/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 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.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
+public class SeqPanel extends JPanel implements MouseListener,
+ MouseMotionListener, MouseWheelListener, SequenceListener,
+ SelectionListener
{
/** DOCUMENT ME!! */
/** 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
- //////////////////////////////////////////
+ // ////////////////////////////////////////
+ // ///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("<html>");
+
String tmpString;
EditCommand editCommand;
StructureSelectionManager ssm;
-
/**
* Creates a new SeqPanel object.
- *
- * @param avp DOCUMENT ME!
- * @param p DOCUMENT ME!
+ *
+ * @param avp
+ * DOCUMENT ME!
+ * @param p
+ * 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);
}
}
int startWrapBlock = -1;
+
int wrappedBlock = -1;
+
int findRes(MouseEvent evt)
{
int res = 0;
hgap += av.charHeight;
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + seqCanvas.getAnnotationHeight();
int y = evt.getY();
y -= hgap;
}
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();
}
hgap += av.charHeight;
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + seqCanvas.getAnnotationHeight();
y -= hgap;
- seq = Math.min( (y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.alignment.getHeight() - 1);
}
else
{
- seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
+ av.alignment.getHeight() - 1);
}
return seq;
for (int i = 0; i < features.length; i++)
{
if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(features[i].getType()))
+ || !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())
+ && 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))
+ if ((features[i].getBegin() <= res)
+ && (features[i].getEnd() >= res))
{
tmp.addElement(features[i]);
}
return features;
}
-
void endEditing()
{
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null,
- av.getAlignment().getSequences());
+ av.firePropertyChange("alignment", null, av.getAlignment()
+ .getSequences());
}
startseq = -1;
void setCursorPosition()
{
- SequenceI sequence =
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(
- getKeyboardNo1() - 1
- );
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
scrollToVisible();
}
int maxWidth = av.alignment.getWidth();
while (!av.colSel.isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth
- && seqCanvas.cursorX > 0)
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
+ || !av.colSel.isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
}
if (!av.wrapAlignment)
{
- while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+ while (seqCanvas.cursorX < av.colSel
+ .adjustForHiddenColumns(av.startRes))
{
if (!ap.scrollRight(false))
{
break;
}
}
- while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+ while (seqCanvas.cursorX > av.colSel
+ .adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
{
}
}
setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
- seqCanvas.cursorX, seqCanvas.cursorY);
+ seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
}
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence =
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
SequenceGroup sg = av.selectionGroup;
- //Find the top and bottom of this group
+ // Find the top and bottom of this group
int min = av.alignment.getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
}
ap.paintAlignment(false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
return;
}
- if (evt.isShiftDown() || evt.isAltDown() ||
- evt.isControlDown())
+ if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
{
if (evt.isAltDown() || evt.isControlDown())
{
return;
}
- if ( (seq < av.getAlignment().getHeight()) &&
- (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ if ((seq < av.getAlignment().getHeight())
+ && (res < av.getAlignment().getSequenceAt(seq).getLength()))
{
startseq = seq;
lastres = res;
}
String lastMessage;
+
public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
- String tmp = sequence.hashCode()+" "+index+" "+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;
}
-
public void highlightSequence(SearchResults results)
{
- seqCanvas.highlightSearchResults(results);
+ if (av.followHighlight)
+ {
+ if (ap.scrollToPosition(results, false))
+ {
+ seqCanvas.revalidate();
+ }
+ }
+ seqCanvas.highlightSearchResults(results);
}
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
- //repaint();
+ // repaint();
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
}
pos = setStatusMessage(sequence, res, seq);
- if (ssm != null && pos>-1)
+ if (ssm != null && pos > -1)
mouseOverSequence(sequence, res, pos);
-
tooltipText.setLength(6); // Cuts the buffer back to <html>
SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
tooltipText.append("<br>");
}
- if (!groups[g].getName().startsWith("JTreeGroup") &&
- !groups[g].getName().startsWith("JGroup"))
+ if (!groups[g].getName().startsWith("JTreeGroup")
+ && !groups[g].getName().startsWith("JGroup"))
{
tooltipText.append(groups[g].getName());
}
// use aa to see if the mouse pointer is on a
if (av.showSequenceFeatures)
{
+ int rpos;
SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(), sequence.findPosition(res));
+ 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();
+ }
+
+ }
+
+ }
+
+ 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;
+ }
- if (features != null)
+ /**
+ * 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 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)
