2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 import java.util.List;
24 import java.awt.event.*;
28 import jalview.commands.*;
29 import jalview.datamodel.*;
30 import jalview.schemes.*;
31 import jalview.structure.*;
37 * @version $Revision: 1.130 $
39 public class SeqPanel extends JPanel implements MouseListener,
40 MouseMotionListener, MouseWheelListener, SequenceListener,
45 public SeqCanvas seqCanvas;
48 public AlignmentPanel ap;
50 protected int lastres;
52 protected int startseq;
54 protected AlignViewport av;
56 ScrollThread scrollThread = null;
58 boolean mouseDragging = false;
60 boolean editingSeqs = false;
62 boolean groupEditing = false;
64 // ////////////////////////////////////////
65 // ///Everything below this is for defining the boundary of the rubberband
66 // ////////////////////////////////////////
69 boolean changeEndSeq = false;
71 boolean changeStartSeq = false;
73 boolean changeEndRes = false;
75 boolean changeStartRes = false;
77 SequenceGroup stretchGroup = null;
79 boolean remove = false;
83 boolean mouseWheelPressed = false;
85 StringBuffer keyboardNo1;
87 StringBuffer keyboardNo2;
89 java.net.URL linkImageURL;
91 StringBuffer tooltipText = new StringBuffer("<html>");
95 EditCommand editCommand;
97 StructureSelectionManager ssm;
100 * Creates a new SeqPanel object.
107 public SeqPanel(AlignViewport av, AlignmentPanel ap)
109 linkImageURL = getClass().getResource("/images/link.gif");
110 ToolTipManager.sharedInstance().registerComponent(this);
111 ToolTipManager.sharedInstance().setInitialDelay(0);
112 ToolTipManager.sharedInstance().setDismissDelay(10000);
114 setBackground(Color.white);
116 seqCanvas = new SeqCanvas(ap);
117 setLayout(new BorderLayout());
118 add(seqCanvas, BorderLayout.CENTER);
124 addMouseMotionListener(this);
125 addMouseListener(this);
126 addMouseWheelListener(this);
127 ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
128 ssm.addStructureViewerListener(this);
129 ssm.addSelectionListener(this);
133 int startWrapBlock = -1;
135 int wrappedBlock = -1;
137 int findRes(MouseEvent evt)
142 if (av.wrapAlignment)
145 int hgap = av.charHeight;
146 if (av.scaleAboveWrapped)
148 hgap += av.charHeight;
151 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
152 + seqCanvas.getAnnotationHeight();
156 x -= seqCanvas.LABEL_WEST;
158 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
164 wrappedBlock = y / cHeight;
165 wrappedBlock += av.getStartRes() / cwidth;
167 res = wrappedBlock * cwidth + x / av.getCharWidth();
172 if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
174 // make sure we calculate relative to visible alignment, rather than right-hand gutter
175 x = seqCanvas.getX()+seqCanvas.getWidth();
177 res = (x / av.getCharWidth()) + av.getStartRes();
180 if (av.hasHiddenColumns())
182 res = av.getColumnSelection().adjustForHiddenColumns(res);
189 int findSeq(MouseEvent evt)
194 if (av.wrapAlignment)
196 int hgap = av.charHeight;
197 if (av.scaleAboveWrapped)
199 hgap += av.charHeight;
202 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
203 + seqCanvas.getAnnotationHeight();
207 seq = Math.min((y % cHeight) / av.getCharHeight(),
208 av.getAlignment().getHeight() - 1);
212 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
213 av.getAlignment().getHeight() - 1);
219 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
221 Vector tmp = new Vector();
222 SequenceFeature[] features = sequence.getSequenceFeatures();
223 if (features != null)
225 for (int i = 0; i < features.length; i++)
227 if (av.featuresDisplayed == null
228 || !av.featuresDisplayed.containsKey(features[i].getType()))
233 if (features[i].featureGroup != null
234 && seqCanvas.fr.featureGroups != null
235 && seqCanvas.fr.featureGroups
236 .containsKey(features[i].featureGroup)
237 && !((Boolean) seqCanvas.fr.featureGroups
238 .get(features[i].featureGroup)).booleanValue())
241 if ((features[i].getBegin() <= res)
242 && (features[i].getEnd() >= res))
