2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
24 import java.awt.event.*;
\r
25 import javax.swing.*;
\r
27 import jalview.commands.*;
\r
28 import jalview.datamodel.*;
\r
29 import jalview.schemes.*;
\r
30 import jalview.structure.*;
\r
36 * @version $Revision$
\r
38 public class SeqPanel
\r
39 extends JPanel implements MouseListener,
\r
40 MouseMotionListener, MouseWheelListener, SequenceListener
\r
43 /** DOCUMENT ME!! */
\r
44 public SeqCanvas seqCanvas;
\r
46 /** DOCUMENT ME!! */
\r
47 public AlignmentPanel ap;
\r
48 protected int lastres;
\r
49 protected int startseq;
\r
50 protected AlignViewport av;
\r
52 ScrollThread scrollThread = null;
\r
53 boolean mouseDragging = false;
\r
54 boolean editingSeqs = false;
\r
55 boolean groupEditing = false;
\r
57 //////////////////////////////////////////
\r
58 /////Everything below this is for defining the boundary of the rubberband
\r
59 //////////////////////////////////////////
\r
61 boolean changeEndSeq = false;
\r
62 boolean changeStartSeq = false;
\r
63 boolean changeEndRes = false;
\r
64 boolean changeStartRes = false;
\r
65 SequenceGroup stretchGroup = null;
\r
66 boolean remove = false;
\r
68 Point lastMousePress;
\r
69 boolean mouseWheelPressed = false;
\r
70 StringBuffer keyboardNo1;
\r
71 StringBuffer keyboardNo2;
\r
73 java.net.URL linkImageURL;
\r
75 StringBuffer tooltipText = new StringBuffer("<html>");
\r
78 EditCommand editCommand;
\r
80 StructureSelectionManager ssm;
\r
84 * Creates a new SeqPanel object.
\r
86 * @param avp DOCUMENT ME!
\r
87 * @param p DOCUMENT ME!
\r
89 public SeqPanel(AlignViewport av, AlignmentPanel ap)
\r
91 linkImageURL = getClass().getResource("/images/link.gif");
\r
92 ToolTipManager.sharedInstance().registerComponent(this);
\r
93 ToolTipManager.sharedInstance().setInitialDelay(0);
\r
94 ToolTipManager.sharedInstance().setDismissDelay(10000);
\r
96 setBackground(Color.white);
\r
98 seqCanvas = new SeqCanvas(ap);
\r
99 setLayout(new BorderLayout());
\r
100 add(seqCanvas, BorderLayout.CENTER);
\r
104 if (!av.isDataset())
\r
106 addMouseMotionListener(this);
\r
107 addMouseListener(this);
\r
108 addMouseWheelListener(this);
\r
109 ssm = StructureSelectionManager.getStructureSelectionManager();
\r
110 ssm.addStructureViewerListener(this);
\r
114 int startWrapBlock = -1;
\r
115 int wrappedBlock = -1;
\r
116 int findRes(MouseEvent evt)
\r
119 int x = evt.getX();
\r
121 if (av.wrapAlignment)
\r
124 int hgap = av.charHeight;
\r
125 if (av.scaleAboveWrapped)
\r
127 hgap += av.charHeight;
\r
130 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
131 + hgap + seqCanvas.getAnnotationHeight();
\r
133 int y = evt.getY();
\r
135 x -= seqCanvas.LABEL_WEST;
\r
137 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
\r
143 wrappedBlock = y / cHeight;
\r
144 wrappedBlock += av.getStartRes() / cwidth;
\r
146 res = wrappedBlock * cwidth + x / av.getCharWidth();
\r
151 res = (x / av.getCharWidth()) + av.getStartRes();
\r
154 if (av.hasHiddenColumns)
\r
156 res = av.getColumnSelection().adjustForHiddenColumns(res);
\r
163 int findSeq(MouseEvent evt)
\r
166 int y = evt.getY();
\r
168 if (av.wrapAlignment)
\r
170 int hgap = av.charHeight;
\r
171 if (av.scaleAboveWrapped)
\r
173 hgap += av.charHeight;
\r
176 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
177 + hgap + seqCanvas.getAnnotationHeight();
\r
181 seq = Math.min( (y % cHeight) / av.getCharHeight(),
\r
182 av.alignment.getHeight() - 1);
\r
186 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
\r
187 av.alignment.getHeight() - 1);
