/*
- * 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
+ * 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
+ *
+ * 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 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
+ * 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/>.
*/
package jalview.gui;
import java.util.*;
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import jalview.commands.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
*/
public class SeqPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener, SequenceListener, SelectionListener
+ MouseMotionListener, MouseWheelListener, SequenceListener,
+ SelectionListener
{
/** DOCUMENT ME!! */
/**
* Creates a new SeqPanel object.
- *
+ *
* @param avp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param p
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
}
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)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
- .getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.getAlignment().getHeight() - 1);
}
else
{
seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
+ av.getAlignment().getHeight() - 1);
}
return seq;
void setCursorPosition()
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
- int maxWidth = av.alignment.getWidth();
+ int maxWidth = av.getAlignment().getWidth();
- while (!av.colSel.isVisible(seqCanvas.cursorX)
+ while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
+ || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
{
seqCanvas.cursorX = 0;
}
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
{
- seqCanvas.cursorX = av.alignment.getWidth() - 1;
+ seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
}
if (seqCanvas.cursorY < 0)
{
seqCanvas.cursorY = 0;
}
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
{
- seqCanvas.cursorY = av.alignment.getHeight() - 1;
+ seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
}
endEditing();
}
if (!av.wrapAlignment)
{
- while (seqCanvas.cursorX < av.colSel
+ while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
{
if (!ap.scrollRight(false))
break;
}
}
- while (seqCanvas.cursorX > av.colSel
+ while (seqCanvas.cursorX > av.getColumnSelection()
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
}
}
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
- SequenceGroup sg = av.selectionGroup;
+ SequenceGroup sg = av.getSelectionGroup();
// Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
+ int min = av.getAlignment().getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
- int index = av.alignment.findIndex(sg.getSequenceAt(i));
+ int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
if (index > max)
{
max = index;
sg.getSequences(null).clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
- editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+ editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX + getKeyboardNo1();
- editSequence(false, seqCanvas.cursorX);
+ 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)
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
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);
+ ssm.mouseOverSequence(sequence, index, pos, av);
}
lastMessage = tmp;
}
+ @Override
public void highlightSequence(SearchResults results)
{
if (av.followHighlight)
{
- ap.scrollToPosition(results, false);
+ if (ap.scrollToPosition(results, false))
+ {
+ seqCanvas.revalidate();
+ }
}
seqCanvas.highlightSearchResults(results);
}
+ @Override
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
if (editingSeqs)
tooltipText.setLength(6); // Cuts the buffer back to <html>
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
if (av.showSequenceFeatures)
{
int rpos;
- SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), rpos = sequence.findPosition(res));
- appendFeatures(tooltipText, linkImageURL.toString(), rpos, features);
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
+ appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
+ this.ap.seqPanel.seqCanvas.fr.minmax);
}
if (tooltipText.length() == 6) // <html></html>
{
setToolTipText(null);
+ lastTooltip = null;
}
else
{
tooltipText.append("</html>");
if (lastTooltip == null
|| !lastTooltip.equals(tooltipText.toString()))
+ {
setToolTipText(tooltipText.toString());
+ lastTooltip = tooltipText.toString();
+ }
- 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;
+ }
+
/**
- * appends the features at rpos to the given stringbuffer ready for display in a tooltip
+ * 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.
+ * TODO refactor to Jalview 'utilities' somehow.
