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 = 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 = 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());
543 public void mouseReleased(MouseEvent evt)
545 mouseDragging = false;
546 mouseWheelPressed = false;
550 doMouseReleasedDefineMode(evt);
564 public void mousePressed(MouseEvent evt)
566 lastMousePress = evt.getPoint();
568 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
570 mouseWheelPressed = true;
574 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
576 if (evt.isAltDown() || evt.isControlDown())
584 doMousePressedDefineMode(evt);
588 int seq = findSeq(evt);
589 int res = findRes(evt);
591 if (seq < 0 || res < 0)
596 if ((seq < av.getAlignment().getHeight())
597 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
614 public void mouseOverSequence(SequenceI sequence, int index, int pos)
616 String tmp = sequence.hashCode() + " " + index + " " + pos;
618 if (lastMessage == null || !lastMessage.equals(tmp))
620 // System.err.println("mouseOver Sequence: "+tmp);
621 ssm.mouseOverSequence(sequence, index, pos, av);
627 public void highlightSequence(SearchResults results)
629 if (av.followHighlight)
631 if (ap.scrollToPosition(results, false))
633 seqCanvas.revalidate();
636 seqCanvas.highlightSearchResults(results);
640 public void updateColours(SequenceI seq, int index)
642 System.out.println("update the seqPanel colours");
653 public void mouseMoved(MouseEvent evt)
657 // This is because MacOSX creates a mouseMoved
658 // If control is down, other platforms will not.
662 int res = findRes(evt);
663 int seq = findSeq(evt);
665 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
670 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
672 if (res >= sequence.getLength())
677 pos = setStatusMessage(sequence, res, seq);
678 if (ssm != null && pos > -1)
679 mouseOverSequence(sequence, res, pos);
681 tooltipText.setLength(6); // Cuts the buffer back to <html>
683 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
686 for (int g = 0; g < groups.length; g++)
688 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
690 if (tooltipText.length() > 6)
692 tooltipText.append("<br>");
695 if (!groups[g].getName().startsWith("JTreeGroup")
696 && !groups[g].getName().startsWith("JGroup"))
698 tooltipText.append(groups[g].getName());
701 if (groups[g].getDescription() != null)
703 tooltipText.append(": " + groups[g].getDescription());
709 // use aa to see if the mouse pointer is on a
710 if (av.showSequenceFeatures)
713 SequenceFeature[] features = findFeaturesAtRes(
714 sequence.getDatasetSequence(),
715 rpos = sequence.findPosition(res));
716 appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
717 this.ap.seqPanel.seqCanvas.fr.minmax);
719 if (tooltipText.length() == 6) // <html></html>
721 setToolTipText(null);
726 tooltipText.append("</html>");
727 if (lastTooltip == null
728 || !lastTooltip.equals(tooltipText.toString()))
730 setToolTipText(tooltipText.toString());
731 lastTooltip = tooltipText.toString();
738 private Point lastp = null;
743 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
745 public Point getToolTipLocation(MouseEvent event)
747 int x = event.getX(), w = getWidth();
748 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
751 if (!event.isShiftDown() || p == null)
753 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
754 event.getX() + wdth, event.getY() - 20) : null;
757 * TODO: try to modify position region is not obcured by tooltip
763 * appends the features at rpos to the given stringbuffer ready for display in
766 * @param tooltipText2
767 * @param linkImageURL
770 * TODO refactor to Jalview 'utilities' somehow.
