features = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ seqARep.appendFeatures(tooltipText, pos, features,
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
- if (tooltipText.length() == 6) //
+ if (tooltipText.length() == 6) //
{
setToolTipText(null);
lastTooltip = null;
}
else
{
- tooltipText.append("");
- if (lastTooltip == null
- || !lastTooltip.equals(tooltipText.toString()))
+ String textString = tooltipText.toString();
+ if (lastTooltip == null || !lastTooltip.equals(textString))
{
- setToolTipText(tooltipText.toString());
- lastTooltip = tooltipText.toString();
+ String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+ textString);
+ setToolTipText(formattedTooltipText);
+ lastTooltip = textString;
}
-
}
-
}
private Point lastp = null;
@@ -783,6 +829,7 @@ public class SeqPanel extends JPanel implements MouseListener,
*
* @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
*/
+ @Override
public Point getToolTipLocation(MouseEvent event)
{
int x = event.getX(), w = getWidth();
@@ -791,8 +838,9 @@ public class SeqPanel extends JPanel implements MouseListener,
Point p = lastp;
if (!event.isShiftDown() || p == null)
{
- p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
- event.getX() + wdth, event.getY() - 20) : null;
+ p = (tooltipText != null && tooltipText.length() > 6)
+ ? new Point(event.getX() + wdth, event.getY() - 20)
+ : null;
}
/*
* TODO: try to modify position region is not obcured by tooltip
@@ -803,78 +851,169 @@ public class SeqPanel extends JPanel implements MouseListener,
String lastTooltip;
/**
- * Set status message in alignment panel
+ * set when the current UI interaction has resulted in a change that requires
+ * overview shading to be recalculated. this could be changed to something
+ * more expressive that indicates what actually has changed, so selective
+ * redraws can be applied
+ */
+ private boolean needOverviewUpdate = 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 res
+ * @param column
* alignment column
- * @param seq
+ * @param seqIndex
* index of sequence in alignment
- * @return position of res in sequence
+ * @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)
*/
- int setStatusMessage(SequenceI sequence, int res, int seq)
+ protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ char sequenceChar, int residuePos)
{
- int pos = -1;
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
- + sequence.getName());
+ 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());
- Object obj = null;
- if (av.getAlignment().isNucleotide())
+ String residue = null;
+
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ boolean isGapped = Comparison.isGap(sequenceChar);
+
+ if (!isGapped)
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
- + "");
- if (obj != null)
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ String displayChar = String.valueOf(sequenceChar);
+ if (nucleotide)
{
- text.append(" Nucleotide: ");
+ residue = ResidueProperties.nucleotideName.get(displayChar);
}
- }
- else
- {
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
+ else
{
- text.append(" Residue: ");
+ 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.statusBar.setText(text.toString());
+ }
- if (obj != null)
+ /**
+ * 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)
{
- pos = sequence.findPosition(res);
- if (obj != "")
+ 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)
{
- text.append(obj + " (" + pos + ")");
+ int start = m.getStart();
+ setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+ start);
+ return;
}
}
- ap.alignFrame.statusBar.setText(text.toString());
- return pos;
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ 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()))
+ 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++;
}
@@ -883,26 +1022,60 @@ public class SeqPanel extends JPanel implements MouseListener,
fontSize = 1;
}
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
- ap.fontChanged();
+ 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
{
- if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ /*
+ * on drag left or right, decrement or increment character width
+ */
+ int newWidth = 0;
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.charWidth--;
+ newWidth = av.getCharWidth() - 1;
+ av.setCharWidth(newWidth);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.charWidth++;
+ newWidth = av.getCharWidth() + 1;
+ av.setCharWidth(newWidth);
+ }
+ if (newWidth > 0)
+ {
+ ap.paintAlignment(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();
+ }
}
-
- ap.paintAlignment(false);
}
FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
@@ -915,7 +1088,7 @@ public class SeqPanel extends JPanel implements MouseListener,
return;
}
- int res = findRes(evt);
+ int res = findColumn(evt);
if (res < 0)
{
@@ -938,7 +1111,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
mouseDragging = true;
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
scrollThread.setEvent(evt);
}
@@ -965,13 +1138,14 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- StringBuffer message = new StringBuffer();
+ StringBuilder message = new StringBuilder(64);
if (groupEditing)
{
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
@@ -984,7 +1158,9 @@ public class SeqPanel extends JPanel implements MouseListener,
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+ editCommand = new EditCommand(MessageManager
+ .formatMessage("label.edit_params", new String[]
+ { label }));
}
}
@@ -1001,9 +1177,8 @@ public class SeqPanel extends JPanel implements MouseListener,
ap.alignFrame.statusBar.setText(message.toString());
// Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.getHiddenRepSequences())