*/
- public static void appendFeatures(StringBuffer tooltipText2, String linkImageURL,
- int rpos, SequenceFeature[] features)
+ public void appendFeatures(StringBuffer tooltipText2,
+ String linkImageURL, int rpos, SequenceFeature[] features)
+ {
+ appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
+ }
+
+ public void appendFeatures(StringBuffer tooltipText2, String string,
+ int rpos, SequenceFeature[] features, Hashtable minmax)
{
String tmpString;
if (features != null)
{
tooltipText2.append("<br>");
}
-
- 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()))
+ // TODO: remove this hack to display link only features
+ boolean linkOnly = features[i].getValue("linkonly") != null;
+ if (!linkOnly)
{
- tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("<HTML>");
- if (startTag > -1)
- {
- tmpString = tmpString.substring(startTag + 6);
- }
- int endTag = tmpString.toUpperCase().indexOf("</BODY>");
- if (endTag > -1)
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
{
- tmpString = tmpString.substring(0, endTag);
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
}
- endTag = tmpString.toUpperCase().indexOf("</HTML>");
- if (endTag > -1)
+ if (features[i].begin != features[i].end)
{
- tmpString = tmpString.substring(0, endTag);
+ tooltipText2.append(" " + features[i].end);
}
- if (startTag > -1)
- {
- tooltipText2.append("; " + tmpString);
- }
- else
+ if (features[i].getDescription() != null
+ && !features[i].description.equals(features[i]
+ .getType()))
{
- if (tmpString.indexOf("<") > -1
- || tmpString.indexOf(">") > -1)
+ tmpString = features[i].getDescription();
+ String tmp2up=tmpString.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -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);
+ tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag+6);
+ }
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
+ if (startTag > -1)
+ {
+ tooltipText2.append("; " + tmpString);
}
else
{
- tooltipText2.append("; " + tmpString);
+ 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].getValue("status") != null)
- {
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
+ // check score should be shown
+ if (features[i].getScore() != Float.NaN)
{
- tooltipText2.append("; (" + features[i].getValue("status")
- + ")");
+ float[][] rng = (minmax == null) ? null : ((float[][]) minmax
+ .get(features[i].getType()));
+ if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
+ {
+ 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(" <img src=\"" + linkImageURL + "\">");
/**
* Set status message in alignment panel
- *
+ *
* @param sequence
- * aligned sequence object
+ * aligned sequence object
* @param res
- * alignment column
+ * alignment column
* @param seq
- * index of sequence in alignment
+ * index of sequence in alignment
* @return position of res in sequence
*/
int setStatusMessage(SequenceI sequence, int res, int seq)
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
- .getX()
- - lastMousePress.getX()))
+ .getX() - lastMousePress.getX()))
{
int fontSize = av.font.getSize();
fontSize = 1;
}
- av
- .setFont(new Font(av.font.getName(), av.font.getStyle(),
- fontSize));
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
av.charWidth = oldWidth;
ap.fontChanged();
}
if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
- editSequence(false, res);
+ editSequence(false, false,res);
}
else
{
- editSequence(true, res);
+ editSequence(true, false,res);
}
mouseDragging = true;
}
}
- synchronized void editSequence(boolean insertGap, 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;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
// No group, but the sequence may represent a group
- if (!groupEditing && av.hasHiddenRows)
+ if (!groupEditing && av.hasHiddenRows())
{
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
// Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences)
+ || (sg != null && sg.getSequences(av.getHiddenRepSequences())
.contains(seq)))
{
fixedColumns = true;
// but the sequence represents a group
if (sg == null)
{
- if (av.hiddenRepSequences == null
- || !av.hiddenRepSequences.containsKey(seq))
+ if (!av.isHiddenRepSequence(seq))
{
endEditing();
return;
}
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
}
fixedLeft = sg.getStartRes();
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+ List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
int g, groupSize = vseqs.size();
SequenceI[] groupSeqs = new SequenceI[groupSize];
for (g = 0; g < groupSeqs.length; g++)
{
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+ groupSeqs[g] = vseqs.get(g);
}
// drag to right
// 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.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
if (!blank)
{
- if (sg.getSize() == av.alignment.getHeight())
+ if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns && startres < av.getColumnSelection()
+ if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
.getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
- int alWidth = av.alignment.getWidth();
- if (av.hasHiddenRows)
+ int alWidth = av.getAlignment().getWidth();
+ if (av.hasHiddenRows())
{
- int hwidth = av.alignment.getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences().getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
else
{
editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.alignment, true);
+ startres, startres - lastres, av.getAlignment(), true);
}
}
else
else
{
editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.alignment, true);
+ startres, lastres - startres, av.getAlignment(), true);
}
}
else
{
editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.alignment, true);
- }
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ }
}
else
{
+ if(!editSeq){
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
if (max > 0)
{
editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.alignment, true);
+ { seq }, startres, max, av.getAlignment(), true);
}
}
+ }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);
+ }
+ }
}
}
}
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
- av.alignment, true);
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
+ editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
- av.alignment, true);
+ av.getAlignment(), true);
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
/**
* DOCUMENT ME!