\r
193 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
\r
195 Vector tmp = new Vector();
\r
196 SequenceFeature[] features = sequence.getSequenceFeatures();
\r
197 if (features != null)
\r
199 for (int i = 0; i < features.length; i++)
\r
201 if (av.featuresDisplayed == null
\r
202 || !av.featuresDisplayed.containsKey(features[i].getType()))
\r
207 if (features[i].featureGroup != null
\r
208 && seqCanvas.fr.featureGroups!=null
\r
209 && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)
\r
210 && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())
\r
214 if ( (features[i].getBegin() <= res) &&
\r
215 (features[i].getEnd() >= res))
\r
217 tmp.addElement(features[i]);
\r
222 features = new SequenceFeature[tmp.size()];
\r
223 tmp.copyInto(features);
\r
231 if (editCommand != null && editCommand.getSize() > 0)
\r
233 ap.alignFrame.addHistoryItem(editCommand);
\r
234 av.firePropertyChange("alignment", null,
\r
235 av.getAlignment().getSequences());
\r
240 editingSeqs = false;
\r
241 groupEditing = false;
\r
242 keyboardNo1 = null;
\r
243 keyboardNo2 = null;
\r
244 editCommand = null;
\r
247 void setCursorRow()
\r
249 seqCanvas.cursorY = getKeyboardNo1() - 1;
\r
253 void setCursorColumn()
\r
255 seqCanvas.cursorX = getKeyboardNo1() - 1;
\r
259 void setCursorRowAndColumn()
\r
261 if (keyboardNo2 == null)
\r
263 keyboardNo2 = new StringBuffer();
\r
267 seqCanvas.cursorX = getKeyboardNo1() - 1;
\r
268 seqCanvas.cursorY = getKeyboardNo2() - 1;
\r
273 void setCursorPosition()
\r
275 SequenceI sequence =
\r
276 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
\r
278 seqCanvas.cursorX = sequence.findIndex(
\r
279 getKeyboardNo1() - 1
\r
284 void moveCursor(int dx, int dy)
\r
286 seqCanvas.cursorX += dx;
\r
287 seqCanvas.cursorY += dy;
\r
288 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
\r
290 int original = seqCanvas.cursorX - dx;
\r
291 int maxWidth = av.alignment.getWidth();
\r
293 while (!av.colSel.isVisible(seqCanvas.cursorX)
\r
294 && seqCanvas.cursorX < maxWidth
\r
295 && seqCanvas.cursorX > 0)
\r
297 seqCanvas.cursorX += dx;
\r
300 if (seqCanvas.cursorX >= maxWidth
\r
301 || !av.colSel.isVisible(seqCanvas.cursorX))
\r
303 seqCanvas.cursorX = original;
\r
310 void scrollToVisible()
\r
312 if (seqCanvas.cursorX < 0)
\r
314 seqCanvas.cursorX = 0;
\r
316 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
\r
318 seqCanvas.cursorX = av.alignment.getWidth() - 1;
\r
321 if (seqCanvas.cursorY < 0)
\r
323 seqCanvas.cursorY = 0;
\r
325 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
\r
327 seqCanvas.cursorY = av.alignment.getHeight() - 1;
\r
331 if (av.wrapAlignment)
\r
333 ap.scrollToWrappedVisible(seqCanvas.cursorX);
\r
337 while (seqCanvas.cursorY < av.startSeq)
\r
341 while (seqCanvas.cursorY + 1 > av.endSeq)
\r
343 ap.scrollUp(false);
\r
345 if (!av.wrapAlignment)
\r
347 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
\r
349 if (!ap.scrollRight(false))
\r
354 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
\r
356 if (!ap.scrollRight(true))
\r
363 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
\r
364 seqCanvas.cursorX, seqCanvas.cursorY);
\r
366 seqCanvas.repaint();
\r
369 void setSelectionAreaAtCursor(boolean topLeft)
\r
371 SequenceI sequence =
\r
372 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
\r
374 if (av.getSelectionGroup() != null)
\r
376 SequenceGroup sg = av.selectionGroup;
\r
377 //Find the top and bottom of this group
\r
378 int min = av.alignment.getHeight(), max = 0;
\r
379 for (int i = 0; i < sg.getSize(); i++)