- .contains(seq)))
+ if (groupEditing || (sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
{
fixedColumns = true;
@@ -1046,8 +1221,10 @@ public class SeqPanel extends JPanel implements MouseListener,
if (av.hasHiddenColumns())
{
fixedColumns = true;
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+ int y1 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryLeft(startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryRight(startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
@@ -1097,7 +1274,7 @@ public class SeqPanel extends JPanel implements MouseListener,
// Find the next gap before the end
// of the visible region boundary
boolean blank = false;
- for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
+ for (; fixedRight > lastres; fixedRight--)
{
blank = true;
@@ -1105,8 +1282,7 @@ public class SeqPanel extends JPanel implements MouseListener,
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(groupSeqs[g]
- .getCharAt(fixedRight - j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
{
blank = false;
break;
@@ -1123,8 +1299,8 @@ public class SeqPanel extends JPanel implements MouseListener,
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av
- .getColumnSelection().getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av.getAlignment()
+ .getHiddenColumns().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
@@ -1168,7 +1344,7 @@ public class SeqPanel extends JPanel implements MouseListener,
continue;
}
- if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
@@ -1190,8 +1366,8 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres);
}
}
else
@@ -1206,8 +1382,8 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres);
}
}
@@ -1222,14 +1398,13 @@ public class SeqPanel extends JPanel implements MouseListener,
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
else
@@ -1241,13 +1416,12 @@ public class SeqPanel extends JPanel implements MouseListener,
{
for (int j = lastres; j > startres; j--)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ if (!Comparison.isGap(seq.getCharAt(startres)))
{
endEditing();
break;
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
+ deleteChar(startres, new SequenceI[] { seq }, fixedRight);
}
}
else
@@ -1256,7 +1430,7 @@ public class SeqPanel extends JPanel implements MouseListener,
int max = 0;
for (int m = startres; m < lastres; m++)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ if (!Comparison.isGap(seq.getCharAt(m)))
{
break;
}
@@ -1265,9 +1439,8 @@ public class SeqPanel extends JPanel implements MouseListener,
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- new SequenceI[]
- { seq }, startres, max, av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+ startres, max);
}
}
}
@@ -1277,14 +1450,13 @@ public class SeqPanel extends JPanel implements MouseListener,
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
}
@@ -1304,7 +1476,7 @@ public class SeqPanel extends JPanel implements MouseListener,
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
{
- if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
{
// Theres a space, so break and insert the gap
break;
@@ -1319,22 +1491,36 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
- av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
+
+ appendEdit(Action.INSERT_GAP, seq, j, 1);
+
+ }
+
+ /**
+ * Helper method to add and perform one edit action.
+ *
+ * @param action
+ * @param seq
+ * @param pos
+ * @param count
+ */
+ protected void appendEdit(Action action, SequenceI[] seq, int pos,
+ int count)
+ {
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
- av.getAlignment(), true);
+ final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+ av.getAlignment().getGapCharacter());
+ editCommand.appendEdit(edit, av.getAlignment(), true, null);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
- av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, seq, j, 1);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
- av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
}
/**
@@ -1351,9 +1537,9 @@ public class SeqPanel extends JPanel implements MouseListener,
oldSeq = 0;
}
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
scrollThread = null;
}
}
@@ -1372,12 +1558,17 @@ public class SeqPanel extends JPanel implements MouseListener,
return;
}
- if (mouseDragging)
+ 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)
{
@@ -1392,23 +1583,34 @@ public class SeqPanel extends JPanel implements MouseListener,
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt)));
+ int column = findColumn(evt);
- if (features != null && features.length > 0)
- {
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(),
- features[0].getEnd());
- seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.length > 0)
+ /*
+ * find features at the position (if not gapped), or straddling
+ * the position (if at a gap)
+ */
+ List features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+
+ if (!features.isEmpty())
{
- seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
- { sequence }, features, false, ap);
+ /*
+ * 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);
- seqCanvas.highlightSearchResults(null);
+ /*
+ * 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
}
}
}
@@ -1421,23 +1623,23 @@ public class SeqPanel extends JPanel implements MouseListener,
{
if (e.isShiftDown())
{
- ap.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
- else
+ else if (!av.getWrapAlignment())
{
- ap.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
- ap.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
- else
+ else if (!av.getWrapAlignment())
{
- ap.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
}
// TODO Update tooltip for new position.
