/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
+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.SearchResults;
+import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+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.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.*;
-import jalview.structure.*;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision: 1.130 $
*/
StringBuffer keyboardNo2;
java.net.URL linkImageURL;
+
private final SequenceAnnotationReport seqARep;
- StringBuffer tooltipText = new StringBuffer("<html>");
+
+ StringBuffer tooltipText = new StringBuffer();
String tmpString;
StructureSelectionManager ssm;
+ SearchResults lastSearchResults;
+
/**
* Creates a new SeqPanel object.
- *
+ *
* @param avp
* DOCUMENT ME!
* @param p
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
linkImageURL = getClass().getResource("/images/link.gif");
- seqARep=new SequenceAnnotationReport(linkImageURL.toString());
+ seqARep = new SequenceAnnotationReport(linkImageURL.toString());
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
int wrappedBlock = -1;
+ /**
+ * Returns the aligned sequence position (base 0) at the mouse position, or
+ * the closest visible one
+ *
+ * @param evt
+ * @return
+ */
int findRes(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
- + seqCanvas.getAnnotationHeight();
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap + seqCanvas.getAnnotationHeight();
int y = evt.getY();
y -= hgap;
}
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();
+ // make sure we calculate relative to visible alignment, rather than
+ // right-hand gutter
+ x = seqCanvas.getX() + seqCanvas.getWidth();
}
res = (x / av.getCharWidth()) + av.getStartRes();
+ if (res > av.getEndRes())
+ {
+ // moused off right
+ res = av.getEndRes();
+ }
}
if (av.hasHiddenColumns())
int seq = 0;
int y = evt.getY();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
- + seqCanvas.getAnnotationHeight();
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap + seqCanvas.getAnnotationHeight();
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.getAlignment().getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+ .getHeight() - 1);
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.getAlignment().getHeight() - 1);
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ .getAlignment().getHeight() - 1);
}
return seq;
}
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ /**
+ * When all of a sequence of edits are complete, put the resulting edit list
+ * on the history stack (undo list), and reset flags for editing in progress.
+ */
+ void endEditing()
{
- Vector tmp = new Vector();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
+ try
{
- for (int i = 0; i < features.length; i++)
+ if (editCommand != null && editCommand.getSize() > 0)
{
- if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && seqCanvas.fr.featureGroups != null
- && seqCanvas.fr.featureGroups
- .containsKey(features[i].featureGroup)
- && !((Boolean) seqCanvas.fr.featureGroups
- .get(features[i].featureGroup)).booleanValue())
- continue;
-
- if ((features[i].getBegin() <= res)
- && (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null, av.getAlignment()
+ .getSequences());
}
- }
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
- }
-
- void endEditing()
- {
- if (editCommand != null && editCommand.getSize() > 0)
+ } finally
{
- ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null, av.getAlignment()
- .getSequences());
+ /*
+ * Tidy up come what may...
+ */
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
}
-
- startseq = -1;
- lastres = -1;
- editingSeqs = false;
- groupEditing = false;
- keyboardNo1 = null;
- keyboardNo2 = null;
- editCommand = null;
}
void setCursorRow()
void setCursorPosition()
{
- SequenceI sequence = av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns()
+ && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
}
endEditing();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
ap.scrollToWrappedVisible(seqCanvas.cursorX);
}
{
ap.scrollUp(false);
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
endEditing();
}
- void insertNucAtCursor(boolean group,String nuc){
- groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX;
- editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
- endEditing();
+ void insertNucAtCursor(boolean group, String nuc)
+ {
+ // TODO not called - delete?
