/*
* 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
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
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.List;
import java.util.Vector;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
import jalview.api.AlignViewportI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
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.viewmodel.AlignmentViewport;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision: 1.130 $
*/
public class SeqPanel extends JPanel implements MouseListener,
MouseMotionListener, MouseWheelListener, SequenceListener,
SelectionListener
{
/** DOCUMENT ME!! */
public SeqCanvas seqCanvas;
/** DOCUMENT ME!! */
public AlignmentPanel ap;
protected int lastres;
protected int startseq;
protected AlignViewport av;
ScrollThread scrollThread = null;
boolean mouseDragging = false;
boolean editingSeqs = false;
boolean groupEditing = false;
// ////////////////////////////////////////
// ///Everything below this is for defining the boundary of the rubberband
// ////////////////////////////////////////
int oldSeq = -1;
boolean changeEndSeq = false;
boolean changeStartSeq = false;
boolean changeEndRes = false;
boolean changeStartRes = false;
SequenceGroup stretchGroup = null;
boolean remove = false;
Point lastMousePress;
boolean mouseWheelPressed = false;
StringBuffer keyboardNo1;
StringBuffer keyboardNo2;
java.net.URL linkImageURL;
private final SequenceAnnotationReport seqARep;
StringBuffer tooltipText = new StringBuffer();
String tmpString;
EditCommand editCommand;
StructureSelectionManager ssm;
/**
* Creates a new SeqPanel object.
*
* @param avp
* DOCUMENT ME!
* @param p
* DOCUMENT ME!
*/
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
linkImageURL = getClass().getResource("/images/link.gif");
seqARep = new SequenceAnnotationReport(linkImageURL.toString());
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
this.av = av;
setBackground(Color.white);
seqCanvas = new SeqCanvas(ap);
setLayout(new BorderLayout());
add(seqCanvas, BorderLayout.CENTER);
this.ap = ap;
if (!av.isDataset())
{
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
}
int startWrapBlock = -1;
int wrappedBlock = -1;
int findRes(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
if (av.getWrapAlignment())
{
int hgap = av.getCharHeight();
if (av.getScaleAboveWrapped())
{
hgap += av.getCharHeight();
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ hgap
+ seqCanvas.getAnnotationHeight();
int y = evt.getY();
y -= hgap;
x -= seqCanvas.LABEL_WEST;
int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
if (cwidth < 1)
{
return 0;
}
wrappedBlock = y / cHeight;
wrappedBlock += av.getStartRes() / cwidth;
res = wrappedBlock * cwidth + x / av.getCharWidth();
}
else
{
if (x > seqCanvas.getWidth() + 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 (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
return res;
}
int findSeq(MouseEvent evt)
{
int seq = 0;
int y = evt.getY();
if (av.getWrapAlignment())
{
int hgap = av.getCharHeight();
if (av.getScaleAboveWrapped())
{
hgap += av.getCharHeight();
}
int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ hgap
+ seqCanvas.getAnnotationHeight();
y -= hgap;
seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
.getHeight() - 1);
}
else
{
seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
.getAlignment().getHeight() - 1);
}
return seq;
}
/**
* 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()
{
try
{
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
av.firePropertyChange("alignment", null, av.getAlignment()
.getSequences());
}
} finally
{
/*
* Tidy up come what may...