- *
+ *
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceGroup sg = null;
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
- if (av.getSelectionGroup().getSize() == 1
- && av.getSelectionGroup().getEndRes()
- - av.getSelectionGroup().getStartRes() < 2)
+ sg = av.getSelectionGroup();
+ if (sg != null && sg.getSize() == 1
+ && sg.getEndRes() - sg.getStartRes() < 2)
{
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(findRes(evt)));
+ 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());
+ highlight.addResult(sequence, features[0].getBegin(),
+ features[0].getEnd());
seqCanvas.highlightSearchResults(highlight);
}
if (features != null && features.length > 0)
}
}
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
{
ap.scrollUp(true);
}
+ // TODO Update tooltip for new position.
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
startWrapBlock = wrappedBlock;
- if (av.wrapAlignment && seq > av.alignment.getHeight())
+ if (av.wrapAlignment && seq > av.getAlignment().getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
"Cannot edit annotations in wrapped view.",
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if ((sequence == null) || (res > sequence.getLength()))
{
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
&& (res < stretchGroup.getEndRes()))
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(res));
+ SequenceFeature[] allFeatures = findFeaturesAtRes(
+ sequence.getDatasetSequence(), sequence.findPosition(res));
Vector links = new Vector();
for (int i = 0; i < allFeatures.length; i++)
{
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
-
+
stretchGroup = sg;
if (av.getConservationSelected())
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMouseReleasedDefineMode(MouseEvent evt)
{
return;
}
+ stretchGroup.recalcConservation(); // always do this - annotation has own
+ // state
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();
+ ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
+ stretchGroup,av.getHiddenRepSequences());
}
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
- .getName());
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
else
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
- .getName());
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
}
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ ap.paintAlignment(true);
changeEndRes = false;
changeStartRes = false;
/**
* DOCUMENT ME!
- *
+ *
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
return;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.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.
running = false;
}
+ @Override
public void run()
{
running = true;
}
if (mouseDragging && (evt.getY() >= getHeight())
- && (av.alignment.getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getEndSeq()))
{
running = ap.scrollUp(false);
}
}
}
}
+
/**
* 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...
- if (av==source)
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ if (av == source
+ || !av.followSelection
+ || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ || (source instanceof AlignViewport && ((AlignViewport) source)
+ .getSequenceSetId().equals(av.getSequenceSetId())))
{
return;
}
- // do we want to thread this ? (contention with seqsel and colsel locks, I suspect)
- boolean repaint=false;
- if (av.followSelection)
+ // 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))
{
- if (av.selectionGroup==null || !av.isSelectionGroupChanged())
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize()>0)
{
- SequenceGroup sgroup = (seqsel!=null) ? seqsel.intersect(av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences : null)
- : null;
- if (sgroup!=null && sgroup.getSize()>0)
+ if (av.getAlignment() == null)
+ {
+ jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+ if ((sgroup == null || sgroup.getSize() == 0)
+ || (colsel == null || colsel.size() == 0))
{
- av.setSelectionGroup(sgroup);
- } else {
- av.setSelectionGroup(null);
+ // don't copy columns if the region didn't intersect.
+ copycolsel = false;
}
- repaint = av.isSelectionGroupChanged();
}
- if (av.colSel==null || !av.isColSelChanged())
+ 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)
{
- // Check to see if the current selection is from a previous message
- if (colsel==null || colsel.size()==0)
+ if (av.getColumnSelection() != null)
{
- av.colSel.clear();
- } else {
- av.colSel = new ColumnSelection(colsel);
- }
- repaint |= av.isColSelChanged();
+ 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)
{
git://source.jalview.org / jalview.git / blobdiff