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
}
void numberPressed(char value)
int getKeyboardNo1()
{
- if (keyboardNo1 == null)
- return 1;
- else
+ try
+ {
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ } catch (Exception x)
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
}
+ keyboardNo1 = null;
+ return 1;
}
int getKeyboardNo2()
{
- if (keyboardNo2 == null)
- return 1;
- else
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ } catch (Exception x)
{
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
}
+ keyboardNo2 = null;
+ return 1;
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
mouseDragging = false;
mouseWheelPressed = false;
+ if (evt.isPopupTrigger()) // Windows: mouseReleased
+ {
+ showPopupMenu(evt);
+ evt.consume();
+ return;
+ }
+
if (!editingSeqs)
{
doMouseReleasedDefineMode(evt);
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
{
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
{
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)
{
- if (av.followHighlight)
+ if (results == null || results.equals(lastSearchResults))
+ {
+ return;
+ }
+ lastSearchResults = results;
+
+ if (av.isFollowHighlight())
{
+ /*
+ * if scrollToPosition requires a scroll adjustment, this flag prevents
+ * another scroll event being propagated back to the originator
+ *
+ * @see AlignmentPanel#adjustmentValueChanged
+ */
+ ap.setDontScrollComplement(true);
if (ap.scrollToPosition(results, false))
{
- seqCanvas.revalidate();
+ seqCanvas.revalidate();
}
}
+ setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
}
@Override
+ public VamsasSource getVamsasSource()
+ {
+ return this.ap == null ? null : this.ap.av;
+ }
+
+ @Override
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
pos = setStatusMessage(sequence, res, seq);
if (ssm != null && pos > -1)
+ {
mouseOverSequence(sequence, res, pos);
+ }
tooltipText.setLength(6); // Cuts the buffer back to <html>
{
if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
{
- if (tooltipText.length() > 6)
- {
- tooltipText.append("<br>");
- }
-
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
}
// use aa to see if the mouse pointer is on a
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
int rpos;
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(),
- rpos = sequence.findPosition(res));
- seqARep.appendFeatures(tooltipText, rpos, features,
- this.ap.seqPanel.seqCanvas.fr.minmax);
+ List<SequenceFeature> features = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
+ seqARep.appendFeatures(tooltipText, rpos, features,
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
if (tooltipText.length() == 6) // <html></html>
{
}
else
{
- tooltipText.append("</html>");
if (lastTooltip == null
|| !lastTooltip.equals(tooltipText.toString()))
{
- setToolTipText(tooltipText.toString());
+ String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltipText.toString());
+ // String formatedTooltipText = tooltipText.toString();
+ setToolTipText(formatedTooltipText);
lastTooltip = tooltipText.toString();
}
*
* @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
*/
+ @Override
public Point getToolTipLocation(MouseEvent event)
{
int x = event.getX(), w = getWidth();
return lastp = p;
}
-
String lastTooltip;
/**
+ * 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
+
+ /**
* Set status message in alignment panel
- *
+ *
* @param sequence
* aligned sequence object
* @param res
*/
int setStatusMessage(SequenceI sequence, int res, int seq)
{
- 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 = seq == -1 ? "" : " " + (seq + 1);
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
- Object obj = null;
+ String residue = null;
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ final String displayChar = String.valueOf(sequence.getCharAt(res));
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
- + "");
- if (obj != null)
+ residue = ResidueProperties.nucleotideName.get(displayChar);
+ if (residue != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(residue);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
+ residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+ .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
+ .get(displayChar));
+ if (residue != null)
{
- text.append(" Residue: ");
+ text.append(" Residue: ").append(residue);
}
}
- if (obj != null)
+ int pos = -1;
+ if (residue != null)
{
pos = sequence.findPosition(res);
- if (obj != "")
- {
- text.append(obj + " (" + pos + ")");
- }
+ text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
return pos;
}
/**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResults results)
+ {
+ AlignmentI al = this.av.getAlignment();
+ int sequenceIndex = al.findIndex(results);
+ if (sequenceIndex == -1)
+ {
+ return;
+ }
+ SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ for (Match m : results.getResults())
+ {
+ SequenceI seq = m.getSequence();
+ if (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+
+ 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!