\r
381 int index = av.alignment.findIndex(sg.getSequenceAt(i));
\r
396 sg.setStartRes(seqCanvas.cursorX);
\r
397 if (sg.getEndRes() < seqCanvas.cursorX)
\r
399 sg.setEndRes(seqCanvas.cursorX);
\r
402 min = seqCanvas.cursorY;
\r
406 sg.setEndRes(seqCanvas.cursorX);
\r
407 if (sg.getStartRes() > seqCanvas.cursorX)
\r
409 sg.setStartRes(seqCanvas.cursorX);
\r
412 max = seqCanvas.cursorY + 1;
\r
417 // Only the user can do this
\r
418 av.setSelectionGroup(null);
\r
422 // Now add any sequences between min and max
\r
423 sg.getSequences(null).clear();
\r
424 for (int i = min; i < max; i++)
\r
426 sg.addSequence(av.alignment.getSequenceAt(i), false);
\r
431 if (av.getSelectionGroup() == null)
\r
433 SequenceGroup sg = new SequenceGroup();
\r
434 sg.setStartRes(seqCanvas.cursorX);
\r
435 sg.setEndRes(seqCanvas.cursorX);
\r
436 sg.addSequence(sequence, false);
\r
437 av.setSelectionGroup(sg);
\r
440 ap.paintAlignment(false);
\r
443 void insertGapAtCursor(boolean group)
\r
445 groupEditing = group;
\r
446 startseq = seqCanvas.cursorY;
\r
447 lastres = seqCanvas.cursorX;
\r
448 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
\r
452 void deleteGapAtCursor(boolean group)
\r
454 groupEditing = group;
\r
455 startseq = seqCanvas.cursorY;
\r
456 lastres = seqCanvas.cursorX + getKeyboardNo1();
\r
457 editSequence(false, seqCanvas.cursorX);
\r
461 void numberPressed(char value)
\r
463 if (keyboardNo1 == null)
\r
465 keyboardNo1 = new StringBuffer();
\r
468 if (keyboardNo2 != null)
\r
470 keyboardNo2.append(value);
\r
474 keyboardNo1.append(value);
\r
478 int getKeyboardNo1()
\r
480 if (keyboardNo1 == null)
\r
484 int value = Integer.parseInt(keyboardNo1.toString());
\r
485 keyboardNo1 = null;
\r
490 int getKeyboardNo2()
\r
492 if (keyboardNo2 == null)
\r
496 int value = Integer.parseInt(keyboardNo2.toString());
\r
497 keyboardNo2 = null;
\r
505 * @param evt DOCUMENT ME!
\r
507 public void mouseReleased(MouseEvent evt)
\r
509 mouseDragging = false;
\r
510 mouseWheelPressed = false;
\r
514 doMouseReleasedDefineMode(evt);
\r
524 * @param evt DOCUMENT ME!
\r
526 public void mousePressed(MouseEvent evt)
\r
528 lastMousePress = evt.getPoint();
\r
530 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
\r
532 mouseWheelPressed = true;
\r
536 if (evt.isShiftDown() || evt.isAltDown() ||
\r
537 evt.isControlDown())
\r
539 if (evt.isAltDown() || evt.isControlDown())
\r
541 groupEditing = true;
\r
543 editingSeqs = true;
\r
547 doMousePressedDefineMode(evt);
\r
551 int seq = findSeq(evt);
\r
552 int res = findRes(evt);
\r
554 if (seq < 0 || res < 0)
\r
559 if ( (seq < av.getAlignment().getHeight()) &&
\r
560 (res < av.getAlignment().getSequenceAt(seq).getLength()))
\r
574 String lastMessage;
\r
575 public void mouseOverSequence(SequenceI sequence, int index)
\r
577 String tmp = sequence.hashCode()+index+"";
\r
578 if (lastMessage == null || !lastMessage.equals(tmp))
\r
579 ssm.mouseOverSequence(sequence, index);
\r
585 public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
\r
587 if(av.alignment.findIndex(seq)>-1)
\r
589 SearchResults highlight = new SearchResults();
\r
590 highlight.addResult(seq,index,index);
\r
591 seqCanvas.highlightSearchResults(highlight);
\r
595 public void updateColours(SequenceI seq, int index)
\r
597 System.out.println("update the seqPanel colours");
\r
604 * @param evt DOCUMENT ME!
\r
606 public void mouseMoved(MouseEvent evt)
\r
610 // This is because MacOSX creates a mouseMoved
\r
611 // If control is down, other platforms will not.