244 tmp.addElement(features[i]);
249 features = new SequenceFeature[tmp.size()];
250 tmp.copyInto(features);
257 if (editCommand != null && editCommand.getSize() > 0)
259 ap.alignFrame.addHistoryItem(editCommand);
260 av.firePropertyChange("alignment", null, av.getAlignment()
267 groupEditing = false;
275 seqCanvas.cursorY = getKeyboardNo1() - 1;
279 void setCursorColumn()
281 seqCanvas.cursorX = getKeyboardNo1() - 1;
285 void setCursorRowAndColumn()
287 if (keyboardNo2 == null)
289 keyboardNo2 = new StringBuffer();
293 seqCanvas.cursorX = getKeyboardNo1() - 1;
294 seqCanvas.cursorY = getKeyboardNo2() - 1;
299 void setCursorPosition()
301 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
304 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
308 void moveCursor(int dx, int dy)
310 seqCanvas.cursorX += dx;
311 seqCanvas.cursorY += dy;
312 if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
314 int original = seqCanvas.cursorX - dx;
315 int maxWidth = av.getAlignment().getWidth();
317 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
318 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
320 seqCanvas.cursorX += dx;
323 if (seqCanvas.cursorX >= maxWidth
324 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
326 seqCanvas.cursorX = original;
333 void scrollToVisible()
335 if (seqCanvas.cursorX < 0)
337 seqCanvas.cursorX = 0;
339 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
341 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
344 if (seqCanvas.cursorY < 0)
346 seqCanvas.cursorY = 0;
348 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
350 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
354 if (av.wrapAlignment)
356 ap.scrollToWrappedVisible(seqCanvas.cursorX);
360 while (seqCanvas.cursorY < av.startSeq)
364 while (seqCanvas.cursorY + 1 > av.endSeq)
368 if (!av.wrapAlignment)
370 while (seqCanvas.cursorX < av.getColumnSelection()
371 .adjustForHiddenColumns(av.startRes))
373 if (!ap.scrollRight(false))
378 while (seqCanvas.cursorX > av.getColumnSelection()
379 .adjustForHiddenColumns(av.endRes))
381 if (!ap.scrollRight(true))
388 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
389 seqCanvas.cursorX, seqCanvas.cursorY);
394 void setSelectionAreaAtCursor(boolean topLeft)
396 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
399 if (av.getSelectionGroup() != null)
401 SequenceGroup sg = av.getSelectionGroup();
402 // Find the top and bottom of this group
403 int min = av.getAlignment().getHeight(), max = 0;
404 for (int i = 0; i < sg.getSize(); i++)
406 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
421 sg.setStartRes(seqCanvas.cursorX);
422 if (sg.getEndRes() < seqCanvas.cursorX)
424 sg.setEndRes(seqCanvas.cursorX);
427 min = seqCanvas.cursorY;
431 sg.setEndRes(seqCanvas.cursorX);
432 if (sg.getStartRes() > seqCanvas.cursorX)
434 sg.setStartRes(seqCanvas.cursorX);
437 max = seqCanvas.cursorY + 1;
442 // Only the user can do this
443 av.setSelectionGroup(null);
447 // Now add any sequences between min and max
448 sg.getSequences(null).clear();
449 for (int i = min; i < max; i++)
451 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
456 if (av.getSelectionGroup() == null)
458 SequenceGroup sg = new SequenceGroup();
459 sg.setStartRes(seqCanvas.cursorX);
460 sg.setEndRes(seqCanvas.cursorX);
461 sg.addSequence(sequence, false);
462 av.setSelectionGroup(sg);
465 ap.paintAlignment(false);
469 void insertGapAtCursor(boolean group)
471 groupEditing = group;
472 startseq = seqCanvas.cursorY;
473 lastres = seqCanvas.cursorX;
474 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
478 void deleteGapAtCursor(boolean group)
480 groupEditing = group;
481 startseq = seqCanvas.cursorY;
482 lastres = seqCanvas.cursorX + getKeyboardNo1();
483 editSequence(false, false, seqCanvas.cursorX);
487 void insertNucAtCursor(boolean group,String nuc){
488 groupEditing = group;
489 startseq = seqCanvas.cursorY;
490 lastres = seqCanvas.cursorX;
