2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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/>.
23 import java.awt.event.*;
27 import jalview.commands.*;
28 import jalview.datamodel.*;
29 import jalview.schemes.*;
30 import jalview.structure.*;
38 public class SeqPanel extends JPanel implements MouseListener,
39 MouseMotionListener, MouseWheelListener, SequenceListener,
44 public SeqCanvas seqCanvas;
47 public AlignmentPanel ap;
49 protected int lastres;
51 protected int startseq;
53 protected AlignViewport av;
55 ScrollThread scrollThread = null;
57 boolean mouseDragging = false;
59 boolean editingSeqs = false;
61 boolean groupEditing = false;
63 // ////////////////////////////////////////
64 // ///Everything below this is for defining the boundary of the rubberband
65 // ////////////////////////////////////////
68 boolean changeEndSeq = false;
70 boolean changeStartSeq = false;
72 boolean changeEndRes = false;
74 boolean changeStartRes = false;
76 SequenceGroup stretchGroup = null;
78 boolean remove = false;
82 boolean mouseWheelPressed = false;
84 StringBuffer keyboardNo1;
86 StringBuffer keyboardNo2;
88 java.net.URL linkImageURL;
90 StringBuffer tooltipText = new StringBuffer("<html>");
94 EditCommand editCommand;
96 StructureSelectionManager ssm;
99 * Creates a new SeqPanel object.
106 public SeqPanel(AlignViewport av, AlignmentPanel ap)
108 linkImageURL = getClass().getResource("/images/link.gif");
109 ToolTipManager.sharedInstance().registerComponent(this);
110 ToolTipManager.sharedInstance().setInitialDelay(0);
111 ToolTipManager.sharedInstance().setDismissDelay(10000);
113 setBackground(Color.white);
115 seqCanvas = new SeqCanvas(ap);
116 setLayout(new BorderLayout());
117 add(seqCanvas, BorderLayout.CENTER);
123 addMouseMotionListener(this);
124 addMouseListener(this);
125 addMouseWheelListener(this);
126 ssm = StructureSelectionManager.getStructureSelectionManager();
127 ssm.addStructureViewerListener(this);
128 ssm.addSelectionListener(this);
132 int startWrapBlock = -1;
134 int wrappedBlock = -1;
136 int findRes(MouseEvent evt)
141 if (av.wrapAlignment)
144 int hgap = av.charHeight;
145 if (av.scaleAboveWrapped)
147 hgap += av.charHeight;
150 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
151 + seqCanvas.getAnnotationHeight();
155 x -= seqCanvas.LABEL_WEST;
157 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
163 wrappedBlock = y / cHeight;
164 wrappedBlock += av.getStartRes() / cwidth;
166 res = wrappedBlock * cwidth + x / av.getCharWidth();
171 if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
173 // make sure we calculate relative to visible alignment, rather than right-hand gutter
174 x = seqCanvas.getX()+seqCanvas.getWidth();
176 res = (x / av.getCharWidth()) + av.getStartRes();
179 if (av.hasHiddenColumns)
181 res = av.getColumnSelection().adjustForHiddenColumns(res);
188 int findSeq(MouseEvent evt)
193 if (av.wrapAlignment)
195 int hgap = av.charHeight;
196 if (av.scaleAboveWrapped)
198 hgap += av.charHeight;
201 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
202 + seqCanvas.getAnnotationHeight();
206 seq = Math.min((y % cHeight) / av.getCharHeight(),
207 av.alignment.getHeight() - 1);
211 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
212 av.alignment.getHeight() - 1);
218 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
220 Vector tmp = new Vector();
221 SequenceFeature[] features = sequence.getSequenceFeatures();
222 if (features != null)
224 for (int i = 0; i < features.length; i++)
226 if (av.featuresDisplayed == null
227 || !av.featuresDisplayed.containsKey(features[i].getType()))
232 if (features[i].featureGroup != null
233 && seqCanvas.fr.featureGroups != null
234 && seqCanvas.fr.featureGroups
235 .containsKey(features[i].featureGroup)
236 && !((Boolean) seqCanvas.fr.featureGroups
237 .get(features[i].featureGroup)).booleanValue())
