/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
* Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program 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 2
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.gui;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.structure.*;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
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;
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");
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 = StructureSelectionManager.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.wrapAlignment)
{
int hgap = av.charHeight;
if (av.scaleAboveWrapped)
{
hgap += av.charHeight;
}
int cHeight = av.getAlignment().getHeight() * av.charHeight + 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
{
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.wrapAlignment)
{
int hgap = av.charHeight;
if (av.scaleAboveWrapped)
{
hgap += av.charHeight;
}
int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ seqCanvas.getAnnotationHeight();
y -= hgap;
seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
.getHeight() - 1);
}
else
{
seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
av.alignment.getHeight() - 1);
}
return seq;
}
SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
{
Vector tmp = new Vector();
SequenceFeature[] features = sequence.getSequenceFeatures();
if (features != null)
{
for (int i = 0; i < features.length; i++)
{
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]);
}
}
}
features = new SequenceFeature[tmp.size()];
tmp.copyInto(features);
return features;
}
void endEditing()
{
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
av.firePropertyChange("alignment", null, av.getAlignment()
.getSequences());
}
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 = (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.colSel.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.alignment.getWidth();
while (!av.colSel.isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
|| !av.colSel.isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
}
scrollToVisible();
}
void scrollToVisible()
{
if (seqCanvas.cursorX < 0)
{
seqCanvas.cursorX = 0;
}
else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
{
seqCanvas.cursorX = av.alignment.getWidth() - 1;
}
if (seqCanvas.cursorY < 0)
{
seqCanvas.cursorY = 0;
}
else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
{
seqCanvas.cursorY = av.alignment.getHeight() - 1;
}
endEditing();
if (av.wrapAlignment)
{
ap.scrollToWrappedVisible(seqCanvas.cursorX);
}
else
{
while (seqCanvas.cursorY < av.startSeq)
{
ap.scrollUp(true);
}
while (seqCanvas.cursorY + 1 > av.endSeq)
{
ap.scrollUp(false);
}
if (!av.wrapAlignment)
{
while (seqCanvas.cursorX < av.colSel
.adjustForHiddenColumns(av.startRes))
{
if (!ap.scrollRight(false))
{
break;
}
}
while (seqCanvas.cursorX > av.colSel
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
{
break;
}
}
}
}
setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
}
void setSelectionAreaAtCursor(boolean topLeft)
{
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
SequenceGroup sg = av.selectionGroup;
// Find the top and bottom of this group
int min = av.alignment.getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
int index = av.alignment.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.alignment.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, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
void deleteGapAtCursor(boolean group)
{
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX + getKeyboardNo1();
editSequence(false, seqCanvas.cursorX);
endEditing();
}
void numberPressed(char value)
{
if (keyboardNo1 == null)
{
keyboardNo1 = new StringBuffer();
}
if (keyboardNo2 != null)
{
keyboardNo2.append(value);
}
else
{
keyboardNo1.append(value);
}
}
int getKeyboardNo1()
{
if (keyboardNo1 == null)
return 1;
else
{
int value = Integer.parseInt(keyboardNo1.toString());
keyboardNo1 = null;
return value;
}
}
int getKeyboardNo2()
{
if (keyboardNo2 == null)
return 1;
else
{
int value = Integer.parseInt(keyboardNo2.toString());
keyboardNo2 = null;
return value;
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
mouseWheelPressed = false;
if (!editingSeqs)
{
doMouseReleasedDefineMode(evt);
return;
}
endEditing();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
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;
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);
}
lastMessage = tmp;
}
public void highlightSequence(SearchResults results)
{
if (av.followHighlight)
{
ap.scrollToPosition(results, false);
}
seqCanvas.highlightSearchResults(results);
}
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
// repaint();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
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.alignment.findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
{
if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
{
if (tooltipText.length() > 6)
{
tooltipText.append("
");
}
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.showSequenceFeatures)
{
int rpos;
SequenceFeature[] features = findFeaturesAtRes(sequence
.getDatasetSequence(), rpos = sequence.findPosition(res));
appendFeatures(tooltipText, linkImageURL.toString(), rpos, features);
}
if (tooltipText.length() == 6) //
{
setToolTipText(null);
}
else
{
tooltipText.append("");
if (lastTooltip == null
|| !lastTooltip.equals(tooltipText.toString()))
setToolTipText(tooltipText.toString());
lastTooltip = tooltipText.toString();
}
}
/**
* appends the features at rpos to the given stringbuffer ready for display in a tooltip
* @param tooltipText2
* @param linkImageURL
* @param rpos
* @param features
* TODO refactor to Jalview 'utilities' somehow.