491 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
495 void numberPressed(char value)
497 if (keyboardNo1 == null)
499 keyboardNo1 = new StringBuffer();
502 if (keyboardNo2 != null)
504 keyboardNo2.append(value);
508 keyboardNo1.append(value);
514 if (keyboardNo1 == null)
518 int value = Integer.parseInt(keyboardNo1.toString());
526 if (keyboardNo2 == null)
530 int value = Integer.parseInt(keyboardNo2.toString());
542 public void mouseReleased(MouseEvent evt)
544 mouseDragging = false;
545 mouseWheelPressed = false;
549 doMouseReleasedDefineMode(evt);
562 public void mousePressed(MouseEvent evt)
564 lastMousePress = evt.getPoint();
566 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
568 mouseWheelPressed = true;
572 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
574 if (evt.isAltDown() || evt.isControlDown())
582 doMousePressedDefineMode(evt);
586 int seq = findSeq(evt);
587 int res = findRes(evt);
589 if (seq < 0 || res < 0)
594 if ((seq < av.getAlignment().getHeight())
595 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
611 public void mouseOverSequence(SequenceI sequence, int index, int pos)
613 String tmp = sequence.hashCode() + " " + index + " " + pos;
615 if (lastMessage == null || !lastMessage.equals(tmp))
617 // System.err.println("mouseOver Sequence: "+tmp);
618 ssm.mouseOverSequence(sequence, index, pos, av);
623 public void highlightSequence(SearchResults results)
625 if (av.followHighlight)
627 if (ap.scrollToPosition(results, false))
629 seqCanvas.revalidate();
632 seqCanvas.highlightSearchResults(results);
635 public void updateColours(SequenceI seq, int index)
637 System.out.println("update the seqPanel colours");
647 public void mouseMoved(MouseEvent evt)
651 // This is because MacOSX creates a mouseMoved
652 // If control is down, other platforms will not.
656 int res = findRes(evt);
657 int seq = findSeq(evt);
659 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
664 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
666 if (res >= sequence.getLength())
671 pos = setStatusMessage(sequence, res, seq);
672 if (ssm != null && pos > -1)
673 mouseOverSequence(sequence, res, pos);
675 tooltipText.setLength(6); // Cuts the buffer back to <html>
677 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
680 for (int g = 0; g < groups.length; g++)
682 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
684 if (tooltipText.length() > 6)
686 tooltipText.append("<br>");
689 if (!groups[g].getName().startsWith("JTreeGroup")
690 && !groups[g].getName().startsWith("JGroup"))
692 tooltipText.append(groups[g].getName());
695 if (groups[g].getDescription() != null)
697 tooltipText.append(": " + groups[g].getDescription());
703 // use aa to see if the mouse pointer is on a
704 if (av.showSequenceFeatures)
707 SequenceFeature[] features = findFeaturesAtRes(
708 sequence.getDatasetSequence(),
709 rpos = sequence.findPosition(res));
710 appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
711 this.ap.seqPanel.seqCanvas.fr.minmax);
713 if (tooltipText.length() == 6) // <html></html>
715 setToolTipText(null);
720 tooltipText.append("</html>");
721 if (lastTooltip == null
722 || !lastTooltip.equals(tooltipText.toString()))
724 setToolTipText(tooltipText.toString());
725 lastTooltip = tooltipText.toString();
732 private Point lastp = null;
737 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
739 public Point getToolTipLocation(MouseEvent event)
741 int x = event.getX(), w = getWidth();
742 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
745 if (!event.isShiftDown() || p == null)
747 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
748 event.getX() + wdth, event.getY() - 20) : null;
751 * TODO: try to modify position region is not obcured by tooltip
757 * appends the features at rpos to the given stringbuffer ready for display in
760 * @param tooltipText2
761 * @param linkImageURL
764 * TODO refactor to Jalview 'utilities' somehow.