772 public void appendFeatures(StringBuffer tooltipText2,
773 String linkImageURL, int rpos, SequenceFeature[] features)
775 appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
778 public void appendFeatures(StringBuffer tooltipText2, String string,
779 int rpos, SequenceFeature[] features, Hashtable minmax)
782 if (features != null)
784 for (int i = 0; i < features.length; i++)
786 if (features[i].getType().equals("disulfide bond"))
788 if (features[i].getBegin() == rpos
789 || features[i].getEnd() == rpos)
791 if (tooltipText2.length() > 6)
793 tooltipText2.append("<br>");
795 tooltipText2.append("disulfide bond " + features[i].getBegin()
796 + ":" + features[i].getEnd());
797 if (features[i].links != null)
799 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
805 if (tooltipText2.length() > 6)
807 tooltipText2.append("<br>");
809 // TODO: remove this hack to display link only features
810 boolean linkOnly = features[i].getValue("linkonly") != null;
813 tooltipText2.append(features[i].getType() + " ");
816 // we are marking a positional feature
817 tooltipText2.append(features[i].begin);
819 if (features[i].begin != features[i].end)
821 tooltipText2.append(" " + features[i].end);
824 if (features[i].getDescription() != null
825 && !features[i].description.equals(features[i]
828 tmpString = features[i].getDescription();
829 String tmp2up=tmpString.toUpperCase();
830 int startTag = tmp2up.indexOf("<HTML>");
833 tmpString = tmpString.substring(startTag + 6);
834 tmp2up = tmp2up.substring(startTag+6);
836 int endTag = tmp2up.indexOf("</BODY>");
839 tmpString = tmpString.substring(0, endTag);
840 tmp2up = tmp2up.substring(0, endTag);
842 endTag = tmp2up.indexOf("</HTML>");
845 tmpString = tmpString.substring(0, endTag);
850 tooltipText2.append("; " + tmpString);
854 if (tmpString.indexOf("<") > -1
855 || tmpString.indexOf(">") > -1)
857 // The description does not specify html is to
858 // be used, so we must remove < > symbols
859 tmpString = tmpString.replaceAll("<", "<");
860 tmpString = tmpString.replaceAll(">", ">");
862 tooltipText2.append("; ");
863 tooltipText2.append(tmpString);
868 tooltipText2.append("; " + tmpString);
872 // check score should be shown
873 if (features[i].getScore() != Float.NaN)
875 float[][] rng = (minmax == null) ? null : ((float[][]) minmax
876 .get(features[i].getType()));
877 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
879 tooltipText2.append(" Score=" + features[i].getScore());
882 if (features[i].getValue("status") != null)
884 String status = features[i].getValue("status").toString();
885 if (status.length() > 0)
887 tooltipText2.append("; (" + features[i].getValue("status")
892 if (features[i].links != null)
894 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
905 * Set status message in alignment panel
908 * aligned sequence object
912 * index of sequence in alignment
913 * @return position of res in sequence
915 int setStatusMessage(SequenceI sequence, int res, int seq)
918 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
919 + sequence.getName());
922 if (av.getAlignment().isNucleotide())
924 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
928 text.append(" Nucleotide: ");
933 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
936 text.append(" Residue: ");
942 pos = sequence.findPosition(res);
945 text.append(obj + " (" + pos + ")");
948 ap.alignFrame.statusBar.setText(text.toString());
959 public void mouseDragged(MouseEvent evt)
961 if (mouseWheelPressed)
963 int oldWidth = av.charWidth;
965 // Which is bigger, left-right or up-down?
