package jalview.gui;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ResidueProperties;
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.util.Comparison;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
-import java.util.Vector;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
/**
private final SequenceAnnotationReport seqARep;
- StringBuffer tooltipText = new StringBuffer();
+ StringBuilder tooltipText = new StringBuilder();
String tmpString;
StructureSelectionManager ssm;
+ SearchResultsI lastSearchResults;
+
/**
* Creates a new SeqPanel object.
*
int wrappedBlock = -1;
- int findRes(MouseEvent evt)
+ /**
+ * Returns the aligned sequence position (base 0) at the mouse position, or
+ * the closest visible one
+ *
+ * @param evt
+ * @return
+ */
+ int findColumn(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
+ + hgap + seqCanvas.getAnnotationHeight();
int y = evt.getY();
y -= hgap;
}
wrappedBlock = y / cHeight;
- wrappedBlock += av.getStartRes() / cwidth;
+ wrappedBlock += av.getRanges().getStartRes() / cwidth;
res = wrappedBlock * cwidth + x / av.getCharWidth();
}
else
{
- if (x > seqCanvas.getWidth() + seqCanvas.getWidth())
+ if (x > seqCanvas.getX() + seqCanvas.getWidth())
{
// make sure we calculate relative to visible alignment, rather than
// right-hand gutter
x = seqCanvas.getX() + seqCanvas.getWidth();
}
- res = (x / av.getCharWidth()) + av.getStartRes();
+ res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+ if (res > av.getRanges().getEndRes())
+ {
+ // moused off right
+ res = av.getRanges().getEndRes();
+ }
}
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(res);
}
return res;
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
+ + hgap + seqCanvas.getAnnotationHeight();
y -= hgap;
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ seq = Math.min((y / av.getCharHeight())
+ + av.getRanges().getStartSeq(),
+ av
.getAlignment().getHeight() - 1);
}
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
+
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
if (av.hasHiddenColumns()
- && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ && !hidden.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
- while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+ while (!hidden.isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ || !hidden.isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
endEditing();
if (av.getWrapAlignment())
{
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
}
else
{
- while (seqCanvas.cursorY < av.startSeq)
- {
- ap.scrollUp(true);
- }
- while (seqCanvas.cursorY + 1 > av.endSeq)
- {
- ap.scrollUp(false);
- }
- if (!av.getWrapAlignment())
- {
- while (seqCanvas.cursorX < av.getColumnSelection()
- .adjustForHiddenColumns(av.startRes))
- {
- if (!ap.scrollRight(false))
- {
- break;
- }
- }
- while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.endRes))
- {
- if (!ap.scrollRight(true))
- {
- break;
- }
- }
- }
+ av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
+ av);
}
setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
void insertNucAtCursor(boolean group, String nuc)
{
+ // TODO not called - delete?
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
@Override
public void mouseReleased(MouseEvent evt)
{
+ boolean didDrag = mouseDragging; // did we come here after a drag
mouseDragging = false;
mouseWheelPressed = false;
+ if (evt.isPopupTrigger()) // Windows: mouseReleased
+ {
+ showPopupMenu(evt);
+ evt.consume();
+ return;
+ }
+
if (!editingSeqs)
{
- doMouseReleasedDefineMode(evt);
+ doMouseReleasedDefineMode(evt, didDrag);
return;
}
{
lastMousePress = evt.getPoint();
- if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+ if (SwingUtilities.isMiddleMouseButton(evt))
{
mouseWheelPressed = true;
return;
}
- if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+ boolean isControlDown = Platform.isControlDown(evt);
+ if (evt.isShiftDown() || isControlDown)
{
- if (evt.isAltDown() || evt.isControlDown())
+ editingSeqs = true;
+ if (isControlDown)
{
groupEditing = true;
}
- editingSeqs = true;
}
else
{
}
int seq = findSeq(evt);
- int res = findRes(evt);
+ int res = findColumn(evt);
if (seq < 0 || res < 0)
{
lastMessage = tmp;
}
+ /**
+ * Highlight the mapped region described by the search results object (unless
+ * unchanged). This supports highlight of protein while mousing over linked
+ * cDNA and vice versa. The status bar is also updated to show the location of
+ * the start of the highlighted region.