240 if ((features[i].getBegin() <= res)
241 && (features[i].getEnd() >= res))
243 tmp.addElement(features[i]);
248 features = new SequenceFeature[tmp.size()];
249 tmp.copyInto(features);
256 if (editCommand != null && editCommand.getSize() > 0)
258 ap.alignFrame.addHistoryItem(editCommand);
259 av.firePropertyChange("alignment", null, av.getAlignment()
266 groupEditing = false;
274 seqCanvas.cursorY = getKeyboardNo1() - 1;
278 void setCursorColumn()
280 seqCanvas.cursorX = getKeyboardNo1() - 1;
284 void setCursorRowAndColumn()
286 if (keyboardNo2 == null)
288 keyboardNo2 = new StringBuffer();
292 seqCanvas.cursorX = getKeyboardNo1() - 1;
293 seqCanvas.cursorY = getKeyboardNo2() - 1;
298 void setCursorPosition()
300 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
303 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
307 void moveCursor(int dx, int dy)
309 seqCanvas.cursorX += dx;
310 seqCanvas.cursorY += dy;
311 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
313 int original = seqCanvas.cursorX - dx;
314 int maxWidth = av.alignment.getWidth();
316 while (!av.colSel.isVisible(seqCanvas.cursorX)
317 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
319 seqCanvas.cursorX += dx;
322 if (seqCanvas.cursorX >= maxWidth
323 || !av.colSel.isVisible(seqCanvas.cursorX))
325 seqCanvas.cursorX = original;
332 void scrollToVisible()
334 if (seqCanvas.cursorX < 0)
336 seqCanvas.cursorX = 0;
338 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
340 seqCanvas.cursorX = av.alignment.getWidth() - 1;
343 if (seqCanvas.cursorY < 0)
345 seqCanvas.cursorY = 0;
347 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
349 seqCanvas.cursorY = av.alignment.getHeight() - 1;
353 if (av.wrapAlignment)
355 ap.scrollToWrappedVisible(seqCanvas.cursorX);
359 while (seqCanvas.cursorY < av.startSeq)
363 while (seqCanvas.cursorY + 1 > av.endSeq)
367 if (!av.wrapAlignment)
369 while (seqCanvas.cursorX < av.colSel
370 .adjustForHiddenColumns(av.startRes))
372 if (!ap.scrollRight(false))
377 while (seqCanvas.cursorX > av.colSel
378 .adjustForHiddenColumns(av.endRes))
380 if (!ap.scrollRight(true))
387 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
388 seqCanvas.cursorX, seqCanvas.cursorY);
393 void setSelectionAreaAtCursor(boolean topLeft)
395 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
398 if (av.getSelectionGroup() != null)
400 SequenceGroup sg = av.selectionGroup;
401 // Find the top and bottom of this group
402 int min = av.alignment.getHeight(), max = 0;
403 for (int i = 0; i < sg.getSize(); i++)
405 int index = av.alignment.findIndex(sg.getSequenceAt(i));
420 sg.setStartRes(seqCanvas.cursorX);
421 if (sg.getEndRes() < seqCanvas.cursorX)
423 sg.setEndRes(seqCanvas.cursorX);
426 min = seqCanvas.cursorY;
430 sg.setEndRes(seqCanvas.cursorX);
431 if (sg.getStartRes() > seqCanvas.cursorX)
433 sg.setStartRes(seqCanvas.cursorX);
436 max = seqCanvas.cursorY + 1;
441 // Only the user can do this
442 av.setSelectionGroup(null);
446 // Now add any sequences between min and max
447 sg.getSequences(null).clear();
448 for (int i = min; i < max; i++)
450 sg.addSequence(av.alignment.getSequenceAt(i), false);
455 if (av.getSelectionGroup() == null)
457 SequenceGroup sg = new SequenceGroup();
458 sg.setStartRes(seqCanvas.cursorX);
459 sg.setEndRes(seqCanvas.cursorX);
460 sg.addSequence(sequence, false);
461 av.setSelectionGroup(sg);
464 ap.paintAlignment(false);
468 void insertGapAtCursor(boolean group)
470 groupEditing = group;
471 startseq = seqCanvas.cursorY;
472 lastres = seqCanvas.cursorX;
473 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
477 void deleteGapAtCursor(boolean group)
479 groupEditing = group;
480 startseq = seqCanvas.cursorY;
481 lastres = seqCanvas.cursorX + getKeyboardNo1();
482 editSequence(false, seqCanvas.cursorX);
486 void numberPressed(char value)