766 public void appendFeatures(StringBuffer tooltipText2,
767 String linkImageURL, int rpos, SequenceFeature[] features)
769 appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
772 public void appendFeatures(StringBuffer tooltipText2, String string,
773 int rpos, SequenceFeature[] features, Hashtable minmax)
776 if (features != null)
778 for (int i = 0; i < features.length; i++)
780 if (features[i].getType().equals("disulfide bond"))
782 if (features[i].getBegin() == rpos
783 || features[i].getEnd() == rpos)
785 if (tooltipText2.length() > 6)
787 tooltipText2.append("<br>");
789 tooltipText2.append("disulfide bond " + features[i].getBegin()
790 + ":" + features[i].getEnd());
791 if (features[i].links != null)
793 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
799 if (tooltipText2.length() > 6)
801 tooltipText2.append("<br>");
803 // TODO: remove this hack to display link only features
804 boolean linkOnly = features[i].getValue("linkonly") != null;
807 tooltipText2.append(features[i].getType() + " ");
810 // we are marking a positional feature
811 tooltipText2.append(features[i].begin);
813 if (features[i].begin != features[i].end)
815 tooltipText2.append(" " + features[i].end);
818 if (features[i].getDescription() != null
819 && !features[i].description.equals(features[i]
822 tmpString = features[i].getDescription();
823 String tmp2up=tmpString.toUpperCase();
824 int startTag = tmp2up.indexOf("<HTML>");
827 tmpString = tmpString.substring(startTag + 6);
828 tmp2up = tmp2up.substring(startTag+6);
830 int endTag = tmp2up.indexOf("</BODY>");
833 tmpString = tmpString.substring(0, endTag);
834 tmp2up = tmp2up.substring(0, endTag);
836 endTag = tmp2up.indexOf("</HTML>");
839 tmpString = tmpString.substring(0, endTag);
844 tooltipText2.append("; " + tmpString);
848 if (tmpString.indexOf("<") > -1
849 || tmpString.indexOf(">") > -1)
851 // The description does not specify html is to
852 // be used, so we must remove < > symbols
853 tmpString = tmpString.replaceAll("<", "<");
854 tmpString = tmpString.replaceAll(">", ">");
856 tooltipText2.append("; ");
857 tooltipText2.append(tmpString);
862 tooltipText2.append("; " + tmpString);
866 // check score should be shown
867 if (features[i].getScore() != Float.NaN)
869 float[][] rng = (minmax == null) ? null : ((float[][]) minmax
870 .get(features[i].getType()));
871 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
873 tooltipText2.append(" Score=" + features[i].getScore());
876 if (features[i].getValue("status") != null)
878 String status = features[i].getValue("status").toString();
879 if (status.length() > 0)
881 tooltipText2.append("; (" + features[i].getValue("status")
886 if (features[i].links != null)
888 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
899 * Set status message in alignment panel
902 * aligned sequence object
906 * index of sequence in alignment
907 * @return position of res in sequence
909 int setStatusMessage(SequenceI sequence, int res, int seq)
912 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
913 + sequence.getName());
916 if (av.getAlignment().isNucleotide())
918 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
922 text.append(" Nucleotide: ");
927 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
930 text.append(" Residue: ");
936 pos = sequence.findPosition(res);
939 text.append(obj + " (" + pos + ")");
942 ap.alignFrame.statusBar.setText(text.toString());
952 public void mouseDragged(MouseEvent evt)
954 if (mouseWheelPressed)
956 int oldWidth = av.charWidth;
958 // Which is bigger, left-right or up-down?