+ */
@Override
- public void highlightSequence(SearchResults results)
+ public void highlightSequence(SearchResultsI results)
{
- if (av.followHighlight)
+ if (results == null || results.equals(lastSearchResults))
+ {
+ return;
+ }
+ lastSearchResults = results;
+
+ if (av.isFollowHighlight())
{
+ // don't allow highlight of protein/cDNA to also scroll a complementary
+ // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+ // over residue to change abruptly, causing highlighted residue in panel 2
+ // to change, causing a scroll in panel 1 etc)
+ ap.setToScrollComplementPanel(false);
if (ap.scrollToPosition(results, false))
{
seqCanvas.revalidate();
}
+ ap.setToScrollComplementPanel(true);
}
setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
{
return this.ap == null ? null : this.ap.av;
}
+
@Override
public void updateColours(SequenceI seq, int index)
{
mouseDragged(evt);
}
- int res = findRes(evt);
+ final int column = findColumn(evt);
int seq = findSeq(evt);
- int pos;
- if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
return;
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res >= sequence.getLength())
+ if (column >= sequence.getLength())
{
return;
}
- pos = setStatusMessage(sequence, res, seq);
+ /*
+ * set status bar message, returning residue position in sequence
+ */
+ final int pos = setStatusMessage(sequence, column, seq);
if (ssm != null && pos > -1)
{
- mouseOverSequence(sequence, res, pos);
+ mouseOverSequence(sequence, column, pos);
}
tooltipText.setLength(6); // Cuts the buffer back to <html>
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ if (groups[g].getStartRes() <= column
+ && groups[g].getEndRes() >= column)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
}
}
- // use aa to see if the mouse pointer is on a
- if (av.isShowSequenceFeatures())
+ if (av.isShowSequenceFeatures() && pos != -1)
{
- int rpos;
- List<SequenceFeature> features = ap.getFeatureRenderer().findFeaturesAtRes(
- sequence.getDatasetSequence(),
- rpos = sequence.findPosition(res));
- seqARep.appendFeatures(tooltipText, rpos, features,
+ List<SequenceFeature> features = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+ seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
- if (tooltipText.length() == 6) // <html></html>
+ if (tooltipText.length() == 6) // <html>
{
setToolTipText(null);
lastTooltip = null;
*
* @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
*/
+ @Override
public Point getToolTipLocation(MouseEvent event)
{
int x = event.getX(), w = getWidth();
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, residue and residue position for the given sequence and
+ * column position. Returns the calculated residue position in the sequence,
+ * or -1 for a gapped column position.
*
* @param sequence
* aligned sequence object
- * @param res
+ * @param column
* alignment column
* @param seq
* index of sequence in alignment
- * @return position of res in sequence
+ * @return position of column in sequence or -1 if at a gap
*/
- int setStatusMessage(SequenceI sequence, int res, int seq)
+ int setStatusMessage(SequenceI sequence, final int column, int seq)
{
StringBuilder text = new StringBuilder(32);
* Sequence number (if known), and sequence name.
*/
String seqno = seq == -1 ? "" : " " + (seq + 1);
- text.append("Sequence" + seqno + " ID: " + sequence.getName());
+ 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).