966 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
967 .getX() - lastMousePress.getX()))
969 int fontSize = av.font.getSize();
971 if (evt.getY() < lastMousePress.getY())
975 else if (evt.getY() > lastMousePress.getY())
985 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
986 av.charWidth = oldWidth;
991 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
995 else if (evt.getX() > lastMousePress.getX())
1000 ap.paintAlignment(false);
1003 FontMetrics fm = getFontMetrics(av.getFont());
1004 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
1006 lastMousePress = evt.getPoint();
1013 doMouseDraggedDefineMode(evt);
1017 int res = findRes(evt);
1024 if ((lastres == -1) || (lastres == res))
1029 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1031 // dragLeft, delete gap
1032 editSequence(false, false,res);
1036 editSequence(true, false,res);
1039 mouseDragging = true;
1040 if (scrollThread != null)
1042 scrollThread.setEvent(evt);
1046 //TODO: Make it more clever than many booleans
1047 synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
1050 int fixedRight = -1;
1051 boolean fixedColumns = false;
1052 SequenceGroup sg = av.getSelectionGroup();
1054 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1056 // No group, but the sequence may represent a group
1057 if (!groupEditing && av.hasHiddenRows())
1059 if (av.isHiddenRepSequence(seq))
1061 sg = av.getRepresentedSequences(seq);
1062 groupEditing = true;
1066 StringBuffer message = new StringBuffer();
1069 message.append("Edit group:");
1070 if (editCommand == null)
1072 editCommand = new EditCommand("Edit Group");
1077 message.append("Edit sequence: " + seq.getName());
1078 String label = seq.getName();
1079 if (label.length() > 10)
1081 label = label.substring(0, 10);
1083 if (editCommand == null)
1085 editCommand = new EditCommand("Edit " + label);
1091 message.append(" insert ");
1095 message.append(" delete ");
1098 message.append(Math.abs(startres - lastres) + " gaps.");
1099 ap.alignFrame.statusBar.setText(message.toString());
1101 // Are we editing within a selection group?
1103 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1106 fixedColumns = true;
1108 // sg might be null as the user may only see 1 sequence,
1109 // but the sequence represents a group
1112 if (!av.isHiddenRepSequence(seq))
1117 sg = av.getRepresentedSequences(seq);
1120 fixedLeft = sg.getStartRes();
1121 fixedRight = sg.getEndRes();
1123 if ((startres < fixedLeft && lastres >= fixedLeft)
1124 || (startres >= fixedLeft && lastres < fixedLeft)
1125 || (startres > fixedRight && lastres <= fixedRight)
1126 || (startres <= fixedRight && lastres > fixedRight))
1132 if (fixedLeft > startres)
1134 fixedRight = fixedLeft - 1;
1137 else if (fixedRight < startres)
1139 fixedLeft = fixedRight;
1144 if (av.hasHiddenColumns())
1146 fixedColumns = true;
1147 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1148 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1150 if ((insertGap && startres > y1 && lastres < y1)
1151 || (!insertGap && startres < y2 && lastres > y2))
1157 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1158 // Selection spans a hidden region
1159 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1167 fixedRight = y2 - 1;
1174 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1175 int g, groupSize = vseqs.size();
1176 SequenceI[] groupSeqs = new SequenceI[groupSize];
1177 for (g = 0; g < groupSeqs.length; g++)
1179 groupSeqs[g] = vseqs.get(g);
1185 // If the user has selected the whole sequence, and is dragging to
1186 // the right, we can still extend the alignment and selectionGroup
1187 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1188 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1190 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1191 fixedRight = sg.getEndRes();
1194 // Is it valid with fixed columns??
1195 // Find the next gap before the end
1196 // of the visible region boundary
1197 boolean blank = false;
1198 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1202 for (g = 0; g < groupSize; g++)
1204 for (int j = 0; j < startres - lastres; j++)
1206 if (!jalview.util.Comparison.isGap(groupSeqs[g]
1207 .getCharAt(fixedRight - j)))
1222 if (sg.getSize() == av.getAlignment().getHeight())
1224 if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
1225 .getHiddenBoundaryRight(startres)))
1231 int alWidth = av.getAlignment().getWidth();
1232 if (av.hasHiddenRows())
1234 int hwidth = av.getAlignment().getHiddenSequences().getWidth();
1235 if (hwidth > alWidth)
1240 // We can still insert gaps if the selectionGroup
1241 // contains all the sequences
1242 sg.setEndRes(sg.getEndRes() + startres - lastres);
1243 fixedRight = alWidth + startres - lastres;
1254 else if (!insertGap)
1256 // / Are we able to delete?
1257 // ie are all columns blank?