959 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
960 .getX() - lastMousePress.getX()))
962 int fontSize = av.font.getSize();
964 if (evt.getY() < lastMousePress.getY())
968 else if (evt.getY() > lastMousePress.getY())
978 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
979 av.charWidth = oldWidth;
984 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
988 else if (evt.getX() > lastMousePress.getX())
993 ap.paintAlignment(false);
996 FontMetrics fm = getFontMetrics(av.getFont());
997 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
999 lastMousePress = evt.getPoint();
1006 doMouseDraggedDefineMode(evt);
1010 int res = findRes(evt);
1017 if ((lastres == -1) || (lastres == res))
1022 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1024 // dragLeft, delete gap
1025 editSequence(false, false,res);
1029 editSequence(true, false,res);
1032 mouseDragging = true;
1033 if (scrollThread != null)
1035 scrollThread.setEvent(evt);
1039 //TODO: Make it more clever than many booleans
1040 synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
1043 int fixedRight = -1;
1044 boolean fixedColumns = false;
1045 SequenceGroup sg = av.getSelectionGroup();
1047 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1049 // No group, but the sequence may represent a group
1050 if (!groupEditing && av.hasHiddenRows())
1052 if (av.isHiddenRepSequence(seq))
1054 sg = av.getRepresentedSequences(seq);
1055 groupEditing = true;
1059 StringBuffer message = new StringBuffer();
1062 message.append("Edit group:");
1063 if (editCommand == null)
1065 editCommand = new EditCommand("Edit Group");
1070 message.append("Edit sequence: " + seq.getName());
1071 String label = seq.getName();
1072 if (label.length() > 10)
1074 label = label.substring(0, 10);
1076 if (editCommand == null)
1078 editCommand = new EditCommand("Edit " + label);
1084 message.append(" insert ");
1088 message.append(" delete ");
1091 message.append(Math.abs(startres - lastres) + " gaps.");
1092 ap.alignFrame.statusBar.setText(message.toString());
1094 // Are we editing within a selection group?
1096 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1099 fixedColumns = true;
1101 // sg might be null as the user may only see 1 sequence,
1102 // but the sequence represents a group
1105 if (!av.isHiddenRepSequence(seq))
1110 sg = av.getRepresentedSequences(seq);
1113 fixedLeft = sg.getStartRes();
1114 fixedRight = sg.getEndRes();
1116 if ((startres < fixedLeft && lastres >= fixedLeft)
1117 || (startres >= fixedLeft && lastres < fixedLeft)
1118 || (startres > fixedRight && lastres <= fixedRight)
1119 || (startres <= fixedRight && lastres > fixedRight))
1125 if (fixedLeft > startres)
1127 fixedRight = fixedLeft - 1;
1130 else if (fixedRight < startres)
1132 fixedLeft = fixedRight;
1137 if (av.hasHiddenColumns())
1139 fixedColumns = true;
1140 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1141 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1143 if ((insertGap && startres > y1 && lastres < y1)
1144 || (!insertGap && startres < y2 && lastres > y2))
1150 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1151 // Selection spans a hidden region
1152 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1160 fixedRight = y2 - 1;
1167 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1168 int g, groupSize = vseqs.size();
1169 SequenceI[] groupSeqs = new SequenceI[groupSize];
1170 for (g = 0; g < groupSeqs.length; g++)
1172 groupSeqs[g] = (SequenceI) vseqs.get(g);
1178 // If the user has selected the whole sequence, and is dragging to
1179 // the right, we can still extend the alignment and selectionGroup
1180 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1181 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1183 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1184 fixedRight = sg.getEndRes();
1187 // Is it valid with fixed columns??
1188 // Find the next gap before the end
1189 // of the visible region boundary
1190 boolean blank = false;
1191 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1195 for (g = 0; g < groupSize; g++)
1197 for (int j = 0; j < startres - lastres; j++)
1199 if (!jalview.util.Comparison.isGap(groupSeqs[g]
1200 .getCharAt(fixedRight - j)))
1215 if (sg.getSize() == av.getAlignment().getHeight())
1217 if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
1218 .getHiddenBoundaryRight(startres)))
1224 int alWidth = av.getAlignment().getWidth();
1225 if (av.hasHiddenRows())
1227 int hwidth = av.getAlignment().getHiddenSequences().getWidth();
1228 if (hwidth > alWidth)
1233 // We can still insert gaps if the selectionGroup
1234 // contains all the sequences
1235 sg.setEndRes(sg.getEndRes() + startres - lastres);
1236 fixedRight = alWidth + startres - lastres;
1247 else if (!insertGap)
1249 // / Are we able to delete?