*/
- final String displayChar = String.valueOf(sequence.getCharAt(res));
+ final String displayChar = String.valueOf(sequence.getCharAt(column));
if (av.getAlignment().isNucleotide())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
}
else
{
- residue = "X".equalsIgnoreCase(displayChar) ? "X"
- : ResidueProperties.aa2Triplet.get(displayChar);
+ residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+ .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
+ .get(displayChar));
if (residue != null)
{
text.append(" Residue: ").append(residue);
int pos = -1;
if (residue != null)
{
- pos = sequence.findPosition(res);
+ pos = sequence.findPosition(column);
text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
*
* @param results
*/
- private void setStatusMessage(SearchResults results)
+ private void setStatusMessage(SearchResultsI results)
{
- List<Match> matches = results.getResults();
- if (!matches.isEmpty())
+ 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())
{
- Match m = matches.get(0);
SequenceI seq = m.getSequence();
- int sequenceIndex = this.av.getAlignment().findIndex(seq);
+ if (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
- /*
- * Convert position in sequence (base 1) to sequence character array index
- * (base 0)
- */
- int start = m.getStart() - 1;
- setStatusMessage(seq, start, sequenceIndex);
+ if (seq == ds)
+ {
+ /*
+ * Convert position in sequence (base 1) to sequence character array
+ * index (base 0)
+ */
+ int start = m.getStart() - m.getSequence().getStart();
+ setStatusMessage(seq, start, sequenceIndex);
+ return;
+ }
}
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
public void mouseDragged(MouseEvent evt)
{
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++;
}
fontSize = 1;
}
- av.setFont(
- new Font(av.font.getName(), av.font.getStyle(), fontSize),
- true);
- av.setCharWidth(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
{
+ /*
+ * on drag left or right, decrement or increment character width
+ */
+ int newWidth = 0;
if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.setCharWidth(av.getCharWidth() - 1);
+ newWidth = av.getCharWidth() - 1;
+ av.setCharWidth(newWidth);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.setCharWidth(av.getCharWidth() + 1);
+ 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());
return;
}
- int res = findRes(evt);
+ int res = findColumn(evt);
if (res < 0)
{
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
}
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 }));
}
}
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))
{
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;
{
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;
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();
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- appendEdit(Action.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres);
+ appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
else
endEditing();
break;
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
+ deleteChar(startres, new SequenceI[] { seq }, fixedRight);
}
}
else
if (max > 0)
{
- appendEdit(Action.DELETE_GAP, new SequenceI[]
- { seq }, startres, max);
+ appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+ startres, max);
}
}
}
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- appendEdit(Action.INSERT_NUC, new SequenceI[]
- { seq }, lastres, startres - lastres);
+ appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
}
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;
final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
av.getAlignment().getGapCharacter());
- editCommand.appendEdit(edit, av.getAlignment(),
- true, null);
+ editCommand.appendEdit(edit, av.getAlignment(), true, null);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
}
}
+ /**
+ * 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)
{
av.setSelectionGroup(null);
}
- List<SequenceFeature> features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
- sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt)));
+ List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(findColumn(evt)));
- if (features != null && features.size()> 0)
+ if (!features.isEmpty())
{
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features.get(0).getBegin(),
- features.get(0).getEnd());
+ /*
+ * 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);
- }
- if (features != null && features.size()> 0)
- {
- seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
- { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
+ /*
+ * open the Amend Features dialog; clear highlighting afterwards,
+ * whether changes were made or not
+ */
+ List<SequenceI> seqs = Collections.singletonList(sequence);
+ seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+ ap);
seqCanvas.highlightSearchResults(null);
}
}
{
if (e.isShiftDown())
{
- ap.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
else
{
- ap.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
- ap.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
else
{
- ap.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
}
// TODO Update tooltip for new position.
*/
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.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ 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;
}
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())
{
- List<SequenceFeature> allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
- sequence.getDatasetSequence(), sequence.findPosition(res));
- Vector links = new Vector();
- for (SequenceFeature sf:allFeatures)
- {
- if (sf.links != null)
- {
- for (int j = 0; j < sf.links.size(); j++)
- {
- links.addElement(sf.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;
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
-
stretchGroup = sg;
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
}
if (av.getAbovePIDThreshold())
{
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
}
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
{
// Edit end res position of selected group
}
/**
- * DOCUMENT ME!