*/
startseq = -1;
lastres = -1;
editingSeqs = false;
groupEditing = false;
keyboardNo1 = null;
keyboardNo2 = null;
editCommand = null;
}
}
void setCursorRow()
{
seqCanvas.cursorY = getKeyboardNo1() - 1;
scrollToVisible();
}
void setCursorColumn()
{
seqCanvas.cursorX = getKeyboardNo1() - 1;
scrollToVisible();
}
void setCursorRowAndColumn()
{
if (keyboardNo2 == null)
{
keyboardNo2 = new StringBuffer();
}
else
{
seqCanvas.cursorX = getKeyboardNo1() - 1;
seqCanvas.cursorY = getKeyboardNo2() - 1;
scrollToVisible();
}
}
void setCursorPosition()
{
SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
void moveCursor(int dx, int dy)
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
if (av.hasHiddenColumns()
&& !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
|| !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
}
scrollToVisible();
}
void scrollToVisible()
{
if (seqCanvas.cursorX < 0)
{
seqCanvas.cursorX = 0;
}
else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
{
seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
}
if (seqCanvas.cursorY < 0)
{
seqCanvas.cursorY = 0;
}
else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
{
seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
}
endEditing();
if (av.getWrapAlignment())
{
ap.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;
}
}
}
}
setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
}
void setSelectionAreaAtCursor(boolean topLeft)
{
SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
SequenceGroup sg = av.getSelectionGroup();
// Find the top and bottom of this group
int min = av.getAlignment().getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
if (index > max)
{
max = index;
}
if (index < min)
{
min = index;
}
}
max++;
if (topLeft)
{
sg.setStartRes(seqCanvas.cursorX);
if (sg.getEndRes() < seqCanvas.cursorX)
{
sg.setEndRes(seqCanvas.cursorX);
}
min = seqCanvas.cursorY;
}
else
{
sg.setEndRes(seqCanvas.cursorX);
if (sg.getStartRes() > seqCanvas.cursorX)
{
sg.setStartRes(seqCanvas.cursorX);
}
max = seqCanvas.cursorY + 1;
}
if (min > max)
{
// Only the user can do this
av.setSelectionGroup(null);
}
else
{
// Now add any sequences between min and max
sg.getSequences(null).clear();
for (int i = min; i < max; i++)
{
sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
if (av.getSelectionGroup() == null)
{
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(seqCanvas.cursorX);
sg.setEndRes(seqCanvas.cursorX);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
}
ap.paintAlignment(false);
av.sendSelection();
}
void insertGapAtCursor(boolean group)
{
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
void deleteGapAtCursor(boolean group)
{
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX + getKeyboardNo1();
editSequence(false, false, seqCanvas.cursorX);
endEditing();
}
void insertNucAtCursor(boolean group, String nuc)
{
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
void numberPressed(char value)
{
if (keyboardNo1 == null)
{
keyboardNo1 = new StringBuffer();
}
if (keyboardNo2 != null)
{
keyboardNo2.append(value);
}
else
{
keyboardNo1.append(value);
}
}
int getKeyboardNo1()
{
try
{
if (keyboardNo1 != null)
{
int value = Integer.parseInt(keyboardNo1.toString());
keyboardNo1 = null;
return value;
}
} catch (Exception x)
{
}
keyboardNo1 = null;
return 1;
}
int getKeyboardNo2()
{
try
{
if (keyboardNo2 != null)
{
int value = Integer.parseInt(keyboardNo2.toString());
keyboardNo2 = null;
return value;
}
} catch (Exception x)
{
}
keyboardNo2 = null;
return 1;
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
mouseWheelPressed = false;
if (!editingSeqs)
{
doMouseReleasedDefineMode(evt);
return;
}
endEditing();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
{
mouseWheelPressed = true;
return;
}
if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
{
if (evt.isAltDown() || evt.isControlDown())
{
groupEditing = true;
}
editingSeqs = true;
}
else
{
doMousePressedDefineMode(evt);
return;
}
int seq = findSeq(evt);
int res = findRes(evt);
if (seq < 0 || res < 0)
{
return;
}
if ((seq < av.getAlignment().getHeight())
&& (res < av.getAlignment().getSequenceAt(seq).getLength()))
{
startseq = seq;
lastres = res;
}
else
{
startseq = -1;
lastres = -1;
}
return;
}
String lastMessage;
@Override
public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
String tmp = sequence.hashCode() + " " + index + " " + pos;
if (lastMessage == null || !lastMessage.equals(tmp))
{
// System.err.println("mouseOver Sequence: "+tmp);
ssm.mouseOverSequence(sequence, index, pos, av);
}
lastMessage = tmp;
}
@Override
public void highlightSequence(SearchResults results)
{
if (av.isFollowHighlight())
{
if (ap.scrollToPosition(results, false))
{
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");
// repaint();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent evt)
{
if (editingSeqs)
{
// This is because MacOSX creates a mouseMoved
// If control is down, other platforms will not.
