOCUMENT ME!
+ */
+ protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos)
+ {
+ if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+ {
+ return;
+ }
+
+ final int res = pos.column;
+ final int seq = pos.seqIndex;
+ oldSeq = seq;
+ updateOverviewAndStructs = false;
+
+ startWrapBlock = wrappedBlock;
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ if ((sequence == null) || (res > sequence.getLength()))
+ {
+ return;
+ }
+
+ stretchGroup = av.getSelectionGroup();
+
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
+ {
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ if (stretchGroup != null)
+ {
+ // only update the current selection if the popup menu has a group to
+ // focus on
+ av.setSelectionGroup(stretchGroup);
+ }
+ }
+
+ if (evt.isPopupTrigger()) // Mac: mousePressed
+ {
+ showPopupMenu(evt, pos);
+ return;
+ }
+
+ /*
+ * defer right-mouse click handling to mouseReleased on Windows
+ * (where isPopupTrigger() will answer true)
+ * NB isRightMouseButton is also true for Cmd-click on Mac
+ */
+ if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+ {
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = res;
+ seqCanvas.cursorY = seq;
+ seqCanvas.repaint();
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ createStretchGroup(res, sequence);
+ }
+
+ if (stretchGroup != null)
+ {
+ stretchGroup.addPropertyChangeListener(seqCanvas);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ private void createStretchGroup(int res, SequenceI sequence)
+ {
+ // Only if left mouse button do we want to change group sizes
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
+ // or is there a threading issue here?
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+ {
+ // Edit end res position of selected group
+ changeStartRes = true;
+ }
+ stretchGroup.getWidth();
+
+ }
+
+ /**
+ * Build and show a pop-up menu at the right-click mouse position
+ *
+ * @param evt
+ * @param pos
+ */
+ void showPopupMenu(MouseEvent evt, MousePos pos)
+ {
+ final int column = pos.column;
+ final int seq = pos.seqIndex;
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ List features = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+
+ PopupMenu pop = new PopupMenu(ap, null, features);
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * Update the display after mouse up on a selection or group
+ *
+ * @param evt
+ * mouse released event details
+ * @param afterDrag
+ * true if this event is happening after a mouse drag (rather than a
+ * mouse down)
+ */
+ protected void doMouseReleasedDefineMode(MouseEvent evt,
+ boolean afterDrag)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ stretchGroup.removePropertyChangeListener(seqCanvas);
+
+ // always do this - annotation has own state
+ // but defer colourscheme update until hidden sequences are passed in
+ boolean vischange = stretchGroup.recalcConservation(true);
+ updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
+ && afterDrag;
+ if (stretchGroup.cs != null)
+ {
+ if (afterDrag)
+ {
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
+ }
+
+ ResidueShaderI groupColourScheme = stretchGroup
+ .getGroupColourScheme();
+ String name = stretchGroup.getName();
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, groupColourScheme, name);
+ }
+ if (stretchGroup.cs.getThreshold() > 0)
+ {
+ SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
+ }
+ }
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // TODO: structure colours only need updating if stretchGroup used to or now
+ // does contain sequences with structure views
+ ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+ updateOverviewAndStructs = false;
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ av.sendSelection();
+ }
+
+ /**
+ * Resizes the borders of a selection group depending on the direction of
+ * mouse drag
+ *
+ * @param evt
+ */
+ protected void dragStretchGroup(MouseEvent evt)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1)
+ {
+ return;
+ }
+
+ int res = pos.column;
+ int y = pos.seqIndex;
+
+ if (wrappedBlock != startWrapBlock)
+ {
+ return;
+ }
+
+ if (res >= av.getAlignment().getWidth())
+ {
+ res = av.getAlignment().getWidth() - 1;
+ }
+
+ if (stretchGroup.getEndRes() == res)
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if (stretchGroup.getStartRes() == res)
+ {
+ // Edit start res position of selected group
+ changeStartRes = true;
+ }
+
+ if (res < av.getRanges().getStartRes())
+ {
+ res = av.getRanges().getStartRes();
+ }
+
+ if (changeEndRes)
+ {
+ if (res > (stretchGroup.getStartRes() - 1))
+ {
+ stretchGroup.setEndRes(res);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ }
+ else if (changeStartRes)
+ {
+ if (res < (stretchGroup.getEndRes() + 1))
+ {
+ stretchGroup.setStartRes(res);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ }
+
+ int dragDirection = 0;
+
+ if (y > oldSeq)
+ {
+ dragDirection = 1;
+ }
+ else if (y < oldSeq)
+ {
+ dragDirection = -1;
+ }
+
+ while ((y != oldSeq) && (oldSeq > -1)
+ && (y < av.getAlignment().getHeight()))
+ {
+ // This routine ensures we don't skip any sequences, as the
+ // selection is quite slow.