\r
615 int res = findRes(evt);
\r
616 int seq = findSeq(evt);
\r
618 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
\r
623 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
\r
625 if (res > sequence.getLength())
\r
631 mouseOverSequence(sequence, sequence.findPosition(res));
\r
633 setStatusMessage(sequence, res, seq);
\r
635 tooltipText.setLength(6); // Cuts the buffer back to <html>
\r
637 SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
\r
638 if (groups != null)
\r
640 for (int g = 0; g < groups.length; g++)
\r
642 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
\r
644 if (tooltipText.length() > 6)
\r
646 tooltipText.append("<br>");
\r
649 if (!groups[g].getName().startsWith("JTreeGroup") &&
\r
650 !groups[g].getName().startsWith("JGroup"))
\r
652 tooltipText.append(groups[g].getName());
\r
655 if (groups[g].getDescription() != null)
\r
657 tooltipText.append(": " + groups[g].getDescription());
\r
663 // use aa to see if the mouse pointer is on a
\r
664 if (av.showSequenceFeatures)
\r
666 SequenceFeature[] features = findFeaturesAtRes(
\r
667 sequence.getDatasetSequence(), sequence.findPosition(res));
\r
669 if (features != null)
\r
671 for (int i = 0; i < features.length; i++)
\r
673 if (features[i].getType().equals("disulfide bond"))
\r
675 if (features[i].getBegin() == sequence.findPosition(res)
\r
676 || features[i].getEnd() == sequence.findPosition(res))
\r
678 if (tooltipText.length() > 6)
\r
680 tooltipText.append("<br>");
\r
682 tooltipText.append("disulfide bond " + features[i].getBegin() +
\r
684 features[i].getEnd());
\r
685 if (features[i].links != null)
\r
687 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
\r
693 if (tooltipText.length() > 6)
\r
695 tooltipText.append("<br>");
\r
698 tooltipText.append(features[i].getType() + " " +
\r
699 features[i].begin);
\r
700 if (features[i].begin != features[i].end)
\r
702 tooltipText.append(" " + features[i].end);
\r
705 if (features[i].getDescription() != null
\r
706 && !features[i].description.equals(features[i].getType()))
\r
708 tmpString = features[i].getDescription();
\r
709 int startTag = tmpString.toUpperCase().indexOf("<HTML>");
\r
712 tmpString = tmpString.substring(startTag + 6);
\r
714 int endTag = tmpString.toUpperCase().indexOf("</BODY>");
\r
717 tmpString = tmpString.substring(0, endTag);
\r
719 endTag = tmpString.toUpperCase().indexOf("</HTML>");
\r
722 tmpString = tmpString.substring(0, endTag);
\r
727 tooltipText.append("; " + tmpString);
\r
731 if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
\r
733 //The description does not specify html is to
\r
734 //be used, so we must remove < > symbols
\r
735 tmpString = tmpString.replaceAll("<", "<");
\r
736 tmpString = tmpString.replaceAll(">", ">");
\r
738 tooltipText.append("; ");
\r
739 tooltipText.append(tmpString);
\r
744 tooltipText.append("; " + tmpString);
\r
748 if (features[i].getValue("status") != null)
\r
750 String status = features[i].getValue("status").toString();
\r
751 if (status.length() > 0)
\r
753 tooltipText.append("; (" + features[i].getValue("status") + ")");
\r
757 if (features[i].links != null)
\r
759 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
\r
767 if (tooltipText.length() == 6) // <html></html>
\r
769 setToolTipText(null);
\r
773 tooltipText.append("</html>");
\r
774 if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString()))
\r
775 setToolTipText(tooltipText.toString());
\r
777 lastTooltip = tooltipText.toString();
\r
781 String lastTooltip;
\r
783 void setStatusMessage(SequenceI sequence, int res, int seq)
\r
785 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
\r
786 sequence.getName());
\r
789 if (av.alignment.isNucleotide())
\r
791 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
\r
795 text.append(" Nucleotide: ");
\r
800 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
\r
803 text.append(" Residue: ");
\r
812 text.append(obj + " (" + sequence.findPosition(res) +
\r
816 ap.alignFrame.statusBar.setText(text.toString());
\r
823 * @param evt DOCUMENT ME!
\r
825 public void mouseDragged(MouseEvent evt)
\r
827 if (mouseWheelPressed)
\r
829 int oldWidth = av.charWidth;
\r
831 //Which is bigger, left-right or up-down?