1250 // ie are all columns blank?
1252 for (g = 0; g < groupSize; g++)
1254 for (int j = startres; j < lastres; j++)
1256 if (groupSeqs[g].getLength() <= j)
1261 if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
1263 // Not a gap, block edit not valid
1273 // dragging to the right
1274 if (fixedColumns && fixedRight != -1)
1276 for (int j = lastres; j < startres; j++)
1278 insertChar(j, groupSeqs, fixedRight);
1283 editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
1284 startres, startres - lastres, av.getAlignment(), true);
1289 // dragging to the left
1290 if (fixedColumns && fixedRight != -1)
1292 for (int j = lastres; j > startres; j--)
1294 deleteChar(startres, groupSeqs, fixedRight);
1299 editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
1300 startres, lastres - startres, av.getAlignment(), true);
1306 // ///Editing a single sequence///////////
1310 // dragging to the right
1311 if (fixedColumns && fixedRight != -1)
1313 for (int j = lastres; j < startres; j++)
1315 insertChar(j, new SequenceI[]
1316 { seq }, fixedRight);
1321 editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
1322 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1328 // dragging to the left
1329 if (fixedColumns && fixedRight != -1)
1331 for (int j = lastres; j > startres; j--)
1333 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1338 deleteChar(startres, new SequenceI[]
1339 { seq }, fixedRight);
1344 // could be a keyboard edit trying to delete none gaps
1346 for (int m = startres; m < lastres; m++)
1348 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1357 editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
1358 { seq }, startres, max, av.getAlignment(), true);
1361 }else{//insertGap==false AND editSeq==TRUE;
1362 if (fixedColumns && fixedRight != -1)
1364 for (int j = lastres; j < startres; j++)
1366 insertChar(j, new SequenceI[]
1367 { seq }, fixedRight);
1372 editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
1373 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1380 seqCanvas.repaint();
1383 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1385 int blankColumn = fixedColumn;
1386 for (int s = 0; s < seq.length; s++)
1388 // Find the next gap before the end of the visible region boundary
1389 // If lastCol > j, theres a boundary after the gap insertion
1391 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1393 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1395 // Theres a space, so break and insert the gap
1400 if (blankColumn <= j)
1402 blankColumn = fixedColumn;
1408 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
1409 av.getAlignment(), true);
1411 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
1416 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1419 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
1422 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
1423 av.getAlignment(), true);
1432 public void mouseEntered(MouseEvent e)
1439 if (scrollThread != null)
1441 scrollThread.running = false;
1442 scrollThread = null;
1452 public void mouseExited(MouseEvent e)
1454 if (av.getWrapAlignment())
1461 scrollThread = new ScrollThread();
1465 public void mouseClicked(MouseEvent evt)
1467 SequenceGroup sg = null;
1468 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1469 if (evt.getClickCount() > 1)
1471 sg = av.getSelectionGroup();
1472 if (sg != null && sg.getSize() == 1
1473 && sg.getEndRes() - sg.getStartRes() < 2)
1475 av.setSelectionGroup(null);
1478 SequenceFeature[] features = findFeaturesAtRes(
1479 sequence.getDatasetSequence(),
1480 sequence.findPosition(findRes(evt)));
1482 if (features != null && features.length > 0)
1484 SearchResults highlight = new SearchResults();
1485 highlight.addResult(sequence, features[0].getBegin(),
1486 features[0].getEnd());
1487 seqCanvas.highlightSearchResults(highlight);
1489 if (features != null && features.length > 0)
1491 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
1492 { sequence }, features, false, ap);
1494 seqCanvas.highlightSearchResults(null);
1499 public void mouseWheelMoved(MouseWheelEvent e)
1502 if (e.getWheelRotation() > 0)
1510 // TODO Update tooltip for new position.