488 if (keyboardNo1 == null)
490 keyboardNo1 = new StringBuffer();
493 if (keyboardNo2 != null)
495 keyboardNo2.append(value);
499 keyboardNo1.append(value);
505 if (keyboardNo1 == null)
509 int value = Integer.parseInt(keyboardNo1.toString());
517 if (keyboardNo2 == null)
521 int value = Integer.parseInt(keyboardNo2.toString());
533 public void mouseReleased(MouseEvent evt)
535 mouseDragging = false;
536 mouseWheelPressed = false;
540 doMouseReleasedDefineMode(evt);
553 public void mousePressed(MouseEvent evt)
555 lastMousePress = evt.getPoint();
557 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
559 mouseWheelPressed = true;
563 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
565 if (evt.isAltDown() || evt.isControlDown())
573 doMousePressedDefineMode(evt);
577 int seq = findSeq(evt);
578 int res = findRes(evt);
580 if (seq < 0 || res < 0)
585 if ((seq < av.getAlignment().getHeight())
586 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
602 public void mouseOverSequence(SequenceI sequence, int index, int pos)
604 String tmp = sequence.hashCode() + " " + index + " " + pos;
606 if (lastMessage == null || !lastMessage.equals(tmp))
608 // System.err.println("mouseOver Sequence: "+tmp);
609 ssm.mouseOverSequence(sequence, index, pos, av);
614 public void highlightSequence(SearchResults results)
616 if (av.followHighlight)
618 if (ap.scrollToPosition(results, false))
620 seqCanvas.revalidate();
623 seqCanvas.highlightSearchResults(results);
626 public void updateColours(SequenceI seq, int index)
628 System.out.println("update the seqPanel colours");
638 public void mouseMoved(MouseEvent evt)
642 // This is because MacOSX creates a mouseMoved
643 // If control is down, other platforms will not.
647 int res = findRes(evt);
648 int seq = findSeq(evt);
650 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
655 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
657 if (res >= sequence.getLength())
662 pos = setStatusMessage(sequence, res, seq);
663 if (ssm != null && pos > -1)
664 mouseOverSequence(sequence, res, pos);
666 tooltipText.setLength(6); // Cuts the buffer back to <html>
668 SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
671 for (int g = 0; g < groups.length; g++)
673 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
675 if (tooltipText.length() > 6)
677 tooltipText.append("<br>");
680 if (!groups[g].getName().startsWith("JTreeGroup")
681 && !groups[g].getName().startsWith("JGroup"))
683 tooltipText.append(groups[g].getName());
686 if (groups[g].getDescription() != null)
688 tooltipText.append(": " + groups[g].getDescription());
694 // use aa to see if the mouse pointer is on a
695 if (av.showSequenceFeatures)
698 SequenceFeature[] features = findFeaturesAtRes(
699 sequence.getDatasetSequence(),
700 rpos = sequence.findPosition(res));
701 appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
702 this.ap.seqPanel.seqCanvas.fr.minmax);
704 if (tooltipText.length() == 6) // <html></html>
706 setToolTipText(null);
711 tooltipText.append("</html>");
712 if (lastTooltip == null
713 || !lastTooltip.equals(tooltipText.toString()))
715 setToolTipText(tooltipText.toString());
716 lastTooltip = tooltipText.toString();
723 private Point lastp = null;
728 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
730 public Point getToolTipLocation(MouseEvent event)
732 int x = event.getX(), w = getWidth();
733 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
736 if (!event.isShiftDown() || p == null)
738 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
739 event.getX() + wdth, event.getY() - 20) : null;
742 * TODO: try to modify position region is not obcured by tooltip
748 * appends the features at rpos to the given stringbuffer ready for display in
751 * @param tooltipText2
752 * @param linkImageURL
755 * TODO refactor to Jalview 'utilities' somehow.