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ oldSeq += dragDirection;
+
+ if (oldSeq < 0)
+ {
+ break;
+ }
+
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ if (stretchGroup.getSequences(null).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ stretchGroup.addSequence(nextSeq, false);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ }
+
+ if (oldSeq < 0)
+ {
+ oldSeq = -1;
+ }
+
+ mouseDragging = true;
+
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ /*
+ * construct a status message showing the range of the selection
+ */
+ StringBuilder status = new StringBuilder(64);
+ List seqs = stretchGroup.getSequences();
+ String name = seqs.get(0).getName();
+ if (name.length() > 20)
+ {
+ name = name.substring(0, 20);
+ }
+ status.append(name).append(" - ");
+ name = seqs.get(seqs.size() - 1).getName();
+ if (name.length() > 20)
+ {
+ name = name.substring(0, 20);
+ }
+ status.append(name).append(" ");
+ int startRes = stretchGroup.getStartRes();
+ status.append(" cols ").append(String.valueOf(startRes + 1))
+ .append("-");
+ int endRes = stretchGroup.getEndRes();
+ status.append(String.valueOf(endRes + 1));
+ status.append(" (").append(String.valueOf(seqs.size())).append(" x ")
+ .append(String.valueOf(endRes - startRes + 1)).append(")");
+ ap.alignFrame.setStatus(status.toString());
+ }
+
+ void scrollCanvas(MouseEvent evt)
+ {
+ if (evt == null)
+ {
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.stopScrolling();
+ scrollThread = null;
+ }
+ mouseDragging = false;
+ }
+ else
+ {
+ if (scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+
+ mouseDragging = true;
+ scrollThread.setEvent(evt);
+ }
+
+ }
+
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread extends Thread
+ {
+ MouseEvent evt;
+
+ private volatile boolean threadRunning = true;
+
+ public ScrollThread()
+ {
+ start();
+ }
+
+ public void setEvent(MouseEvent e)
+ {
+ evt = e;
+ }
+
+ public void stopScrolling()
+ {
+ threadRunning = false;
+ }
+
+ public boolean isRunning()
+ {
+ return threadRunning;
+ }
+
+ @Override
+ public void run()
+ {
+ while (threadRunning)
+ {
+ if (evt != null)
+ {
+ if (mouseDragging && (evt.getY() < 0)
+ && (av.getRanges().getStartSeq() > 0))
+ {
+ av.getRanges().scrollUp(true);
+ }
+
+ if (mouseDragging && (evt.getY() >= getHeight()) && (av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq()))
+ {
+ av.getRanges().scrollUp(false);
+ }
+
+ if (mouseDragging && (evt.getX() < 0))
+ {
+ av.getRanges().scrollRight(false);
+ }
+ else if (mouseDragging && (evt.getX() >= getWidth()))
+ {
+ av.getRanges().scrollRight(true);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(20);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+
+ /**
+ * modify current selection according to a received message.
+ */
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source)
+ {
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ boolean iSentTheSelection = (av == source
+ || (source instanceof AlignViewport
+ && ((AlignmentViewport) source).getSequenceSetId()
+ .equals(av.getSequenceSetId())));
+
+ if (iSentTheSelection)
+ {
+ // respond to our own event by updating dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ return;
+ }
+
+ // process further ?
+ if (!av.followSelection)
+ {
+ return;
+ }
+
+ /*
+ * Ignore the selection if there is one of our own pending.
+ */
+ if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ {
+ return;
+ }
+
+ /*
+ * Check for selection in a view of which this one is a dna/protein
+ * complement.
+ */
+ if (selectionFromTranslation(seqsel, colsel, hidden, source))
+ {
+ return;
+ }
+
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
+ boolean repaint = false;
+ boolean copycolsel = false;
+
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ if (av.getAlignment() == null)
+ {
+ Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediately.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+ if ((sgroup != null && sgroup.getSize() > 0))
+ {
+ copycolsel = true;
+ }
+ }
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ av.isSelectionGroupChanged(true);
+ repaint = true;
+
+ if (copycolsel)
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.isEmpty())
+ {
+ if (av.getColumnSelection() != null)
+ {
+ av.getColumnSelection().clear();
+ repaint = true;
+ }
+ }
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.getColumnSelection() == null)
+ {
+ av.setColumnSelection(new ColumnSelection(colsel));
+ }
+ else
+ {
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
+ }
+ }
+ av.isColSelChanged(true);
+ repaint = true;
+ }
+
+ if (copycolsel && av.hasHiddenColumns()
+ && (av.getAlignment().getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint) // always true!
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
+ }
+
+ // lastly, update dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ }
+
+ /**
+ * If this panel is a cdna/protein translation view of the selection source,
+ * tries to map the source selection to a local one, and returns true. Else
+ * returns false.
+ *
+ * @param seqsel
+ * @param colsel
+ * @param source
+ */
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
+ {
+ if (!(source instanceof AlignViewportI))
+ {
+ return false;
+ }
+ final AlignViewportI sourceAv = (AlignViewportI) source;
+ if (sourceAv.getCodingComplement() != av
+ && av.getCodingComplement() != sourceAv)
+ {
+ return false;
+ }
+
+ /*
+ * Map sequence selection
+ */
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+ av.setSelectionGroup(sg);
+ av.isSelectionGroupChanged(true);
+
+ /*
+ * Map column selection
+ */
+ // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ // av);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
+ av.setColumnSelection(cs);
+ boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs);
+
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ /*
+ * repaint alignment, and also Overview or Structure
+ * if hidden column selection has changed
+ */
+ ap.paintAlignment(hiddenChanged, hiddenChanged);
+
+ return true;
+ }
+
+ /**
+ *
+ * @return null or last search results handled by this panel
+ */
+ public SearchResultsI getLastSearchResults()
+ {
+ return lastSearchResults;
+ }
+}