@@ -1451,18 +1653,20 @@ public class SeqPanel extends JPanel implements MouseListener,
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
- int seq = findSeq(evt);
+ final int res = findColumn(evt);
+ final int seq = findSeq(evt);
oldSeq = seq;
+ needOverviewUpdate = false;
startWrapBlock = wrappedBlock;
- if (av.wrapAlignment && seq > av.getAlignment().getHeight())
+ if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.cannot_edit_annotations_in_wrapped_view"),
MessageManager.getString("label.wrapped_view_no_edit"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@@ -1480,69 +1684,36 @@ public class SeqPanel extends JPanel implements MouseListener,
stretchGroup = av.getSelectionGroup();
- if (stretchGroup == null)
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
{
- stretchGroup = av.getAlignment().findGroup(sequence);
-
- if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
- && (res < stretchGroup.getEndRes()))
+ 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);
}
- else
- {
- stretchGroup = null;
- }
}
- else if (!stretchGroup.getSequences(null).contains(sequence)
- || (stretchGroup.getStartRes() > res)
- || (stretchGroup.getEndRes() < res))
- {
- stretchGroup = null;
-
- SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
- if (allGroups != null)
- {
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- stretchGroup = allGroups[i];
- break;
- }
- }
- }
-
- av.setSelectionGroup(stretchGroup);
+ if (evt.isPopupTrigger()) // Mac: mousePressed
+ {
+ showPopupMenu(evt);
+ return;
}
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ /*
+ * 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())
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(
- sequence.getDatasetSequence(), sequence.findPosition(res));
- Vector links = new Vector();
- for (int i = 0; i < allFeatures.length; i++)
- {
- if (allFeatures[i].links != null)
- {
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
- }
- }
-
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
- pop.show(this, evt.getX(), evt.getY());
return;
}
if (av.cursorMode)
{
- seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorX = findColumn(evt);
seqCanvas.cursorY = findSeq(evt);
seqCanvas.repaint();
return;
@@ -1550,79 +1721,128 @@ public class SeqPanel extends JPanel implements MouseListener,
if (stretchGroup == null)
{
- // Only if left mouse button do we want to change group sizes
+ createStretchGroup(res, sequence);
+ }
- // define a new group here
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(res);
- sg.setEndRes(res);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
+ if (stretchGroup != null)
+ {
+ stretchGroup.addPropertyChangeListener(seqCanvas);
+ }
- stretchGroup = sg;
+ seqCanvas.repaint();
+ }
- if (av.getConservationSelected())
- {
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
- "Background");
- }
+ 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.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
- }
- if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if ((stretchGroup != null)
- && (stretchGroup.getStartRes() == res))
+ 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 res
+ * @param sequences
+ */
+ void showPopupMenu(MouseEvent evt)
+ {
+ final int column = findColumn(evt);
+ final int seq = findSeq(evt);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ List allFeatures = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ List links = new ArrayList<>();
+ for (SequenceFeature sf : allFeatures)
+ {
+ if (sf.links != null)
{
- // Edit end res position of selected group
- changeStartRes = true;
+ for (String link : sf.links)
+ {
+ links.add(link);
+ }
}
- stretchGroup.getWidth();
}
- seqCanvas.repaint();
+ PopupMenu pop = new PopupMenu(ap, null, links);
+ pop.show(this, evt.getX(), evt.getY());
}
/**
- * DOCUMENT ME!
+ * Update the display after mouse up on a selection or group
*
* @param evt
- * DOCUMENT ME!