757 public void appendFeatures(StringBuffer tooltipText2,
758 String linkImageURL, int rpos, SequenceFeature[] features)
760 appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
763 public void appendFeatures(StringBuffer tooltipText2, String string,
764 int rpos, SequenceFeature[] features, Hashtable minmax)
767 if (features != null)
769 for (int i = 0; i < features.length; i++)
771 if (features[i].getType().equals("disulfide bond"))
773 if (features[i].getBegin() == rpos
774 || features[i].getEnd() == rpos)
776 if (tooltipText2.length() > 6)
778 tooltipText2.append("<br>");
780 tooltipText2.append("disulfide bond " + features[i].getBegin()
781 + ":" + features[i].getEnd());
782 if (features[i].links != null)
784 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
790 if (tooltipText2.length() > 6)
792 tooltipText2.append("<br>");
794 // TODO: remove this hack to display link only features
795 boolean linkOnly = features[i].getValue("linkonly") != null;
798 tooltipText2.append(features[i].getType() + " ");
801 // we are marking a positional feature
802 tooltipText2.append(features[i].begin);
804 if (features[i].begin != features[i].end)
806 tooltipText2.append(" " + features[i].end);
809 if (features[i].getDescription() != null
810 && !features[i].description.equals(features[i]
813 tmpString = features[i].getDescription();
814 int startTag = tmpString.toUpperCase().indexOf("<HTML>");
817 tmpString = tmpString.substring(startTag + 6);
819 int endTag = tmpString.toUpperCase().indexOf("</BODY>");
822 tmpString = tmpString.substring(0, endTag);
824 endTag = tmpString.toUpperCase().indexOf("</HTML>");
827 tmpString = tmpString.substring(0, endTag);
832 tooltipText2.append("; " + tmpString);
836 if (tmpString.indexOf("<") > -1
837 || tmpString.indexOf(">") > -1)
839 // The description does not specify html is to
840 // be used, so we must remove < > symbols
841 tmpString = tmpString.replaceAll("<", "<");
842 tmpString = tmpString.replaceAll(">", ">");
844 tooltipText2.append("; ");
845 tooltipText2.append(tmpString);
850 tooltipText2.append("; " + tmpString);
854 // check score should be shown
855 if (features[i].getScore() != Float.NaN)
857 float[][] rng = (minmax == null) ? null : ((float[][]) minmax
858 .get(features[i].getType()));
859 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
861 tooltipText2.append(" Score=" + features[i].getScore());
864 if (features[i].getValue("status") != null)
866 String status = features[i].getValue("status").toString();
867 if (status.length() > 0)
869 tooltipText2.append("; (" + features[i].getValue("status")
874 if (features[i].links != null)
876 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
887 * Set status message in alignment panel
890 * aligned sequence object
894 * index of sequence in alignment
895 * @return position of res in sequence
897 int setStatusMessage(SequenceI sequence, int res, int seq)
900 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
901 + sequence.getName());
904 if (av.alignment.isNucleotide())
906 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
910 text.append(" Nucleotide: ");
915 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
918 text.append(" Residue: ");
924 pos = sequence.findPosition(res);
927 text.append(obj + " (" + pos + ")");
930 ap.alignFrame.statusBar.setText(text.toString());
940 public void mouseDragged(MouseEvent evt)
942 if (mouseWheelPressed)
944 int oldWidth = av.charWidth;
946 // Which is bigger, left-right or up-down?
947 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
948 .getX() - lastMousePress.getX()))
950 int fontSize = av.font.getSize();
952 if (evt.getY() < lastMousePress.getY())
956 else if (evt.getY() > lastMousePress.getY())
966 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
967 av.charWidth = oldWidth;
972 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
976 else if (evt.getX() > lastMousePress.getX())
981 ap.paintAlignment(false);
984 FontMetrics fm = getFontMetrics(av.getFont());
985 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
987 lastMousePress = evt.getPoint();
994 doMouseDraggedDefineMode(evt);
998 int res = findRes(evt);
1005 if ((lastres == -1) || (lastres == res))
1010 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1012 // dragLeft, delete gap
1013 editSequence(false, res);
1017 editSequence(true, res);
1020 mouseDragging = true;
1021 if (scrollThread != null)
1023 scrollThread.setEvent(evt);
1027 synchronized void editSequence(boolean insertGap, int startres)
1030 int fixedRight = -1;
1031 boolean fixedColumns = false;
1032 SequenceGroup sg = av.getSelectionGroup();
1034 SequenceI seq = av.alignment.getSequenceAt(startseq);
1036 // No group, but the sequence may represent a group
1037 if (!groupEditing && av.hasHiddenRows)
1039 if (av.hiddenRepSequences != null
1040 && av.hiddenRepSequences.containsKey(seq))
1042 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
1043 groupEditing = true;
1047 StringBuffer message = new StringBuffer();
1050 message.append("Edit group:");
1051 if (editCommand == null)
1053 editCommand = new EditCommand("Edit Group");
1058 message.append("Edit sequence: " + seq.getName());
1059 String label = seq.getName();
1060 if (label.length() > 10)
1062 label = label.substring(0, 10);
1064 if (editCommand == null)
1066 editCommand = new EditCommand("Edit " + label);
1072 message.append(" insert ");
1076 message.append(" delete ");
1079 message.append(Math.abs(startres - lastres) + " gaps.");
1080 ap.alignFrame.statusBar.setText(message.toString());
1082 // Are we editing within a selection group?