+ * Build and show a pop-up menu at the right-click mouse position
*
* @param evt
- * DOCUMENT ME!
+ * @param res
+ * @param sequences
*/
- public void doMouseReleasedDefineMode(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt)
+ {
+ final int res = findColumn(evt);
+ final int seq = findSeq(evt);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(res));
+ List<String> links = new ArrayList<>();
+ for (SequenceFeature sf : allFeatures)
+ {
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ links.add(link);
+ }
+ }
+ }
+
+ PopupMenu pop = new PopupMenu(ap, null, links);
+ 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)
+ */
+ public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
{
if (stretchGroup == null)
{
return;
}
-
- stretchGroup.recalcConservation(); // always do this - annotation has own
- // state
+ // 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;
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
+ int res = findColumn(evt);
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)
changeStartRes = true;
}
- if (res < av.getStartRes())
+ if (res < av.getRanges().getStartRes())
{
- res = av.getStartRes();
+ res = av.getRanges().getStartRes();
}
if (changeEndRes)
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
else if (changeStartRes)
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
else
{
}
stretchGroup.addSequence(nextSeq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
{
if (evt != null)
{
- if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
+ if (mouseDragging && (evt.getY() < 0)
+ && (av.getRanges().getStartSeq() > 0))
{
- running = ap.scrollUp(true);
+ running = av.getRanges().scrollUp(true);
}
if (mouseDragging && (evt.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getRanges()
+ .getEndSeq()))
{
- running = ap.scrollUp(false);
+ running = av.getRanges().scrollUp(false);
}
if (mouseDragging && (evt.getX() < 0))
{
- running = ap.scrollRight(false);
+ running = av.getRanges().scrollRight(false);
}
else if (mouseDragging && (evt.getX() >= getWidth()))
{
- running = ap.scrollRight(true);
+ running = av.getRanges().scrollRight(true);
}
}
*/
@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.
- boolean iSentTheSelection = (av == source
- || (source instanceof AlignViewport && ((AlignmentViewport) source)
+ boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())));
- if (iSentTheSelection || !av.followSelection)
+
+ 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;
}
* Check for selection in a view of which this one is a dna/protein
* complement.
*/
- if (selectionFromTranslation(seqsel, colsel, source))
+ 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
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
boolean repaint = false;
- boolean copycolsel = true;
+ boolean copycolsel = false;
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()
+ 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)
- || (colsel == null || colsel.size() == 0))
+ if ((sgroup != null && sgroup.getSize() > 0))
{
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
+ copycolsel = true;
}
}
if (sgroup != null && sgroup.getSize() > 0)
{
// 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)
{
}
else
{
- av.getColumnSelection().setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
}
}
av.isColSelChanged(true);
if (copycolsel
&& av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection()
- .getHiddenColumns() == null))
+ && (av.getAlignment().getHiddenColumns() == null || av
+ .getAlignment().getHiddenColumns().getHiddenRegions() == null))
{
System.err.println("Bad things");
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
// ap.paintAlignment(false);
}
+
+ // lastly, update dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
}
/**
* @param source
*/
protected boolean selectionFromTranslation(SequenceGroup seqsel,
- ColumnSelection colsel, SelectionSource source)
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
- if (!(source instanceof AlignViewportI)) {
+ if (!(source instanceof AlignViewportI))
+ {
return false;
}
final AlignViewportI sourceAv = (AlignViewportI) source;
- if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+ if (sourceAv.getCodingComplement() != av
+ && av.getCodingComplement() != sourceAv)
{
return false;
}
/*
* Map column selection
*/
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
- av);
+ // 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.isColSelChanged(true);
+ av.getAlignment().setHiddenColumns(hs);
+
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
PaintRefresher.Refresh(this, av.getSequenceSetId());
git://source.jalview.org / jalview.git / blobdiff