1259 for (g = 0; g < groupSize; g++)
1261 for (int j = startres; j < lastres; j++)
1263 if (groupSeqs[g].getLength() <= j)
1268 if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
1270 // Not a gap, block edit not valid
1280 // dragging to the right
1281 if (fixedColumns && fixedRight != -1)
1283 for (int j = lastres; j < startres; j++)
1285 insertChar(j, groupSeqs, fixedRight);
1290 editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
1291 startres, startres - lastres, av.getAlignment(), true);
1296 // dragging to the left
1297 if (fixedColumns && fixedRight != -1)
1299 for (int j = lastres; j > startres; j--)
1301 deleteChar(startres, groupSeqs, fixedRight);
1306 editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
1307 startres, lastres - startres, av.getAlignment(), true);
1313 // ///Editing a single sequence///////////
1317 // dragging to the right
1318 if (fixedColumns && fixedRight != -1)
1320 for (int j = lastres; j < startres; j++)
1322 insertChar(j, new SequenceI[]
1323 { seq }, fixedRight);
1328 editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
1329 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1335 // dragging to the left
1336 if (fixedColumns && fixedRight != -1)
1338 for (int j = lastres; j > startres; j--)
1340 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1345 deleteChar(startres, new SequenceI[]
1346 { seq }, fixedRight);
1351 // could be a keyboard edit trying to delete none gaps
1353 for (int m = startres; m < lastres; m++)
1355 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1364 editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
1365 { seq }, startres, max, av.getAlignment(), true);
1368 }else{//insertGap==false AND editSeq==TRUE;
1369 if (fixedColumns && fixedRight != -1)
1371 for (int j = lastres; j < startres; j++)
1373 insertChar(j, new SequenceI[]
1374 { seq }, fixedRight);
1379 editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
1380 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1387 seqCanvas.repaint();
1390 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1392 int blankColumn = fixedColumn;
1393 for (int s = 0; s < seq.length; s++)
1395 // Find the next gap before the end of the visible region boundary
1396 // If lastCol > j, theres a boundary after the gap insertion
1398 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1400 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1402 // Theres a space, so break and insert the gap
1407 if (blankColumn <= j)
1409 blankColumn = fixedColumn;
1415 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
1416 av.getAlignment(), true);
1418 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
1423 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1426 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
1429 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
1430 av.getAlignment(), true);
1440 public void mouseEntered(MouseEvent e)
1447 if (scrollThread != null)
1449 scrollThread.running = false;
1450 scrollThread = null;
1461 public void mouseExited(MouseEvent e)
1463 if (av.getWrapAlignment())
1470 scrollThread = new ScrollThread();
1475 public void mouseClicked(MouseEvent evt)
1477 SequenceGroup sg = null;
1478 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1479 if (evt.getClickCount() > 1)
1481 sg = av.getSelectionGroup();
1482 if (sg != null && sg.getSize() == 1
1483 && sg.getEndRes() - sg.getStartRes() < 2)
1485 av.setSelectionGroup(null);
1488 SequenceFeature[] features = findFeaturesAtRes(
1489 sequence.getDatasetSequence(),
1490 sequence.findPosition(findRes(evt)));
1492 if (features != null && features.length > 0)
1494 SearchResults highlight = new SearchResults();
1495 highlight.addResult(sequence, features[0].getBegin(),
1496 features[0].getEnd());
1497 seqCanvas.highlightSearchResults(highlight);
1499 if (features != null && features.length > 0)
1501 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
1502 { sequence }, features, false, ap);
1504 seqCanvas.highlightSearchResults(null);
1510 public void mouseWheelMoved(MouseWheelEvent e)
1513 if (e.getWheelRotation() > 0)
1521 // TODO Update tooltip for new position.