1084 || (sg != null && sg.getSequences(av.hiddenRepSequences)
1087 fixedColumns = true;
1089 // sg might be null as the user may only see 1 sequence,
1090 // but the sequence represents a group
1093 if (av.hiddenRepSequences == null
1094 || !av.hiddenRepSequences.containsKey(seq))
1099 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
1102 fixedLeft = sg.getStartRes();
1103 fixedRight = sg.getEndRes();
1105 if ((startres < fixedLeft && lastres >= fixedLeft)
1106 || (startres >= fixedLeft && lastres < fixedLeft)
1107 || (startres > fixedRight && lastres <= fixedRight)
1108 || (startres <= fixedRight && lastres > fixedRight))
1114 if (fixedLeft > startres)
1116 fixedRight = fixedLeft - 1;
1119 else if (fixedRight < startres)
1121 fixedLeft = fixedRight;
1126 if (av.hasHiddenColumns)
1128 fixedColumns = true;
1129 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1130 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1132 if ((insertGap && startres > y1 && lastres < y1)
1133 || (!insertGap && startres < y2 && lastres > y2))
1139 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1140 // Selection spans a hidden region
1141 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1149 fixedRight = y2 - 1;
1156 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
1157 int g, groupSize = vseqs.size();
1158 SequenceI[] groupSeqs = new SequenceI[groupSize];
1159 for (g = 0; g < groupSeqs.length; g++)
1161 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
1167 // If the user has selected the whole sequence, and is dragging to
1168 // the right, we can still extend the alignment and selectionGroup
1169 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1170 && sg.getEndRes() == av.alignment.getWidth() - 1)
1172 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
1173 fixedRight = sg.getEndRes();
1176 // Is it valid with fixed columns??
1177 // Find the next gap before the end
1178 // of the visible region boundary
1179 boolean blank = false;
1180 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1184 for (g = 0; g < groupSize; g++)
1186 for (int j = 0; j < startres - lastres; j++)
1188 if (!jalview.util.Comparison.isGap(groupSeqs[g]
1189 .getCharAt(fixedRight - j)))
1204 if (sg.getSize() == av.alignment.getHeight())
1206 if ((av.hasHiddenColumns && startres < av.getColumnSelection()
1207 .getHiddenBoundaryRight(startres)))
1213 int alWidth = av.alignment.getWidth();
1214 if (av.hasHiddenRows)
1216 int hwidth = av.alignment.getHiddenSequences().getWidth();
1217 if (hwidth > alWidth)
1222 // We can still insert gaps if the selectionGroup
1223 // contains all the sequences
1224 sg.setEndRes(sg.getEndRes() + startres - lastres);
1225 fixedRight = alWidth + startres - lastres;
1236 else if (!insertGap)
1238 // / Are we able to delete?
1239 // ie are all columns blank?