\r
832 if (Math.abs(evt.getY() - lastMousePress.getY())
\r
833 > Math.abs(evt.getX() - lastMousePress.getX()))
\r
835 int fontSize = av.font.getSize();
\r
837 if (evt.getY() < lastMousePress.getY())
\r
841 else if (evt.getY() > lastMousePress.getY())
\r
851 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
\r
852 av.charWidth = oldWidth;
\r
857 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
\r
861 else if (evt.getX() > lastMousePress.getX())
\r
866 ap.paintAlignment(false);
\r
869 FontMetrics fm = getFontMetrics(av.getFont());
\r
870 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
\r
872 lastMousePress = evt.getPoint();
\r
879 doMouseDraggedDefineMode(evt);
\r
883 int res = findRes(evt);
\r
890 if ( (lastres == -1) || (lastres == res))
\r
895 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
\r
897 // dragLeft, delete gap
\r
898 editSequence(false, res);
\r
902 editSequence(true, res);
\r
905 mouseDragging = true;
\r
906 if (scrollThread != null)
\r
908 scrollThread.setEvent(evt);
\r
914 synchronized void editSequence(boolean insertGap, int startres)
\r
916 int fixedLeft = -1;
\r
917 int fixedRight = -1;
\r
918 boolean fixedColumns = false;
\r
919 SequenceGroup sg = av.getSelectionGroup();
\r
921 SequenceI seq = av.alignment.getSequenceAt(startseq);
\r
923 //No group, but the sequence may represent a group
\r
924 if (!groupEditing && av.hasHiddenRows)
\r
926 if (av.hiddenRepSequences != null
\r
927 && av.hiddenRepSequences.containsKey(seq))
\r
929 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
\r
930 groupEditing = true;
\r
934 StringBuffer message = new StringBuffer();
\r
937 message.append("Edit group:");
\r
938 if (editCommand == null)
\r
940 editCommand = new EditCommand("Edit Group");
\r
945 message.append("Edit sequence: " + seq.getName());
\r
946 String label = seq.getName();
\r
947 if (label.length() > 10)
\r
949 label = label.substring(0, 10);
\r
951 if (editCommand == null)
\r
953 editCommand = new EditCommand("Edit " + label);
\r
959 message.append(" insert ");
\r
963 message.append(" delete ");
\r
966 message.append(Math.abs(startres - lastres) + " gaps.");
\r
967 ap.alignFrame.statusBar.setText(message.toString());
\r
969 //Are we editing within a selection group?
\r
971 || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
\r
973 fixedColumns = true;
\r
975 //sg might be null as the user may only see 1 sequence,
\r
976 //but the sequence represents a group
\r
979 if (av.hiddenRepSequences == null
\r
980 || !av.hiddenRepSequences.containsKey(seq))
\r
985 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
\r
988 fixedLeft = sg.getStartRes();
\r
989 fixedRight = sg.getEndRes();
\r
991 if ( (startres < fixedLeft && lastres >= fixedLeft)
\r
992 || (startres >= fixedLeft && lastres < fixedLeft)
\r
993 || (startres > fixedRight && lastres <= fixedRight)
\r
994 || (startres <= fixedRight && lastres > fixedRight))
\r
1000 if (fixedLeft > startres)
\r
1002 fixedRight = fixedLeft - 1;
\r
1005 else if (fixedRight < startres)
\r
1007 fixedLeft = fixedRight;
\r
1012 if (av.hasHiddenColumns)
\r
1014 fixedColumns = true;
\r
1015 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
\r
1016 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
\r
1018 if ( (insertGap && startres > y1 && lastres < y1)
\r
1019 || (!insertGap && startres < y2 && lastres > y2))
\r
1025 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
\r
1026 //Selection spans a hidden region
\r
1027 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
\r
1029 if (startres >= y2)
\r
1035 fixedRight = y2 - 1;
\r
1042 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
\r
1043 int g, groupSize = vseqs.size();
\r
1044 SequenceI[] groupSeqs = new SequenceI[groupSize];
\r
1045 for (g = 0; g < groupSeqs.length; g++)
\r
1047 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
\r
1053 //If the user has selected the whole sequence, and is dragging to
\r
1054 // the right, we can still extend the alignment and selectionGroup
\r
1055 if (sg.getStartRes() == 0
\r
1056 && sg.getEndRes() == fixedRight
\r
1057 && sg.getEndRes() == av.alignment.getWidth() - 1
\r
1060 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
\r
1061 fixedRight = sg.getEndRes();
\r
1064 // Is it valid with fixed columns??