1519 public void doMousePressedDefineMode(MouseEvent evt)
1521 int res = findRes(evt);
1522 int seq = findSeq(evt);
1525 startWrapBlock = wrappedBlock;
1527 if (av.wrapAlignment && seq > av.getAlignment().getHeight())
1529 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1530 "Cannot edit annotations in wrapped view.",
1531 "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
1535 if (seq < 0 || res < 0)
1540 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
1542 if ((sequence == null) || (res > sequence.getLength()))
1547 stretchGroup = av.getSelectionGroup();
1549 if (stretchGroup == null)
1551 stretchGroup = av.getAlignment().findGroup(sequence);
1553 if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
1554 && (res < stretchGroup.getEndRes()))
1556 av.setSelectionGroup(stretchGroup);
1560 stretchGroup = null;
1563 else if (!stretchGroup.getSequences(null).contains(sequence)
1564 || (stretchGroup.getStartRes() > res)
1565 || (stretchGroup.getEndRes() < res))
1567 stretchGroup = null;
1569 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1571 if (allGroups != null)
1573 for (int i = 0; i < allGroups.length; i++)
1575 if ((allGroups[i].getStartRes() <= res)
1576 && (allGroups[i].getEndRes() >= res))
1578 stretchGroup = allGroups[i];
1584 av.setSelectionGroup(stretchGroup);
1588 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
1590 SequenceFeature[] allFeatures = findFeaturesAtRes(
1591 sequence.getDatasetSequence(), sequence.findPosition(res));
1592 Vector links = new Vector();
1593 for (int i = 0; i < allFeatures.length; i++)
1595 if (allFeatures[i].links != null)
1597 for (int j = 0; j < allFeatures[i].links.size(); j++)
1599 links.addElement(allFeatures[i].links.elementAt(j));
1604 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
1605 pop.show(this, evt.getX(), evt.getY());
1611 seqCanvas.cursorX = findRes(evt);
1612 seqCanvas.cursorY = findSeq(evt);
1613 seqCanvas.repaint();
1617 if (stretchGroup == null)
1619 // Only if left mouse button do we want to change group sizes
1621 // define a new group here
1622 SequenceGroup sg = new SequenceGroup();
1623 sg.setStartRes(res);
1625 sg.addSequence(sequence, false);
1626 av.setSelectionGroup(sg);
1630 if (av.getConservationSelected())
1632 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1636 if (av.getAbovePIDThreshold())
1638 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1641 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1643 // Edit end res position of selected group
1644 changeEndRes = true;
1646 else if ((stretchGroup != null)
1647 && (stretchGroup.getStartRes() == res))
1649 // Edit end res position of selected group
1650 changeStartRes = true;
1652 stretchGroup.getWidth();
1655 seqCanvas.repaint();
1664 public void doMouseReleasedDefineMode(MouseEvent evt)
1666 if (stretchGroup == null)
1671 stretchGroup.recalcConservation(); // always do this - annotation has own
1673 if (stretchGroup.cs != null)
1675 if (stretchGroup.cs instanceof ClustalxColourScheme)
1677 ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
1678 stretchGroup,av.getHiddenRepSequences());
1681 if (stretchGroup.cs.conservationApplied())
1683 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1684 stretchGroup.getName());
1688 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1689 stretchGroup.getName());
1692 PaintRefresher.Refresh(this, av.getSequenceSetId());
1693 ap.paintAlignment(true);
1695 changeEndRes = false;
1696 changeStartRes = false;
1697 stretchGroup = null;
1707 public void doMouseDraggedDefineMode(MouseEvent evt)
1709 int res = findRes(evt);
1710 int y = findSeq(evt);
1712 if (wrappedBlock != startWrapBlock)
1717 if (stretchGroup == null)
1722 if (res >= av.getAlignment().getWidth())
1724 res = av.getAlignment().getWidth() - 1;
1727 if (stretchGroup.getEndRes() == res)
1729 // Edit end res position of selected group
1730 changeEndRes = true;
1732 else if (stretchGroup.getStartRes() == res)
1734 // Edit start res position of selected group
1735 changeStartRes = true;
1738 if (res < av.getStartRes())
1740 res = av.getStartRes();
1745 if (res > (stretchGroup.getStartRes() - 1))
1747 stretchGroup.setEndRes(res);
1750 else if (changeStartRes)
1752 if (res < (stretchGroup.getEndRes() + 1))
1754 stretchGroup.setStartRes(res);
1758 int dragDirection = 0;
1764 else if (y < oldSeq)
1769 while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
1771 // This routine ensures we don't skip any sequences, as the
1772 // selection is quite slow.