1241 for (g = 0; g < groupSize; g++)
1243 for (int j = startres; j < lastres; j++)
1245 if (groupSeqs[g].getLength() <= j)
1250 if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
1252 // Not a gap, block edit not valid
1262 // dragging to the right
1263 if (fixedColumns && fixedRight != -1)
1265 for (int j = lastres; j < startres; j++)
1267 insertChar(j, groupSeqs, fixedRight);
1272 editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
1273 startres, startres - lastres, av.alignment, true);
1278 // dragging to the left
1279 if (fixedColumns && fixedRight != -1)
1281 for (int j = lastres; j > startres; j--)
1283 deleteChar(startres, groupSeqs, fixedRight);
1288 editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
1289 startres, lastres - startres, av.alignment, true);
1295 // ///Editing a single sequence///////////
1299 // dragging to the right
1300 if (fixedColumns && fixedRight != -1)
1302 for (int j = lastres; j < startres; j++)
1304 insertChar(j, new SequenceI[]
1305 { seq }, fixedRight);
1310 editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
1311 { seq }, lastres, startres - lastres, av.alignment, true);
1316 // dragging to the left
1317 if (fixedColumns && fixedRight != -1)
1319 for (int j = lastres; j > startres; j--)
1321 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1326 deleteChar(startres, new SequenceI[]
1327 { seq }, fixedRight);
1332 // could be a keyboard edit trying to delete none gaps
1334 for (int m = startres; m < lastres; m++)
1336 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1345 editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
1346 { seq }, startres, max, av.alignment, true);
1353 seqCanvas.repaint();
1356 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1358 int blankColumn = fixedColumn;
1359 for (int s = 0; s < seq.length; s++)
1361 // Find the next gap before the end of the visible region boundary
1362 // If lastCol > j, theres a boundary after the gap insertion
1364 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1366 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1368 // Theres a space, so break and insert the gap
1373 if (blankColumn <= j)
1375 blankColumn = fixedColumn;
1381 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
1382 av.alignment, true);
1384 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
1389 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1392 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
1395 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
1396 av.alignment, true);
1405 public void mouseEntered(MouseEvent e)
1412 if (scrollThread != null)
1414 scrollThread.running = false;
1415 scrollThread = null;
1425 public void mouseExited(MouseEvent e)
1427 if (av.getWrapAlignment())
1434 scrollThread = new ScrollThread();
1438 public void mouseClicked(MouseEvent evt)
1440 SequenceGroup sg = null;
1441 SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
1442 if (evt.getClickCount() > 1)
1444 sg = av.getSelectionGroup();
1445 if (sg != null && sg.getSize() == 1
1446 && sg.getEndRes() - sg.getStartRes() < 2)
1448 av.setSelectionGroup(null);
1451 SequenceFeature[] features = findFeaturesAtRes(
1452 sequence.getDatasetSequence(),
1453 sequence.findPosition(findRes(evt)));
1455 if (features != null && features.length > 0)
1457 SearchResults highlight = new SearchResults();
1458 highlight.addResult(sequence, features[0].getBegin(),
1459 features[0].getEnd());
1460 seqCanvas.highlightSearchResults(highlight);
1462 if (features != null && features.length > 0)
1464 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
1465 { sequence }, features, false, ap);
1467 seqCanvas.highlightSearchResults(null);
1472 public void mouseWheelMoved(MouseWheelEvent e)
1475 if (e.getWheelRotation() > 0)
1483 // TODO Update tooltip for new position.
1492 public void doMousePressedDefineMode(MouseEvent evt)
1494 int res = findRes(evt);
1495 int seq = findSeq(evt);
1498 startWrapBlock = wrappedBlock;
1500 if (av.wrapAlignment && seq > av.alignment.getHeight())
1502 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1503 "Cannot edit annotations in wrapped view.",
1504 "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
1508 if (seq < 0 || res < 0)
1513 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
1515 if ((sequence == null) || (res > sequence.getLength()))
1520 stretchGroup = av.getSelectionGroup();
1522 if (stretchGroup == null)
1524 stretchGroup = av.alignment.findGroup(sequence);
1526 if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
1527 && (res < stretchGroup.getEndRes()))
1529 av.setSelectionGroup(stretchGroup);
1533 stretchGroup = null;
1536 else if (!stretchGroup.getSequences(null).contains(sequence)