\r
1065 // Find the next gap before the end
\r
1066 // of the visible region boundary
\r
1067 boolean blank = false;
\r
1068 for (fixedRight = fixedRight;
\r
1069 fixedRight > lastres;
\r
1074 for (g = 0; g < groupSize; g++)
\r
1076 for (int j = 0; j < startres - lastres; j++)
\r
1078 if (!jalview.util.Comparison.isGap(
\r
1079 groupSeqs[g].getCharAt(fixedRight - j)))
\r
1094 if (sg.getSize() == av.alignment.getHeight())
\r
1096 if ( (av.hasHiddenColumns
\r
1098 startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
\r
1104 int alWidth = av.alignment.getWidth();
\r
1105 if (av.hasHiddenRows)
\r
1107 int hwidth = av.alignment.getHiddenSequences().getWidth();
\r
1108 if (hwidth > alWidth)
\r
1113 //We can still insert gaps if the selectionGroup
\r
1114 //contains all the sequences
\r
1115 sg.setEndRes(sg.getEndRes() + startres - lastres);
\r
1116 fixedRight = alWidth + startres - lastres;
\r
1127 else if (!insertGap)
\r
1129 /// Are we able to delete?
\r
1130 // ie are all columns blank?
\r
1132 for (g = 0; g < groupSize; g++)
\r
1134 for (int j = startres; j < lastres; j++)
\r
1136 if (groupSeqs[g].getLength() <= j)
\r
1141 if (!jalview.util.Comparison.isGap(
\r
1142 groupSeqs[g].getCharAt(j)))
\r
1144 // Not a gap, block edit not valid
\r
1154 // dragging to the right
\r
1155 if (fixedColumns && fixedRight != -1)
\r
1157 for (int j = lastres; j < startres; j++)
\r
1159 insertChar(j, groupSeqs, fixedRight);
\r
1164 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1166 startres, startres - lastres,
\r
1173 // dragging to the left
\r
1174 if (fixedColumns && fixedRight != -1)
\r
1176 for (int j = lastres; j > startres; j--)
\r
1178 deleteChar(startres, groupSeqs, fixedRight);
\r
1183 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1185 startres, lastres - startres,
\r
1192 else /////Editing a single sequence///////////
\r
1196 // dragging to the right
\r
1197 if (fixedColumns && fixedRight != -1)
\r
1199 for (int j = lastres; j < startres; j++)
\r
1201 insertChar(j, new SequenceI[]
\r
1202 {seq}, fixedRight);
\r
1207 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1210 lastres, startres - lastres,
\r
1217 // dragging to the left
\r
1218 if (fixedColumns && fixedRight != -1)
\r
1220 for (int j = lastres; j > startres; j--)
\r
1222 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
\r
1227 deleteChar(startres, new SequenceI[]
\r
1228 {seq}, fixedRight);
\r
1233 //could be a keyboard edit trying to delete none gaps
\r
1235 for (int m = startres; m < lastres; m++)
\r
1237 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
\r
1246 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1257 lastres = startres;
\r
1258 seqCanvas.repaint();
\r
1261 void insertChar(int j, SequenceI[] seq, int fixedColumn)
\r
1263 int blankColumn = fixedColumn;
\r
1264 for (int s = 0; s < seq.length; s++)
\r
1266 //Find the next gap before the end of the visible region boundary
\r
1267 //If lastCol > j, theres a boundary after the gap insertion
\r
1269 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1271 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1273 //Theres a space, so break and insert the gap
\r
1278 if (blankColumn <= j)
\r
1280 blankColumn = fixedColumn;
\r
1286 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1288 blankColumn, 1, av.alignment, true);
\r
1290 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1292 j, 1, av.alignment,
\r
1297 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
\r
1300 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1302 j, 1, av.alignment, true);
\r
1304 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1306 fixedColumn, 1, av.alignment, true);
\r
1312 * @param e DOCUMENT ME!
\r
1314 public void mouseEntered(MouseEvent e)
\r
1321 if (scrollThread != null)
\r
1323 scrollThread.running = false;
\r
1324 scrollThread = null;
\r
1331 * @param e DOCUMENT ME!