*/
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
fontSize = 1;
}
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
+ av.setFont(
+ new Font(av.font.getName(), av.font.getStyle(), fontSize),
+ true);
+ av.setCharWidth(oldWidth);
ap.fontChanged();
}
else
{
- if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.charWidth--;
+ av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.charWidth++;
+ av.setCharWidth(av.getCharWidth() + 1);
}
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();
if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
- editSequence(false, false,res);
+ editSequence(false, false, res);
}
else
{
- editSequence(true, false,res);
+ editSequence(true, false, res);
}
mouseDragging = true;
}
}
- //TODO: Make it more clever than many booleans
- synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
+ // TODO: Make it more clever than many booleans
+ synchronized void editSequence(boolean insertGap, boolean editSeq,
+ int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
}
}
- StringBuffer message = new StringBuffer();
+ StringBuilder message = new StringBuilder(64);
if (groupEditing)
{
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[] { label }));
}
}
{
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
+ .getColumnSelection().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
int alWidth = av.getAlignment().getWidth();
if (av.hasHiddenRows())
{
- int hwidth = av.getAlignment().getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences()
+ .getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
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();
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
+ - lastres);
}
}
else
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
+ - startres);
}
}
{
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
{
- if(!editSeq){
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
+ if (!editSeq)
{
- for (int j = lastres; j > startres; j--)
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ for (int j = lastres; j > startres; j--)
{
- endEditing();
- break;
+ if (!Comparison.isGap(seq.getCharAt(startres)))
+ {
+ endEditing();
+ break;
+ }
+ deleteChar(startres, new SequenceI[] { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ // could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < lastres; m++)
+ {
+ if (!Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+ startres, max);
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
}
}
else
- {
- // could be a keyboard edit trying to delete none gaps
- int max = 0;
- for (int m = startres; m < lastres; m++)
+ {// insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ for (int j = lastres; j < startres; j++)
{
- break;
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
- max++;
}
-
- if (max > 0)
+ else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.getAlignment(), true);
+ appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
- }else{//insertGap==false AND editSeq==TRUE;
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j < startres; j++)
- {
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
- }
- }
- else
- {
- editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
- }
- }
}
}
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;
}
}
- 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);
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt)));
+ List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt)));
- if (features != null && features.length > 0)
+ if (features != null && features.size() > 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
}
- if (features != null && features.length > 0)
+ if (features != null && features.size() > 0)
{
- seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
- { sequence }, features, false, ap);
+ seqCanvas.getFeatureRenderer().amendFeatures(
+ new SequenceI[] { sequence },
+ features.toArray(new SequenceFeature[features.size()]),
+ false, ap);
seqCanvas.highlightSearchResults(null);
}
if (e.isShiftDown())
{
ap.scrollRight(true);
-
- } else {
+
+ }
+ else
+ {
ap.scrollUp(false);
}
}
if (e.isShiftDown())
{
ap.scrollRight(false);
- } else {
+ }
+ else
+ {
ap.scrollUp(true);
}
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
- int seq = findSeq(evt);
+ final int res = findRes(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,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
}
av.setSelectionGroup(stretchGroup);
-
}
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger()) // Mac: mousePressed
{
- 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));
- }
- }
- }
+ showPopupMenu(evt);
+ return;
+ }
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
- pop.show(this, evt.getX(), evt.getY());
+ /*
+ * defer right-mouse click handling to mouseReleased on Windows
+ * (where isPopupTrigger() will answer true)
+ * NB isRightMouseButton is also true for Cmd-click on Mac
+ */
+ if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+ {
return;
}
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
-
stretchGroup = sg;
if (av.getConservationSelected())
}
/**
+ * Build and show a pop-up menu at the right-click mouse position
+ *
+ * @param evt
+ * @param res
+ * @param sequence
+ */
+ void showPopupMenu(MouseEvent evt)
+ {
+ final int res = findRes(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<String>();
+ 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());
+ }
+
+ /**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
{
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();
if (stretchGroup.cs != null)
{
- stretchGroup.cs.alignmentChanged(
- stretchGroup,av.getHiddenRepSequences());
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
-
+ ap.paintAlignment(needOverviewUpdate);
+ needOverviewUpdate = false;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
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();
}
}
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
+ while ((y != oldSeq) && (oldSeq > -1)
+ && (y < av.getAlignment().getHeight()))
{
// This routine ensures we don't skip any sequences, as the
// selection is quite slow.
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
else
{
}
stretchGroup.addSequence(nextSeq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
// 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 || !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, 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)
{
- 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)
- {
- 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)
{
av.getColumnSelection().clear();
- repaint=true;
+ repaint = true;
}
}
else
av.isColSelChanged(true);
repaint = true;
}
- if (copycolsel && av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
+
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .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);
}
}
+
+ /**
+ * 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, 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);
+ av.setColumnSelection(cs);
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
+ }
}
git://source.jalview.org / jalview.git / blobdiff