mouseDragged(evt);
}
int res = findRes(evt);
int seq = findSeq(evt);
int pos;
if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
return;
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (res >= sequence.getLength())
{
return;
}
pos = setStatusMessage(sequence, res, seq);
if (ssm != null && pos > -1)
{
mouseOverSequence(sequence, res, pos);
}
tooltipText.setLength(6); // Cuts the buffer back to
SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
{
if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
tooltipText.append(groups[g].getName());
}
if (groups[g].getDescription() != null)
{
tooltipText.append(": " + groups[g].getDescription());
}
}
}
}
// use aa to see if the mouse pointer is on a
if (av.isShowSequenceFeatures())
{
int rpos;
List 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) //
{
setToolTipText(null);
lastTooltip = null;
}
else
{
if (lastTooltip == null
|| !lastTooltip.equals(tooltipText.toString()))
{
String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
tooltipText.toString());
// String formatedTooltipText = tooltipText.toString();
setToolTipText(formatedTooltipText);
lastTooltip = tooltipText.toString();
}
}
}
private Point lastp = null;
/*
* (non-Javadoc)
*
* @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
*/
public Point getToolTipLocation(MouseEvent event)
{
int x = event.getX(), w = getWidth();
int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
// close to edge
Point p = lastp;
if (!event.isShiftDown() || p == 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
*/
return lastp = p;
}
String lastTooltip;
/**
* Set status message in alignment panel
*
* @param sequence
* aligned sequence object
* @param res
* alignment column
* @param seq
* index of sequence in alignment
* @return position of res in sequence
*/
int setStatusMessage(SequenceI sequence, int res, 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());
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())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
if (residue != null)
{
text.append(" Nucleotide: ").append(residue);
}
}
else
{
residue = "X".equalsIgnoreCase(displayChar) ? "X"
: ResidueProperties.aa2Triplet.get(displayChar);
if (residue != null)
{
text.append(" Residue: ").append(residue);
}
}
int pos = -1;
if (residue != null)
{
pos = sequence.findPosition(res);
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)
{
List matches = results.getResults();
if (!matches.isEmpty())
{
Match m = matches.get(0);
SequenceI seq = m.getSequence();
int sequenceIndex = this.av.getAlignment().findIndex(seq);
/*
* Convert position in sequence (base 1) to sequence character array index
* (base 0)
*/
int start = m.getStart() - 1;
setStatusMessage(seq, start, sequenceIndex);
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
@Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
{
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()))
{
int fontSize = av.font.getSize();
if (evt.getY() < lastMousePress.getY())
{
fontSize--;
}
else if (evt.getY() > lastMousePress.getY())
{
fontSize++;
}
if (fontSize < 1)
{
fontSize = 1;
}
av.setFont(
new Font(av.font.getName(), av.font.getStyle(), fontSize),
true);
av.setCharWidth(oldWidth);
ap.fontChanged();
}
else
{
if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.getX())
{
av.setCharWidth(av.getCharWidth() + 1);
}
ap.paintAlignment(false);
}
FontMetrics fm = getFontMetrics(av.getFont());
av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
return;
}
if (!editingSeqs)
{
doMouseDraggedDefineMode(evt);
return;
}
int res = findRes(evt);
if (res < 0)
{
res = 0;
}
if ((lastres == -1) || (lastres == res))
{
return;
}
if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
editSequence(false, false, res);
}
else
{
editSequence(true, false, res);
}
mouseDragging = true;
if (scrollThread != null)
{
scrollThread.setEvent(evt);
}
}
// TODO: Make it more clever than many booleans
synchronized void editSequence(boolean insertGap, boolean editSeq,
int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
SequenceI seq = av.getAlignment().getSequenceAt(startseq);
// No group, but the sequence may represent a group
if (!groupEditing && av.hasHiddenRows())
{
if (av.isHiddenRepSequence(seq))
{
sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
StringBuilder message = new StringBuilder(64);
if (groupEditing)
{
message.append("Edit group:");
if (editCommand == null)
{
editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
}
}
else
{
message.append("Edit sequence: " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
label = label.substring(0, 10);
}
if (editCommand == null)
{
editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
if (insertGap)
{
message.append(" insert ");
}
else
{
message.append(" delete ");
}
message.append(Math.abs(startres - lastres) + " gaps.");
ap.alignFrame.statusBar.setText(message.toString());
// Are we editing within a selection group?