\r
1333 public void mouseExited(MouseEvent e)
\r
1335 if (av.getWrapAlignment())
\r
1340 if (mouseDragging)
\r
1342 scrollThread = new ScrollThread();
\r
1346 public void mouseClicked(MouseEvent evt)
\r
1348 SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
\r
1349 if (evt.getClickCount() > 1)
\r
1351 if (av.getSelectionGroup().getSize() == 1
\r
1352 && av.getSelectionGroup().getEndRes()
\r
1353 - av.getSelectionGroup().getStartRes() < 2)
\r
1355 av.setSelectionGroup(null);
\r
1358 SequenceFeature[] features = findFeaturesAtRes(
\r
1359 sequence.getDatasetSequence(),
\r
1360 sequence.findPosition(findRes(evt))
\r
1363 if (features != null && features.length > 0)
\r
1365 SearchResults highlight = new SearchResults();
\r
1366 highlight.addResult(sequence,
\r
1367 features[0].getBegin(),
\r
1368 features[0].getEnd());
\r
1369 seqCanvas.highlightSearchResults(highlight);
\r
1371 if (features != null && features.length > 0)
\r
1373 seqCanvas.getFeatureRenderer().amendFeatures(
\r
1375 {sequence}, features, false, ap);
\r
1377 seqCanvas.highlightSearchResults(null);
\r
1382 public void mouseWheelMoved(MouseWheelEvent e)
\r
1385 if (e.getWheelRotation() > 0)
\r
1387 ap.scrollUp(false);
\r
1391 ap.scrollUp(true);
\r
1398 * @param evt DOCUMENT ME!
\r
1400 public void doMousePressedDefineMode(MouseEvent evt)
\r
1402 int res = findRes(evt);
\r
1403 int seq = findSeq(evt);
\r
1406 startWrapBlock = wrappedBlock;
\r
1408 if (av.wrapAlignment && seq > av.alignment.getHeight())
\r
1410 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1411 "Cannot edit annotations in wrapped view.",
\r
1412 "Wrapped view - no edit",
\r
1413 JOptionPane.WARNING_MESSAGE);
\r
1417 if (seq < 0 || res < 0)
\r
1422 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1424 if ( (sequence == null) || (res > sequence.getLength()))
\r
1429 stretchGroup = av.getSelectionGroup();
\r
1431 if (stretchGroup == null)
\r
1433 stretchGroup = av.alignment.findGroup(sequence);
\r
1435 if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1436 (res < stretchGroup.getEndRes()))
\r
1438 av.setSelectionGroup(stretchGroup);
\r
1442 stretchGroup = null;
\r
1445 else if (!stretchGroup.getSequences(null).contains(sequence) ||
\r
1446 (stretchGroup.getStartRes() > res) ||
\r
1447 (stretchGroup.getEndRes() < res))
\r
1449 stretchGroup = null;
\r
1451 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1453 if (allGroups != null)
\r
1455 for (int i = 0; i < allGroups.length; i++)
\r
1457 if ( (allGroups[i].getStartRes() <= res) &&
\r
1458 (allGroups[i].getEndRes() >= res))
\r
1460 stretchGroup = allGroups[i];
\r
1466 av.setSelectionGroup(stretchGroup);
\r
1470 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1472 SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),
\r
1473 sequence.findPosition(res));
\r
1474 Vector links = new Vector();
\r
1475 for (int i = 0; i < allFeatures.length; i++)
\r
1477 if (allFeatures[i].links != null)
\r
1479 for (int j = 0; j < allFeatures[i].links.size(); j++)
\r
1481 links.addElement(allFeatures[i].links.elementAt(j));
\r
1486 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1487 pop.show(this, evt.getX(), evt.getY());
\r
1491 if (av.cursorMode)
\r
1493 seqCanvas.cursorX = findRes(evt);
\r
1494 seqCanvas.cursorY = findSeq(evt);
\r
1495 seqCanvas.repaint();
\r
1499 if (stretchGroup == null)
\r
1501 //Only if left mouse button do we want to change group sizes
\r
1503 // define a new group here
\r
1504 SequenceGroup sg = new SequenceGroup();
\r
1505 sg.setStartRes(res);
\r
1506 sg.setEndRes(res);
\r
1507 sg.addSequence(sequence, false);
\r
1508 av.setSelectionGroup(sg);
\r
1509 stretchGroup = sg;
\r
1511 if (av.getConservationSelected())
\r
1513 SliderPanel.setConservationSlider(ap,
\r
1514 av.getGlobalColourScheme(),
\r
1518 if (av.getAbovePIDThreshold())
\r
1520 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1523 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1525 // Edit end res position of selected group
\r
1526 changeEndRes = true;
\r
1528 else if ( (stretchGroup != null) &&
\r
1529 (stretchGroup.getStartRes() == res))
\r
1531 // Edit end res position of selected group
\r
1532 changeStartRes = true;
\r
1534 stretchGroup.getWidth();
\r
1537 seqCanvas.repaint();
\r
1543 * @param evt DOCUMENT ME!