+ * mouse released event details
+ * @param afterDrag
+ * true if this event is happening after a mouse drag (rather than a
+ * mouse down)
*/
- public void doMouseReleasedDefineMode(MouseEvent evt)
+ public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
{
if (stretchGroup == null)
{
return;
}
- stretchGroup.recalcConservation(); // always do this - annotation has own
- // state
+ 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);
+ needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+ && afterDrag;
if (stretchGroup.cs != null)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
av.getHiddenRepSequences());
+ ResidueShaderI groupColourScheme = stretchGroup
+ .getGroupColourScheme();
+ String name = stretchGroup.getName();
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setConservationSlider(ap, groupColourScheme, name);
}
- else
+ if (stretchGroup.cs.getThreshold() > 0)
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
-
+ ap.paintAlignment(needOverviewUpdate);
+ needOverviewUpdate = false;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
@@ -1637,7 +1857,7 @@ public class SeqPanel extends JPanel implements MouseListener,
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
+ int res = findColumn(evt);
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)
@@ -1666,9 +1886,9 @@ public class SeqPanel extends JPanel implements MouseListener,
changeStartRes = true;
}
- if (res < av.getStartRes())
+ if (res < av.getRanges().getStartRes())
{
- res = av.getStartRes();
+ res = av.getRanges().getStartRes();
}
if (changeEndRes)
@@ -1676,6 +1896,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
else if (changeStartRes)
@@ -1683,6 +1904,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
@@ -1716,6 +1938,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
else
{
@@ -1725,6 +1948,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
stretchGroup.addSequence(nextSeq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
@@ -1735,21 +1959,19 @@ public class SeqPanel extends JPanel implements MouseListener,
mouseDragging = true;
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
scrollThread.setEvent(evt);
}
-
- seqCanvas.repaint();
}
void scrollCanvas(MouseEvent evt)
{
if (evt == null)
{
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
scrollThread = null;
}
mouseDragging = false;
@@ -1772,7 +1994,7 @@ public class SeqPanel extends JPanel implements MouseListener,
{
MouseEvent evt;
- boolean running = false;
+ private volatile boolean threadRunning = true;
public ScrollThread()
{
@@ -1786,36 +2008,40 @@ public class SeqPanel extends JPanel implements MouseListener,
public void stopScrolling()
{
- running = false;
+ threadRunning = false;
+ }
+
+ public boolean isRunning()
+ {
+ return threadRunning;
}
@Override
public void run()
{
- running = true;
-
- while (running)
+ while (threadRunning)
{
if (evt != null)
{
- if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
+ if (mouseDragging && (evt.getY() < 0)
+ && (av.getRanges().getStartSeq() > 0))
{
- running = ap.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
- if (mouseDragging && (evt.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ if (mouseDragging && (evt.getY() >= getHeight()) && (av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
- running = ap.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
if (mouseDragging && (evt.getX() < 0))
{
- running = ap.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
else if (mouseDragging && (evt.getX() >= getWidth()))
{
- running = ap.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
}
@@ -1834,63 +2060,93 @@ public class SeqPanel extends JPanel implements MouseListener,
*/
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ 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.
- if (av == source
- || !av.followSelection
- || (av.isSelectionGroupChanged(false) || av
- .isColSelChanged(false))
- || (source instanceof AlignViewport && ((AlignViewport) source)
- .getSequenceSetId().equals(av.getSequenceSetId())))
+ 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)
- // rules are: colsel is copied if there is a real intersection between
- // sequence selection
- boolean repaint = false, copycolsel = true;
- // if (!av.isSelectionGroupChanged(false))
+ /*
+ * 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)
{
- SequenceGroup sgroup = null;
- if (seqsel != null && seqsel.getSize() > 0)
- {
- if (av.getAlignment() == null)
- {
- jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
- + av.getSequenceSetId() + " ViewId=" + av.getViewId()
- + " 's alignment is NULL! returning immediatly.");
- return;
- }
- sgroup = seqsel.intersect(av.getAlignment(),
- (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- || (colsel == null || colsel.size() == 0))
- {
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
- }
- }
- if (sgroup != null && sgroup.getSize() > 0)
+ if (av.getAlignment() == null)
{
- av.setSelectionGroup(sgroup);
+ Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediately.");
+ return;
}
- else
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+ if ((sgroup != null && sgroup.getSize() > 0))
{
- av.setSelectionGroup(null);
+ copycolsel = true;
}
- av.isSelectionGroupChanged(true);
- repaint = 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.size() == 0)
+ if (colsel == null || colsel.isEmpty())
{
if (av.getColumnSelection() != null)
{
@@ -1907,24 +2163,84 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- av.getColumnSelection().setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
}
}
av.isColSelChanged(true);
repaint = true;
}
- if (copycolsel
- && av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection()
- .getHiddenColumns() == null))
+
+ if (copycolsel && av.hasHiddenColumns()
+ && (av.getAlignment().getHiddenColumns() == null))
{
System.err.println("Bad things");
}
- if (repaint)
+ 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);
+ av.getAlignment().setHiddenColumns(hs);
+
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
}
}