*/
public static void appendFeatures(StringBuffer tooltipText2, String linkImageURL,
int rpos, SequenceFeature[] features)
{
String tmpString;
if (features != null)
{
for (int i = 0; i < features.length; i++)
{
if (features[i].getType().equals("disulfide bond"))
{
if (features[i].getBegin() == rpos
|| features[i].getEnd() == rpos)
{
if (tooltipText2.length() > 6)
{
tooltipText2.append("
");
}
tooltipText2.append("disulfide bond " + features[i].getBegin()
+ ":" + features[i].getEnd());
if (features[i].links != null)
{
tooltipText2.append(" ![](\"")
");
}
}
}
else
{
if (tooltipText2.length() > 6)
{
tooltipText2.append("
");
}
tooltipText2.append(features[i].getType() + " ");
if (rpos!=0)
{
// we are marking a positional feature
tooltipText2.append(features[i].begin);
}
if (features[i].begin != features[i].end)
{
tooltipText2.append(" " + features[i].end);
}
if (features[i].getDescription() != null
&& !features[i].description.equals(features[i]
.getType()))
{
tmpString = features[i].getDescription();
int startTag = tmpString.toUpperCase().indexOf("");
if (startTag > -1)
{
tmpString = tmpString.substring(startTag + 6);
}
int endTag = tmpString.toUpperCase().indexOf("");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
}
endTag = tmpString.toUpperCase().indexOf("");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
}
if (startTag > -1)
{
tooltipText2.append("; " + tmpString);
}
else
{
if (tmpString.indexOf("<") > -1
|| tmpString.indexOf(">") > -1)
{
// The description does not specify html is to
// be used, so we must remove < > symbols
tmpString = tmpString.replaceAll("<", "<");
tmpString = tmpString.replaceAll(">", ">");
tooltipText2.append("; ");
tooltipText2.append(tmpString);
}
else
{
tooltipText2.append("; " + tmpString);
}
}
}
if (features[i].getScore()!=Float.NaN)
{
tooltipText2.append(" Score="+features[i].getScore());
}
if (features[i].getValue("status") != null)
{
String status = features[i].getValue("status").toString();
if (status.length() > 0)
{
tooltipText2.append("; (" + features[i].getValue("status")
+ ")");
}
}
if (features[i].links != null)
{
tooltipText2.append(" ");
}
}
}
}
}
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)
{
int pos = -1;
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+ sequence.getName());
Object obj = null;
if (av.alignment.isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
if (obj != null)
{
text.append(" Nucleotide: ");
}
}
else
{
obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
if (obj != null)
{
text.append(" Residue: ");
}
}
if (obj != null)
{
pos = sequence.findPosition(res);
if (obj != "")
{
text.append(obj + " (" + pos + ")");
}
}
ap.alignFrame.statusBar.setText(text.toString());
return pos;
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
{
int oldWidth = av.charWidth;
// 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));
av.charWidth = oldWidth;
ap.fontChanged();
}
else
{
if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
{
av.charWidth--;
}
else if (evt.getX() > lastMousePress.getX())
{
av.charWidth++;
}
ap.paintAlignment(false);
}
FontMetrics fm = getFontMetrics(av.getFont());
av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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, res);
}
else
{
editSequence(true, res);
}
mouseDragging = true;
if (scrollThread != null)
{
scrollThread.setEvent(evt);
}
}
synchronized void editSequence(boolean insertGap, int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
SequenceI seq = av.alignment.getSequenceAt(startseq);
// No group, but the sequence may represent a group
if (!groupEditing && av.hasHiddenRows)
{
if (av.hiddenRepSequences != null
&& av.hiddenRepSequences.containsKey(seq))
{
sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
groupEditing = true;
}
}
StringBuffer message = new StringBuffer();
if (groupEditing)
{
message.append("Edit group:");
if (editCommand == null)
{
editCommand = new EditCommand("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("Edit " + 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.hiddenRepSequences)
.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.hiddenRepSequences == null
|| !av.hiddenRepSequences.containsKey(seq))
{
endEditing();
return;
}
sg = (SequenceGroup) av.hiddenRepSequences.get(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)
{
Vector vseqs = sg.getSequences(av.hiddenRepSequences);
int g, groupSize = vseqs.size();
SequenceI[] groupSeqs = new SequenceI[groupSize];
for (g = 0; g < groupSeqs.length; g++)
{
groupSeqs[g] = (SequenceI) vseqs.elementAt(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.alignment.getWidth() - 1)
{
sg.setEndRes(av.alignment.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.alignment.getHeight())
{
if ((av.hasHiddenColumns && startres < av.getColumnSelection()
.getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
int alWidth = av.alignment.getWidth();
if (av.hasHiddenRows)
{
int hwidth = av.alignment.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
{
editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
startres, startres - lastres, av.alignment, true);
}
}
else
{
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j > startres; j--)