if (groupEditing
|| (sg != null && sg.getSequences(av.getHiddenRepSequences())
.contains(seq)))
{
fixedColumns = true;
// sg might be null as the user may only see 1 sequence,
// but the sequence represents a group
if (sg == null)
{
if (!av.isHiddenRepSequence(seq))
{
endEditing();
return;
}
sg = av.getRepresentedSequences(seq);
}
fixedLeft = sg.getStartRes();
fixedRight = sg.getEndRes();
if ((startres < fixedLeft && lastres >= fixedLeft)
|| (startres >= fixedLeft && lastres < fixedLeft)
|| (startres > fixedRight && lastres <= fixedRight)
|| (startres <= fixedRight && lastres > fixedRight))
{
endEditing();
return;
}
if (fixedLeft > startres)
{
fixedRight = fixedLeft - 1;
fixedLeft = 0;
}
else if (fixedRight < startres)
{
fixedLeft = fixedRight;
fixedRight = -1;
}
}
if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
{
endEditing();
return;
}
// System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
// Selection spans a hidden region
if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
{
if (startres >= y2)
{
fixedLeft = y2;
}
else
{
fixedRight = y2 - 1;
}
}
}
if (groupEditing)
{
List vseqs = sg.getSequences(av.getHiddenRepSequences());
int g, groupSize = vseqs.size();
SequenceI[] groupSeqs = new SequenceI[groupSize];
for (g = 0; g < groupSeqs.length; g++)
{
groupSeqs[g] = vseqs.get(g);
}
// drag to right
if (insertGap)
{
// If the user has selected the whole sequence, and is dragging to
// the right, we can still extend the alignment and selectionGroup
if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
&& sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
// Is it valid with fixed columns??
// Find the next gap before the end
// of the visible region boundary
boolean blank = false;
for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
{
blank = true;
for (g = 0; g < groupSize; g++)
{
for (int j = 0; j < startres - lastres; j++)
{
if (!jalview.util.Comparison.isGap(groupSeqs[g]
.getCharAt(fixedRight - j)))
{
blank = false;
break;
}
}
}
if (blank)
{
break;
}
}
if (!blank)
{
if (sg.getSize() == av.getAlignment().getHeight())
{
if ((av.hasHiddenColumns() && startres < av
.getColumnSelection().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
int alWidth = av.getAlignment().getWidth();
if (av.hasHiddenRows())
{
int hwidth = av.getAlignment().getHiddenSequences()
.getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
}
}
// We can still insert gaps if the selectionGroup
// contains all the sequences
sg.setEndRes(sg.getEndRes() + startres - lastres);
fixedRight = alWidth + startres - lastres;
}
else
{
endEditing();
return;
}
}
}
// drag to left
else if (!insertGap)
{
// / Are we able to delete?