1530 public void doMousePressedDefineMode(MouseEvent evt)
1532 int res = findRes(evt);
1533 int seq = findSeq(evt);
1536 startWrapBlock = wrappedBlock;
1538 if (av.wrapAlignment && seq > av.getAlignment().getHeight())
1540 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1541 "Cannot edit annotations in wrapped view.",
1542 "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
1546 if (seq < 0 || res < 0)
1551 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1553 if ((sequence == null) || (res > sequence.getLength()))
1558 stretchGroup = av.getSelectionGroup();
1560 if (stretchGroup == null)
1562 stretchGroup = av.getAlignment().findGroup(sequence);
1564 if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
1565 && (res < stretchGroup.getEndRes()))
1567 av.setSelectionGroup(stretchGroup);
1571 stretchGroup = null;
1574 else if (!stretchGroup.getSequences(null).contains(sequence)
1575 || (stretchGroup.getStartRes() > res)
1576 || (stretchGroup.getEndRes() < res))
1578 stretchGroup = null;
1580 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1582 if (allGroups != null)
1584 for (int i = 0; i < allGroups.length; i++)
1586 if ((allGroups[i].getStartRes() <= res)
1587 && (allGroups[i].getEndRes() >= res))
1589 stretchGroup = allGroups[i];
1595 av.setSelectionGroup(stretchGroup);
1599 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
1601 SequenceFeature[] allFeatures = findFeaturesAtRes(
1602 sequence.getDatasetSequence(), sequence.findPosition(res));
1603 Vector links = new Vector();
1604 for (int i = 0; i < allFeatures.length; i++)
1606 if (allFeatures[i].links != null)
1608 for (int j = 0; j < allFeatures[i].links.size(); j++)
1610 links.addElement(allFeatures[i].links.elementAt(j));
1615 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
1616 pop.show(this, evt.getX(), evt.getY());
1622 seqCanvas.cursorX = findRes(evt);
1623 seqCanvas.cursorY = findSeq(evt);
1624 seqCanvas.repaint();
1628 if (stretchGroup == null)
1630 // Only if left mouse button do we want to change group sizes
1632 // define a new group here
1633 SequenceGroup sg = new SequenceGroup();
1634 sg.setStartRes(res);
1636 sg.addSequence(sequence, false);
1637 av.setSelectionGroup(sg);
1641 if (av.getConservationSelected())
1643 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1647 if (av.getAbovePIDThreshold())
1649 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1652 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1654 // Edit end res position of selected group
1655 changeEndRes = true;
1657 else if ((stretchGroup != null)
1658 && (stretchGroup.getStartRes() == res))
1660 // Edit end res position of selected group
1661 changeStartRes = true;
1663 stretchGroup.getWidth();
1666 seqCanvas.repaint();
1675 public void doMouseReleasedDefineMode(MouseEvent evt)
1677 if (stretchGroup == null)
1682 stretchGroup.recalcConservation(); // always do this - annotation has own
1684 if (stretchGroup.cs != null)
1686 if (stretchGroup.cs instanceof ClustalxColourScheme)
1688 ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
1689 stretchGroup,av.getHiddenRepSequences());
1692 if (stretchGroup.cs.conservationApplied())
1694 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1695 stretchGroup.getName());
1699 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1700 stretchGroup.getName());
1703 PaintRefresher.Refresh(this, av.getSequenceSetId());
1704 ap.paintAlignment(true);
1706 changeEndRes = false;
1707 changeStartRes = false;
1708 stretchGroup = null;
1718 public void doMouseDraggedDefineMode(MouseEvent evt)
1720 int res = findRes(evt);
1721 int y = findSeq(evt);
1723 if (wrappedBlock != startWrapBlock)
1728 if (stretchGroup == null)
1733 if (res >= av.getAlignment().getWidth())
1735 res = av.getAlignment().getWidth() - 1;
1738 if (stretchGroup.getEndRes() == res)
1740 // Edit end res position of selected group
1741 changeEndRes = true;
1743 else if (stretchGroup.getStartRes() == res)
1745 // Edit start res position of selected group
1746 changeStartRes = true;
1749 if (res < av.getStartRes())
1751 res = av.getStartRes();
1756 if (res > (stretchGroup.getStartRes() - 1))
1758 stretchGroup.setEndRes(res);
1761 else if (changeStartRes)
1763 if (res < (stretchGroup.getEndRes() + 1))
1765 stretchGroup.setStartRes(res);
1769 int dragDirection = 0;
1775 else if (y < oldSeq)
1780 while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
1782 // This routine ensures we don't skip any sequences, as the
1783 // selection is quite slow.