{
deleteChar(startres, groupSeqs, fixedRight);
}
}
else
{
editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
startres, lastres - startres, av.alignment, true);
}
}
}
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
{
editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.alignment, true);
}
}
else
{
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
for (int j = lastres; j > startres; j--)
{
if (!jalview.util.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 (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
{
break;
}
max++;
}
if (max > 0)
{
editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
{ seq }, startres, max, av.alignment, true);
}
}
}
}
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;
}
}
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
av.alignment, true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
av.alignment, true);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
{
oldSeq = 0;
}
if (scrollThread != null)
{
scrollThread.running = false;
scrollThread = null;
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
{
return;
}
if (mouseDragging)
{
scrollThread = new ScrollThread();
}
}
public void mouseClicked(MouseEvent evt)
{
SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
if (av.getSelectionGroup().getSize() == 1
&& av.getSelectionGroup().getEndRes()
- av.getSelectionGroup().getStartRes() < 2)
{
av.setSelectionGroup(null);
}
SequenceFeature[] features = findFeaturesAtRes(sequence
.getDatasetSequence(), sequence.findPosition(findRes(evt)));
if (features != null && features.length > 0)
{
SearchResults highlight = new SearchResults();
highlight.addResult(sequence, features[0].getBegin(), features[0]
.getEnd());
seqCanvas.highlightSearchResults(highlight);
}
if (features != null && features.length > 0)
{
seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
{ sequence }, features, false, ap);
seqCanvas.highlightSearchResults(null);
}
}
}
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
if (e.getWheelRotation() > 0)
{
ap.scrollUp(false);
}
else
{
ap.scrollUp(true);
}
}
/**
* 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.wrapAlignment && seq > av.alignment.getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
"Cannot edit annotations in wrapped view.",
"Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
return;
}
if (seq < 0 || res < 0)
{
return;
}
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
if ((sequence == null) || (res > sequence.getLength()))
{
return;
}
stretchGroup = av.getSelectionGroup();
if (stretchGroup == null)
{
stretchGroup = av.alignment.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.alignment.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))
{
SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
.getDatasetSequence(), sequence.findPosition(res));
Vector links = new Vector();
for (int i = 0; i < allFeatures.length; i++)
{
if (allFeatures[i].links != null)
{
for (int j = 0; j < allFeatures[i].links.size(); j++)
{
links.addElement(allFeatures[i].links.elementAt(j));
}
}
}
jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
pop.show(this, evt.getX(), evt.getY());
return;
}
if (av.cursorMode)
{
seqCanvas.cursorX = findRes(evt);
seqCanvas.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;
}
if (stretchGroup.cs != null)
{
if (stretchGroup.cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
.getSequences(av.hiddenRepSequences), stretchGroup
.getWidth());
}
if (stretchGroup.cs instanceof Blosum62ColourScheme
|| stretchGroup.cs instanceof PIDColourScheme
|| stretchGroup.cs.conservationApplied()
|| stretchGroup.cs.getThreshold() > 0)
{
stretchGroup.recalcConservation();
}
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.alignment.getWidth())
{
res = av.alignment.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.alignment.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;
}
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.alignment.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.
*/
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
SelectionSource source)
{
// TODO: fix this hack - source of messages is align viewport, but SeqPanel handles selection messages...
if (av==source)
{
return;
}
// do we want to thread this ? (contention with seqsel and colsel locks, I suspect)
boolean repaint=false;
if (av.followSelection)
{
if (av.selectionGroup==null || !av.isSelectionGroupChanged())
{
SequenceGroup sgroup = (seqsel!=null) ? seqsel.intersect(av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences : null)
: null;
if (sgroup!=null && sgroup.getSize()>0)
{
av.setSelectionGroup(sgroup);
} else {
av.setSelectionGroup(null);
}
repaint = av.isSelectionGroupChanged();
}
if (av.colSel==null || !av.isColSelChanged())
{
// Check to see if the current selection is from a previous message
if (colsel==null || colsel.size()==0)
{
av.colSel.clear();
} else {
av.colSel = new ColumnSelection(colsel);
}
repaint |= av.isColSelChanged();
}
}
if (repaint)
{
// probably finessing with multiple redraws here
PaintRefresher.Refresh(this, av.getSequenceSetId());
// ap.paintAlignment(false);
}
}
}