+ {
+ for (int i = 0; i < features.length; i++)
{
- for (int i = 0; i < features.length; i++)
+ if (features[i].getType().equals("disulfide bond"))
{
- if (features[i].getType().equals("disulfide bond"))
+ if (features[i].getBegin() == rpos
+ || features[i].getEnd() == rpos)
{
- if (features[i].getBegin() == sequence.findPosition(res)
- || features[i].getEnd() == sequence.findPosition(res))
+ if (tooltipText2.length() > 6)
{
- if (tooltipText.length() > 6)
- {
- tooltipText.append("<br>");
- }
- tooltipText.append("disulfide bond " + features[i].getBegin() +
- ":" +
- features[i].getEnd());
- if (features[i].links != null)
- {
- tooltipText.append(" <img src=\"" + linkImageURL + "\">");
- }
+ tooltipText2.append("<br>");
+ }
+ tooltipText2.append("disulfide bond " + features[i].getBegin()
+ + ":" + features[i].getEnd());
+ if (features[i].links != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
}
}
- else
+ }
+ else
+ {
+ if (tooltipText2.length() > 6)
{
- if (tooltipText.length() > 6)
+ tooltipText2.append("<br>");
+ }
+ // TODO: remove this hack to display link only features
+ boolean linkOnly = features[i].getValue("linkonly") != null;
+ if (!linkOnly)
+ {
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
{
- tooltipText.append("<br>");
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
}
-
- tooltipText.append(features[i].getType() + " " +
- features[i].begin);
if (features[i].begin != features[i].end)
{
- tooltipText.append(" " + features[i].end);
+ tooltipText2.append(" " + features[i].end);
}
if (features[i].getDescription() != null
- && !features[i].description.equals(features[i].getType()))
+ && !features[i].description.equals(features[i]
+ .getType()))
{
tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+ String tmp2up=tmpString.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
{
tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag+6);
}
- int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+ int endTag = tmp2up.indexOf("</BODY>");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
}
- endTag = tmpString.toUpperCase().indexOf("</HTML>");
+ endTag = tmp2up.indexOf("</HTML>");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
if (startTag > -1)
{
- tooltipText.append("; " + tmpString);
+ tooltipText2.append("; " + tmpString);
}
else
{
- if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
+ if (tmpString.indexOf("<") > -1
+ || tmpString.indexOf(">") > -1)
{
- //The description does not specify html is to
- //be used, so we must remove < > symbols
+ // The description does not specify html is to
+ // be used, so we must remove < > symbols
tmpString = tmpString.replaceAll("<", "<");
tmpString = tmpString.replaceAll(">", ">");
- tooltipText.append("; ");
- tooltipText.append(tmpString);
+ tooltipText2.append("; ");
+ tooltipText2.append(tmpString);
}
else
{
- tooltipText.append("; " + tmpString);
+ tooltipText2.append("; " + tmpString);
}
}
}
+ // check score should be shown
+ if (features[i].getScore() != Float.NaN)
+ {
+ 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)
{
- tooltipText.append("; (" + features[i].getValue("status") + ")");
+ tooltipText2.append("; (" + features[i].getValue("status")
+ + ")");
}
}
-
- if (features[i].links != null)
- {
- tooltipText.append(" <img src=\"" + linkImageURL + "\">");
- }
-
}
+ if (features[i].links != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+ }
+
}
}
}
-
- if (tooltipText.length() == 6) // <html></html>
- {
- setToolTipText(null);
- }
- else
- {
- tooltipText.append("</html>");
- if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString()))
- setToolTipText(tooltipText.toString());
-
- lastTooltip = tooltipText.toString();
- }
-
}
+
String lastTooltip;
/**
* Set status message in alignment panel
- * @param sequence aligned sequence object
- * @param res alignment column
- * @param seq index of sequence in alignment
+ *
+ * @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());
+ 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) +
- "");
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ + "");
if (obj != null)
{
text.append(" Nucleotide: ");
if (obj != null)
{
- pos=sequence.findPosition(res);
+ pos = sequence.findPosition(res);
if (obj != "")
{
- text.append(obj + " (" + pos +
- ")");
+ text.append(obj + " (" + pos + ")");
}
}
ap.alignFrame.statusBar.setText(text.toString());
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
{
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()))
+ // 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();
res = 0;
}
- if ( (lastres == -1) || (lastres == res))
+ if ((lastres == -1) || (lastres == res))
{
return;
}
- if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+ if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
editSequence(false, res);
}
}
-
-
synchronized void editSequence(boolean insertGap, int startres)
{
int fixedLeft = -1;
SequenceI seq = av.alignment.getSequenceAt(startseq);
- //No group, but the sequence may represent a group
+ // No group, but the sequence may represent a group
if (!groupEditing && av.hasHiddenRows)
{
if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ && av.hiddenRepSequences.containsKey(seq))
{
sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
groupEditing = true;
message.append(Math.abs(startres - lastres) + " gaps.");
ap.alignFrame.statusBar.setText(message.toString());
- //Are we editing within a selection group?
+ // Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+ || (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
+ // 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))
+ || !av.hiddenRepSequences.containsKey(seq))
{
endEditing();
return;
fixedLeft = sg.getStartRes();
fixedRight = sg.getEndRes();
- if ( (startres < fixedLeft && lastres >= fixedLeft)
- || (startres >= fixedLeft && lastres < fixedLeft)
- || (startres > fixedRight && lastres <= fixedRight)
- || (startres <= fixedRight && lastres > fixedRight))
+ if ((startres < fixedLeft && lastres >= fixedLeft)
+ || (startres >= fixedLeft && lastres < fixedLeft)
+ || (startres > fixedRight && lastres <= fixedRight)
+ || (startres <= fixedRight && lastres > fixedRight))
{
endEditing();
return;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
- if ( (insertGap && startres > y1 && lastres < y1)
- || (!insertGap && startres < y2 && lastres > y2))
+ 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
+ // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ // Selection spans a hidden region
if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
{
if (startres >= y2)
// drag to right
if (insertGap)
{
- //If the user has selected the whole sequence, and is dragging to
+ // 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
- )
+ if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
+ && sg.getEndRes() == av.alignment.getWidth() - 1)
{
sg.setEndRes(av.alignment.getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
// Find the next gap before the end
// of the visible region boundary
boolean blank = false;
- for (fixedRight = fixedRight;
- fixedRight > lastres;
- fixedRight--)
+ for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
{
blank = true;
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(fixedRight - j)))
+ if (!jalview.util.Comparison.isGap(groupSeqs[g]
+ .getCharAt(fixedRight - j)))
{
blank = false;
break;
{
if (sg.getSize() == av.alignment.getHeight())
{
- if ( (av.hasHiddenColumns
- &&
- startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns && startres < av.getColumnSelection()
+ .getHiddenBoundaryRight(startres)))
{
endEditing();
return;
alWidth = hwidth;
}
}
- //We can still insert gaps if the selectionGroup
- //contains all the sequences
+ // We can still insert gaps if the selectionGroup
+ // contains all the sequences
sg.setEndRes(sg.getEndRes() + startres - lastres);
fixedRight = alWidth + startres - lastres;
}
// drag to left
else if (!insertGap)
{
- /// Are we able to delete?
+ // / Are we able to delete?
// ie are all columns blank?
for (g = 0; g < groupSize; g++)
continue;
}
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- groupSeqs,
- startres, startres - lastres,
- av.alignment,
- true);
+ editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ startres, startres - lastres, av.alignment, true);
}
}
else
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- groupSeqs,
- startres, lastres - startres,
- av.alignment,
- true);
+ editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ startres, lastres - startres, av.alignment, true);
}
}
}
- else /////Editing a single sequence///////////
+ else
+ // ///Editing a single sequence///////////
{
if (insertGap)
{
for (int j = lastres; j < startres; j++)
{
insertChar(j, new SequenceI[]
- {seq}, fixedRight);
+ { seq }, fixedRight);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- new SequenceI[]
- {seq},
- lastres, startres - lastres,
- av.alignment,
- true);
+ editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.alignment, true);
}
}
else
break;
}
deleteChar(startres, new SequenceI[]
- {seq}, fixedRight);
+ { seq }, fixedRight);
}
}
else
{
- //could be a keyboard edit trying to delete none gaps
+ // could be a keyboard edit trying to delete none gaps
int max = 0;
for (int m = startres; m < lastres; m++)
{
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- new SequenceI[]
- {seq},
- startres, max,
- av.alignment,
- true);
+ editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+ { seq }, startres, max, av.alignment, true);
}
}
}
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
+ // 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
+ // Theres a space, so break and insert the gap
break;
}
}
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- blankColumn, 1, av.alignment, true);
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ av.alignment, true);
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- j, 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.DELETE_GAP, seq, j, 1, av.alignment,
+ true);
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- fixedColumn, 1, av.alignment, true);
+ editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ av.alignment, true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent e)
{
public void mouseClicked(MouseEvent evt)
{
+ SequenceGroup sg = null;
SequenceI sequence = av.alignment.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))
- );
+ 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)
{
- seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[]
- {sequence}, features, false, ap);
+ 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);
- }
+ if (e.getWheelRotation() > 0)
+ {
+ ap.scrollUp(false);
+ }
+ else
+ {
+ ap.scrollUp(true);
+ }
+ // TODO Update tooltip for new position.