1773 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1775 oldSeq += dragDirection;
1782 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1784 if (stretchGroup.getSequences(null).contains(nextSeq))
1786 stretchGroup.deleteSequence(seq, false);
1792 stretchGroup.addSequence(seq, false);
1795 stretchGroup.addSequence(nextSeq, false);
1804 mouseDragging = true;
1806 if (scrollThread != null)
1808 scrollThread.setEvent(evt);
1811 seqCanvas.repaint();
1814 void scrollCanvas(MouseEvent evt)
1818 if (scrollThread != null)
1820 scrollThread.running = false;
1821 scrollThread = null;
1823 mouseDragging = false;
1827 if (scrollThread == null)
1829 scrollThread = new ScrollThread();
1832 mouseDragging = true;
1833 scrollThread.setEvent(evt);
1838 // this class allows scrolling off the bottom of the visible alignment
1839 class ScrollThread extends Thread
1843 boolean running = false;
1845 public ScrollThread()
1850 public void setEvent(MouseEvent e)
1855 public void stopScrolling()
1868 if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
1870 running = ap.scrollUp(true);
1873 if (mouseDragging && (evt.getY() >= getHeight())
1874 && (av.getAlignment().getHeight() > av.getEndSeq()))
1876 running = ap.scrollUp(false);
1879 if (mouseDragging && (evt.getX() < 0))
1881 running = ap.scrollRight(false);
1883 else if (mouseDragging && (evt.getX() >= getWidth()))
1885 running = ap.scrollRight(true);
1892 } catch (Exception ex)
1900 * modify current selection according to a received message.
1902 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1903 SelectionSource source)
1905 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1906 // handles selection messages...
1907 // TODO: extend config options to allow user to control if selections may be
1908 // shared between viewports.
1910 || !av.followSelection
1911 || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
1912 || (source instanceof AlignViewport && ((AlignViewport) source)
1913 .getSequenceSetId().equals(av.getSequenceSetId())))
1917 // do we want to thread this ? (contention with seqsel and colsel locks, I
1919 // rules are: colsel is copied if there is a real intersection between
1920 // sequence selection
1921 boolean repaint = false, copycolsel = true;
1922 // if (!av.isSelectionGroupChanged(false))
1924 SequenceGroup sgroup = null;
1925 if (seqsel != null && seqsel.getSize()>0)
1927 if (av.getAlignment() == null)
1929 jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
1930 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1931 + " 's alignment is NULL! returning immediatly.");
1934 sgroup = seqsel.intersect(av.getAlignment(),
1935 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1936 if ((sgroup == null || sgroup.getSize() == 0)
1937 || (colsel == null || colsel.size() == 0))
1939 // don't copy columns if the region didn't intersect.
1943 if (sgroup != null && sgroup.getSize() > 0)
1945 av.setSelectionGroup(sgroup);
1949 av.setSelectionGroup(null);
1951 av.isSelectionGroupChanged(true);
1956 // the current selection is unset or from a previous message
1957 // so import the new colsel.
1958 if (colsel == null || colsel.size() == 0)
1960 if (av.getColumnSelection() != null)
1962 av.getColumnSelection().clear();
1968 // TODO: shift colSel according to the intersecting sequences
1969 if (av.getColumnSelection() == null)
1971 av.setColumnSelection(new ColumnSelection(colsel));
1975 av.getColumnSelection().setElementsFrom(colsel);
1978 av.isColSelChanged(true);
1981 if (copycolsel && av.hasHiddenColumns()
1982 && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
1984 System.err.println("Bad things");
1988 // probably finessing with multiple redraws here
1989 PaintRefresher.Refresh(this, av.getSequenceSetId());
1990 // ap.paintAlignment(false);