\r
1545 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1547 if (stretchGroup == null)
\r
1552 if (stretchGroup.cs != null)
\r
1554 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1556 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1557 stretchGroup.getSequences(av.hiddenRepSequences),
\r
1558 stretchGroup.getWidth());
\r
1561 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1562 || stretchGroup.cs instanceof PIDColourScheme
\r
1563 || stretchGroup.cs.conservationApplied()
\r
1564 || stretchGroup.cs.getThreshold() > 0)
\r
1566 stretchGroup.recalcConservation();
\r
1569 if (stretchGroup.cs.conservationApplied())
\r
1571 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1572 stretchGroup.getName());
\r
1576 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1577 stretchGroup.getName());
\r
1579 PaintRefresher.Refresh(this, av.getSequenceSetId());
\r
1580 ap.paintAlignment(true);
\r
1583 changeEndRes = false;
\r
1584 changeStartRes = false;
\r
1585 stretchGroup = null;
\r
1592 * @param evt DOCUMENT ME!
\r
1594 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1596 int res = findRes(evt);
\r
1597 int y = findSeq(evt);
\r
1599 if (wrappedBlock != startWrapBlock)
\r
1604 if (stretchGroup == null)
\r
1609 if (res >= av.alignment.getWidth())
\r
1611 res = av.alignment.getWidth() - 1;
\r
1614 if (stretchGroup.getEndRes() == res)
\r
1616 // Edit end res position of selected group
\r
1617 changeEndRes = true;
\r
1619 else if (stretchGroup.getStartRes() == res)
\r
1621 // Edit start res position of selected group
\r
1622 changeStartRes = true;
\r
1625 if (res < av.getStartRes())
\r
1627 res = av.getStartRes();
\r
1632 if (res > (stretchGroup.getStartRes() - 1))
\r
1634 stretchGroup.setEndRes(res);
\r
1637 else if (changeStartRes)
\r
1639 if (res < (stretchGroup.getEndRes() + 1))
\r
1641 stretchGroup.setStartRes(res);
\r
1645 int dragDirection = 0;
\r
1649 dragDirection = 1;
\r
1651 else if (y < oldSeq)
\r
1653 dragDirection = -1;
\r
1656 while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1658 // This routine ensures we don't skip any sequences, as the
\r
1659 // selection is quite slow.
\r
1660 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1662 oldSeq += dragDirection;
\r
1669 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1671 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1673 stretchGroup.deleteSequence(seq, false);
\r
1679 stretchGroup.addSequence(seq, false);
\r
1682 stretchGroup.addSequence(nextSeq, false);
\r
1691 mouseDragging = true;
\r
1693 if (scrollThread != null)
\r
1695 scrollThread.setEvent(evt);
\r
1698 seqCanvas.repaint();
\r
1701 void scrollCanvas(MouseEvent evt)
\r
1705 if (scrollThread != null)
\r
1707 scrollThread.running = false;
\r
1708 scrollThread = null;
\r
1710 mouseDragging = false;
\r
1714 if (scrollThread == null)
\r
1716 scrollThread = new ScrollThread();
\r
1719 mouseDragging = true;
\r
1720 scrollThread.setEvent(evt);
\r
1725 // this class allows scrolling off the bottom of the visible alignment
\r
1726 class ScrollThread
\r
1730 boolean running = false;
\r
1732 public ScrollThread()
\r
1737 public void setEvent(MouseEvent e)
\r
1742 public void stopScrolling()
\r
1755 if (mouseDragging && (evt.getY() < 0) &&
\r
1756 (av.getStartSeq() > 0))
\r
1758 running = ap.scrollUp(true);
\r
1761 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1762 (av.alignment.getHeight() > av.getEndSeq()))
\r
1764 running = ap.scrollUp(false);
\r
1767 if (mouseDragging && (evt.getX() < 0))
\r
1769 running = ap.scrollRight(false);
\r
1771 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1773 running = ap.scrollRight(true);
\r
1781 catch (Exception ex)
\r