// ie are all columns blank?
for (g = 0; g < groupSize; g++)
{
for (int j = startres; j < lastres; j++)
{
if (groupSeqs[g].getLength() <= j)
{
continue;
}
if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
return;
}
}
}
}
if (insertGap)
{
// dragging to the right
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j < startres; j++)
{
insertChar(j, groupSeqs, fixedRight);
}
}
else
{
appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
- lastres);
}
}
else
{
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j > startres; j--)
{
deleteChar(startres, groupSeqs, fixedRight);
}
}
else
{
appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
- startres);
}
}
}
else
// ///Editing a single sequence///////////
{
if (insertGap)
{
// dragging to the right
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j < startres; j++)
{
insertChar(j, new SequenceI[]
{ seq }, fixedRight);
}
}
else
{
appendEdit(Action.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres);
}
}
else
{
if (!editSeq)
{
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j > startres; j--)
{
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);
}
}
}
else
{// insertGap==false AND editSeq==TRUE;
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j < startres; j++)
{
insertChar(j, new SequenceI[]
{ seq }, fixedRight);
}
}
else
{
appendEdit(Action.INSERT_NUC, new SequenceI[]
{ seq }, lastres, startres - lastres);
}
}
}
}
lastres = startres;
seqCanvas.repaint();
}
void insertChar(int j, SequenceI[] seq, int fixedColumn)
{
int blankColumn = fixedColumn;
for (int s = 0; s < seq.length; s++)
{
// Find the next gap before the end of the visible region boundary
// If lastCol > j, theres a boundary after the gap insertion
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
{
if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
{
// Theres a space, so break and insert the gap
break;
}
}
if (blankColumn <= j)
{
blankColumn = fixedColumn;
endEditing();
return;
}
}
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)
{
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)
{
appendEdit(Action.DELETE_GAP, seq, j, 1);
appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
{
oldSeq = 0;
}
if (scrollThread != null)
{
scrollThread.running = false;
scrollThread = null;
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
{
return;
}
if (mouseDragging)
{
scrollThread = new ScrollThread();
}
}
@Override
public void mouseClicked(MouseEvent evt)
{
SequenceGroup sg = null;
SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
sg = av.getSelectionGroup();
if (sg != null && sg.getSize() == 1
&& sg.getEndRes() - sg.getStartRes() < 2)
{
av.setSelectionGroup(null);
}
List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
sequence.getDatasetSequence(),
sequence.findPosition(findRes(evt)));
if (features != null && features.size()> 0)
{
SearchResults 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);
seqCanvas.highlightSearchResults(null);
}
}
}
@Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
if (e.getWheelRotation() > 0)
{
if (e.isShiftDown())
{
ap.scrollRight(true);
}
else
{
ap.scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
ap.scrollRight(false);
}
else
{
ap.scrollUp(true);
}
}
// TODO Update tooltip for new position.
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
int res = findRes(evt);
int seq = findSeq(evt);
oldSeq = seq;
startWrapBlock = wrappedBlock;
if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.cannot_edit_annotations_in_wrapped_view"),
MessageManager.getString("label.wrapped_view_no_edit"),
JOptionPane.WARNING_MESSAGE);
return;
}
if (seq < 0 || res < 0)
{
return;
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if ((sequence == null) || (res > sequence.getLength()))
{
return;
}
stretchGroup = av.getSelectionGroup();
if (stretchGroup == null)
{
stretchGroup = av.getAlignment().findGroup(sequence);
if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
&& (res < stretchGroup.getEndRes()))
{
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 (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
List 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.cursorY = findSeq(evt);
seqCanvas.repaint();
return;
}
if (stretchGroup == null)
{
// Only if left mouse button do we want to change group sizes
// define a new group here
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(res);
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
stretchGroup = sg;
if (av.getConservationSelected())
{
SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
"Background");
}
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))
{
// Edit end res position of selected group
changeStartRes = true;
}
stretchGroup.getWidth();
}
seqCanvas.repaint();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void doMouseReleasedDefineMode(MouseEvent evt)
{
if (stretchGroup == null)
{
return;
}
stretchGroup.recalcConservation(); // always do this - annotation has own
// state
if (stretchGroup.cs != null)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
stretchGroup.getName());
}
else
{
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
stretchGroup.getName());
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
ap.paintAlignment(true);
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
av.sendSelection();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
int res = findRes(evt);
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)
{
return;
}
if (stretchGroup == null)
{
return;
}
if (res >= av.getAlignment().getWidth())
{
res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
{
// Edit end res position of selected group
changeEndRes = true;
}
else if (stretchGroup.getStartRes() == res)
{
// Edit start res position of selected group
changeStartRes = true;
}
if (res < av.getStartRes())
{
res = av.getStartRes();
}
if (changeEndRes)
{
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
}
}
else if (changeStartRes)
{
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
}
}
int dragDirection = 0;
if (y > oldSeq)
{
dragDirection = 1;
}
else if (y < oldSeq)
{
dragDirection = -1;
}
while ((y != oldSeq) && (oldSeq > -1)
&& (y < av.getAlignment().getHeight()))
{
// This routine ensures we don't skip any sequences, as the
// selection is quite slow.
Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
oldSeq += dragDirection;
if (oldSeq < 0)
{
break;
}
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
}
else
{
if (seq != null)
{
stretchGroup.addSequence(seq, false);
}
stretchGroup.addSequence(nextSeq, false);
}
}
if (oldSeq < 0)
{
oldSeq = -1;
}
mouseDragging = true;
if (scrollThread != null)
{
scrollThread.setEvent(evt);
}
seqCanvas.repaint();
}
void scrollCanvas(MouseEvent evt)
{
if (evt == null)
{
if (scrollThread != null)
{
scrollThread.running = false;
scrollThread = null;
}
mouseDragging = false;
}
else
{
if (scrollThread == null)
{
scrollThread = new ScrollThread();
}
mouseDragging = true;
scrollThread.setEvent(evt);
}
}
// this class allows scrolling off the bottom of the visible alignment
class ScrollThread extends Thread
{
MouseEvent evt;
boolean running = false;
public ScrollThread()
{
start();
}
public void setEvent(MouseEvent e)
{
evt = e;
}
public void stopScrolling()
{
running = false;
}
@Override
public void run()
{
running = true;
while (running)
{
if (evt != null)
{
if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
{
running = ap.scrollUp(true);
}
if (mouseDragging && (evt.getY() >= getHeight())
&& (av.getAlignment().getHeight() > av.getEndSeq()))
{
running = ap.scrollUp(false);
}
if (mouseDragging && (evt.getX() < 0))
{
running = ap.scrollRight(false);
}
else if (mouseDragging && (evt.getX() >= getWidth()))
{
running = ap.scrollRight(true);
}
}
try
{
Thread.sleep(20);
} catch (Exception ex)
{
}
}
}
}
/**
* modify current selection according to a received message.
*/
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
SelectionSource source)
{
// TODO: fix this hack - source of messages is align viewport, but SeqPanel
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
boolean iSentTheSelection = (av == source
|| (source instanceof AlignViewport && ((AlignmentViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())));
if (iSentTheSelection || !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;
boolean copycolsel = true;
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 immediately.");
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);
}
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 (av.getColumnSelection() != null)
{
av.getColumnSelection().clear();
repaint = true;
}
}
else
{
// TODO: shift colSel according to the intersecting sequences
if (av.getColumnSelection() == null)
{
av.setColumnSelection(new ColumnSelection(colsel));
}
else
{
av.getColumnSelection().setElementsFrom(colsel);
}
}
av.isColSelChanged(true);
repaint = true;
}
if (copycolsel
&& av.hasHiddenColumns()
&& (av.getColumnSelection() == null || av.getColumnSelection()
.getHiddenColumns() == null))
{
System.err.println("Bad things");
}
if (repaint) // always true!
{
// probably finessing with multiple redraws here
PaintRefresher.Refresh(this, av.getSequenceSetId());
// ap.paintAlignment(false);
}
}
/**
* 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);
av.isColSelChanged(true);
PaintRefresher.Refresh(this, av.getSequenceSetId());
return true;
}
}