features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr);
/*
* add features in CDS/protein complement at the corresponding
* position if configured to do so
*/
if (av.isShowComplementFeatures())
{
if (!Comparison.isGap(sequence.getCharAt(column)))
{
AlignViewportI complement = ap.getAlignViewport()
.getCodingComplement();
AlignFrame af = Desktop.getAlignFrameFor(complement);
FeatureRendererModel fr2 = af.getFeatureRenderer();
MappedFeatures mf = fr2.findComplementFeaturesAtResidue(sequence,
pos);
if (mf != null)
{
seqARep.appendFeatures(tooltipText, pos, mf, fr2);
}
}
}
}
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))
{
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;
private JToolTip tempTip = new JLabel().createToolTip();
/*
* (non-Javadoc)
*
* @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
*/
@Override
public Point getToolTipLocation(MouseEvent event)
{
// BH 2018
if (tooltipText == null || tooltipText.length() <= 6)
{
return null;
}
if (lastp != null && event.isShiftDown())
{
return lastp;
}
Point p = lastp;
int x = event.getX();
int y = event.getY();
int w = getWidth();
tempTip.setTipText(formattedTooltipText);
int tipWidth = (int) tempTip.getPreferredSize().getWidth();
// was x += (w - x < 200) ? -(w / 2) : 5;
x = (x + tipWidth < w ? x + 10 : w - tipWidth);
p = new Point(x, y + 20); // BH 2018 was - 20?
return lastp = 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.setMousePosition(evt.getPoint());
}
}
/**
* 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);
}
/**
* On reentering the panel, stops any scrolling that was started on dragging
* out of the panel
*
* @param e
*/
@Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
{
oldSeq = 0;
}
stopScrolling();
}
/**
* On leaving the panel, if the mouse is being dragged, starts a thread to
* scroll it until the mouse is released (in unwrapped mode only)
*
* @param e
*/
@Override
public void mouseExited(MouseEvent e)
{
lastMousePosition = null;
ap.alignFrame.setStatus(" ");
if (av.getWrapAlignment())
{
return;
}
if (mouseDragging && scrollThread == null)
{
startScrolling(e.getPoint());
}
}
/**
* 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, true);
/*
* open the Amend Features dialog
*/
new FeatureEditor(ap, Collections.singletonList(sequence), features,
false).showDialog();
}
}
}
@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);
}
}
/*
* 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 (Platform.isWinRightButton(evt))
{
return;
}
if (evt.isPopupTrigger()) // Mac: mousePressed
{
showPopupMenu(evt, pos);
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);
if (sequence != null)
{
PopupMenu pop = new PopupMenu(ap, sequence, column);
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;
}
res = Math.min(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.setMousePosition(evt.getPoint());
}
/*
* 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());
}
/**
* Stops the scroll thread if it is running
*/
void stopScrolling()
{
if (scrollThread != null)
{
scrollThread.stopScrolling();
scrollThread = null;
}
mouseDragging = false;
}
/**
* Starts a thread to scroll the alignment, towards a given mouse position
* outside the panel bounds, unless the alignment is in wrapped mode
*
* @param mousePos
*/
void startScrolling(Point mousePos)
{
/*
* set this.mouseDragging in case this was called from
* a drag in ScalePanel or AnnotationPanel
*/
mouseDragging = true;
if (!av.getWrapAlignment() && scrollThread == null)
{
scrollThread = new ScrollThread();
scrollThread.setMousePosition(mousePos);
if (Platform.isJS())
{
/*
* Javascript - run every 20ms until scrolling stopped
* or reaches the limit of scrollable alignment
*/
Timer t = new Timer(20, new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
if (scrollThread != null)
{
// if (!scrollOnce() {t.stop();}) gives compiler error :-(
scrollThread.scrollOnce();
}
}
});
t.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
if (scrollThread == null)
{
// SeqPanel.stopScrolling called
t.stop();
}
}
});
t.start();
}
else
{
/*
* Java - run in a new thread
*/
scrollThread.start();
}
}
}
/**
* Performs scrolling of the visible alignment left, right, up or down, until
* scrolling is stopped by calling stopScrolling, mouse drag is ended, or the
* limit of the alignment is reached
*/
class ScrollThread extends Thread
{
private Point mousePos;
private volatile boolean keepRunning = true;
/**
* Constructor
*/
public ScrollThread()
{
setName("SeqPanel$ScrollThread");
}
/**
* Sets the position of the mouse that determines the direction of the
* scroll to perform. If this is called as the mouse moves, scrolling should
* respond accordingly. For example, if the mouse is dragged right, scroll
* right should start; if the drag continues down, scroll down should also
* happen.
*
* @param p
*/
public void setMousePosition(Point p)
{
mousePos = p;
}
/**
* Sets a flag that will cause the thread to exit
*/
public void stopScrolling()
{
keepRunning = false;
}
/**
* Scrolls the alignment left or right, and/or up or down, depending on the
* last notified mouse position, until the limit of the alignment is
* reached, or a flag is set to stop the scroll
*/
@Override
public void run()
{
while (keepRunning)
{
if (mousePos != null)
{
keepRunning = scrollOnce();
}
try
{
Thread.sleep(20);
} catch (Exception ex)
{
}
}
SeqPanel.this.scrollThread = null;
}
/**
* Scrolls
*
* - one row up, if the mouse is above the panel
* - one row down, if the mouse is below the panel
* - one column left, if the mouse is left of the panel
* - one column right, if the mouse is right of the panel
*
* Answers true if a scroll was performed, false if not - meaning either
* that the mouse position is within the panel, or the edge of the alignment
* has been reached.
*/
boolean scrollOnce()
{
/*
* quit after mouseUp ensures interrupt in JalviewJS
*/
if (!mouseDragging)
{
return false;
}
boolean scrolled = false;
ViewportRanges ranges = SeqPanel.this.av.getRanges();
/*
* scroll up or down
*/
if (mousePos.y < 0)
{
// mouse is above this panel - try scroll up
scrolled = ranges.scrollUp(true);
}
else if (mousePos.y >= getHeight())
{
// mouse is below this panel - try scroll down
scrolled = ranges.scrollUp(false);
}
/*
* scroll left or right
*/
if (mousePos.x < 0)
{
scrolled |= ranges.scrollRight(false);
}
else if (mousePos.x >= getWidth())
{
scrolled |= ranges.scrollRight(true);
}
return scrolled;
}
}
/**
* 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;
}
}