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
if (av.wrapAlignment && seq > av.alignment.getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit",
- JOptionPane.WARNING_MESSAGE);
+ "Cannot edit annotations in wrapped view.",
+ "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
return;
}
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
- if ( (sequence == null) || (res > sequence.getLength()))
+ if ((sequence == null) || (res > sequence.getLength()))
{
return;
}
{
stretchGroup = av.alignment.findGroup(sequence);
- if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
- (res < stretchGroup.getEndRes()))
+ if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
+ && (res < stretchGroup.getEndRes()))
{
av.setSelectionGroup(stretchGroup);
}
stretchGroup = null;
}
}
- else if (!stretchGroup.getSequences(null).contains(sequence) ||
- (stretchGroup.getStartRes() > res) ||
- (stretchGroup.getEndRes() < res))
+ else if (!stretchGroup.getSequences(null).contains(sequence)
+ || (stretchGroup.getStartRes() > res)
+ || (stretchGroup.getEndRes() < res))
{
stretchGroup = null;
{
for (int i = 0; i < allGroups.length; i++)
{
- if ( (allGroups[i].getStartRes() <= res) &&
- (allGroups[i].getEndRes() >= res))
+ if ((allGroups[i].getStartRes() <= res)
+ && (allGroups[i].getEndRes() >= res))
{
stretchGroup = allGroups[i];
break;
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++)
{
if (stretchGroup == null)
{
- //Only if left mouse button do we want to change group sizes
+ // Only if left mouse button do we want to change group sizes
// define a new group here
SequenceGroup sg = new SequenceGroup();
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
+
stretchGroup = sg;
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap,
- av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+ "Background");
}
if (av.getAbovePIDThreshold())
{
SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ "Background");
}
- if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
{
// Edit end res position of selected group
changeEndRes = true;
}
- else if ( (stretchGroup != null) &&
- (stretchGroup.getStartRes() == res))
+ else if ((stretchGroup != null)
+ && (stretchGroup.getStartRes() == res))
{
// Edit end res position of selected group
changeStartRes = true;
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * 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).resetClustalX(
+ stretchGroup.getSequences(av.hiddenRepSequences),
+ stretchGroup.getWidth());
}
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
+ stretchGroup.getName());
}
else
{
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ stretchGroup.getName());
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
}
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ ap.paintAlignment(true);
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
-
+ av.sendSelection();
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
dragDirection = -1;
}
- while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
{
// This routine ensures we don't skip any sequences, as the
// selection is quite slow.
}
// this class allows scrolling off the bottom of the visible alignment
- class ScrollThread
- extends Thread
+ class ScrollThread extends Thread
{
MouseEvent evt;
+
boolean running = false;
public ScrollThread()
{
if (evt != null)
{
- if (mouseDragging && (evt.getY() < 0) &&
- (av.getStartSeq() > 0))
+ if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
{
running = ap.scrollUp(true);
}
- if (mouseDragging && (evt.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
+ if (mouseDragging && (evt.getY() >= getHeight())
+ && (av.alignment.getHeight() > av.getEndSeq()))
{
running = ap.scrollUp(false);
}
try
{
Thread.sleep(20);
+ } catch (Exception ex)
+ {
}
- 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...
+ // 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)
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false, copycolsel = true;
+ // if (!av.isSelectionGroupChanged(false))
+ {
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize()>0)
+ {
+ if (av.alignment == 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.alignment,
+ (av.hasHiddenRows) ? av.hiddenRepSequences : 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.colSel != null)
+ {
+ av.colSel.clear();
+ repaint=true;
+ }
+ }
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.colSel == null)
+ {
+ av.colSel = new ColumnSelection(colsel);
+ }
+ else
{
+ av.colSel.setElementsFrom(colsel);
}
}
+ av.isColSelChanged(true);
+ repaint = true;
+ }
+ if (copycolsel && av.hasHiddenColumns
+ && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint)
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
}
}
}
git://source.jalview.org / jalview.git / blobdiff