1784 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1786 oldSeq += dragDirection;
1793 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1795 if (stretchGroup.getSequences(null).contains(nextSeq))
1797 stretchGroup.deleteSequence(seq, false);
1803 stretchGroup.addSequence(seq, false);
1806 stretchGroup.addSequence(nextSeq, false);
1815 mouseDragging = true;
1817 if (scrollThread != null)
1819 scrollThread.setEvent(evt);
1822 seqCanvas.repaint();
1825 void scrollCanvas(MouseEvent evt)
1829 if (scrollThread != null)
1831 scrollThread.running = false;
1832 scrollThread = null;
1834 mouseDragging = false;
1838 if (scrollThread == null)
1840 scrollThread = new ScrollThread();
1843 mouseDragging = true;
1844 scrollThread.setEvent(evt);
1849 // this class allows scrolling off the bottom of the visible alignment
1850 class ScrollThread extends Thread
1854 boolean running = false;
1856 public ScrollThread()
1861 public void setEvent(MouseEvent e)
1866 public void stopScrolling()
1880 if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
1882 running = ap.scrollUp(true);
1885 if (mouseDragging && (evt.getY() >= getHeight())
1886 && (av.getAlignment().getHeight() > av.getEndSeq()))
1888 running = ap.scrollUp(false);
1891 if (mouseDragging && (evt.getX() < 0))
1893 running = ap.scrollRight(false);
1895 else if (mouseDragging && (evt.getX() >= getWidth()))
1897 running = ap.scrollRight(true);
1904 } catch (Exception ex)
1912 * modify current selection according to a received message.
1915 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1916 SelectionSource source)
1918 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1919 // handles selection messages...
1920 // TODO: extend config options to allow user to control if selections may be
1921 // shared between viewports.
1923 || !av.followSelection
1924 || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
1925 || (source instanceof AlignViewport && ((AlignViewport) source)
1926 .getSequenceSetId().equals(av.getSequenceSetId())))
1930 // do we want to thread this ? (contention with seqsel and colsel locks, I
1932 // rules are: colsel is copied if there is a real intersection between
1933 // sequence selection
1934 boolean repaint = false, copycolsel = true;
1935 // if (!av.isSelectionGroupChanged(false))
1937 SequenceGroup sgroup = null;
1938 if (seqsel != null && seqsel.getSize()>0)
1940 if (av.getAlignment() == null)
1942 jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
1943 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1944 + " 's alignment is NULL! returning immediatly.");
1947 sgroup = seqsel.intersect(av.getAlignment(),
1948 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1949 if ((sgroup == null || sgroup.getSize() == 0)
1950 || (colsel == null || colsel.size() == 0))
1952 // don't copy columns if the region didn't intersect.
1956 if (sgroup != null && sgroup.getSize() > 0)
1958 av.setSelectionGroup(sgroup);
1962 av.setSelectionGroup(null);
1964 av.isSelectionGroupChanged(true);
1969 // the current selection is unset or from a previous message
1970 // so import the new colsel.
1971 if (colsel == null || colsel.size() == 0)
1973 if (av.getColumnSelection() != null)
1975 av.getColumnSelection().clear();
1981 // TODO: shift colSel according to the intersecting sequences
1982 if (av.getColumnSelection() == null)
1984 av.setColumnSelection(new ColumnSelection(colsel));
1988 av.getColumnSelection().setElementsFrom(colsel);
1991 av.isColSelChanged(true);
1994 if (copycolsel && av.hasHiddenColumns()
1995 && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
1997 System.err.println("Bad things");
2001 // probably finessing with multiple redraws here
2002 PaintRefresher.Refresh(this, av.getSequenceSetId());
2003 // ap.paintAlignment(false);