1537 || (stretchGroup.getStartRes() > res)
1538 || (stretchGroup.getEndRes() < res))
1540 stretchGroup = null;
1542 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
1544 if (allGroups != null)
1546 for (int i = 0; i < allGroups.length; i++)
1548 if ((allGroups[i].getStartRes() <= res)
1549 && (allGroups[i].getEndRes() >= res))
1551 stretchGroup = allGroups[i];
1557 av.setSelectionGroup(stretchGroup);
1561 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
1563 SequenceFeature[] allFeatures = findFeaturesAtRes(
1564 sequence.getDatasetSequence(), sequence.findPosition(res));
1565 Vector links = new Vector();
1566 for (int i = 0; i < allFeatures.length; i++)
1568 if (allFeatures[i].links != null)
1570 for (int j = 0; j < allFeatures[i].links.size(); j++)
1572 links.addElement(allFeatures[i].links.elementAt(j));
1577 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
1578 pop.show(this, evt.getX(), evt.getY());
1584 seqCanvas.cursorX = findRes(evt);
1585 seqCanvas.cursorY = findSeq(evt);
1586 seqCanvas.repaint();
1590 if (stretchGroup == null)
1592 // Only if left mouse button do we want to change group sizes
1594 // define a new group here
1595 SequenceGroup sg = new SequenceGroup();
1596 sg.setStartRes(res);
1598 sg.addSequence(sequence, false);
1599 av.setSelectionGroup(sg);
1603 if (av.getConservationSelected())
1605 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1609 if (av.getAbovePIDThreshold())
1611 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1614 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1616 // Edit end res position of selected group
1617 changeEndRes = true;
1619 else if ((stretchGroup != null)
1620 && (stretchGroup.getStartRes() == res))
1622 // Edit end res position of selected group
1623 changeStartRes = true;
1625 stretchGroup.getWidth();
1628 seqCanvas.repaint();
1637 public void doMouseReleasedDefineMode(MouseEvent evt)
1639 if (stretchGroup == null)
1644 stretchGroup.recalcConservation(); // always do this - annotation has own
1646 if (stretchGroup.cs != null)
1648 if (stretchGroup.cs instanceof ClustalxColourScheme)
1650 ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
1651 stretchGroup.getSequences(av.hiddenRepSequences),
1652 stretchGroup.getWidth());
1655 if (stretchGroup.cs.conservationApplied())
1657 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1658 stretchGroup.getName());
1662 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1663 stretchGroup.getName());
1666 PaintRefresher.Refresh(this, av.getSequenceSetId());
1667 ap.paintAlignment(true);
1669 changeEndRes = false;
1670 changeStartRes = false;
1671 stretchGroup = null;
1681 public void doMouseDraggedDefineMode(MouseEvent evt)
1683 int res = findRes(evt);
1684 int y = findSeq(evt);
1686 if (wrappedBlock != startWrapBlock)
1691 if (stretchGroup == null)
1696 if (res >= av.alignment.getWidth())
1698 res = av.alignment.getWidth() - 1;
1701 if (stretchGroup.getEndRes() == res)
1703 // Edit end res position of selected group
1704 changeEndRes = true;
1706 else if (stretchGroup.getStartRes() == res)
1708 // Edit start res position of selected group
1709 changeStartRes = true;
1712 if (res < av.getStartRes())
1714 res = av.getStartRes();
1719 if (res > (stretchGroup.getStartRes() - 1))
1721 stretchGroup.setEndRes(res);
1724 else if (changeStartRes)
1726 if (res < (stretchGroup.getEndRes() + 1))
1728 stretchGroup.setStartRes(res);
1732 int dragDirection = 0;
1738 else if (y < oldSeq)
1743 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
1745 // This routine ensures we don't skip any sequences, as the
1746 // selection is quite slow.
1747 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1749 oldSeq += dragDirection;
1756 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1758 if (stretchGroup.getSequences(null).contains(nextSeq))
1760 stretchGroup.deleteSequence(seq, false);
1766 stretchGroup.addSequence(seq, false);
1769 stretchGroup.addSequence(nextSeq, false);
1778 mouseDragging = true;
1780 if (scrollThread != null)
1782 scrollThread.setEvent(evt);
1785 seqCanvas.repaint();
1788 void scrollCanvas(MouseEvent evt)
1792 if (scrollThread != null)
1794 scrollThread.running = false;
1795 scrollThread = null;
1797 mouseDragging = false;
1801 if (scrollThread == null)
1803 scrollThread = new ScrollThread();
1806 mouseDragging = true;
1807 scrollThread.setEvent(evt);
1812 // this class allows scrolling off the bottom of the visible alignment
1813 class ScrollThread extends Thread
1817 boolean running = false;
1819 public ScrollThread()
1824 public void setEvent(MouseEvent e)
1829 public void stopScrolling()
1842 if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
1844 running = ap.scrollUp(true);
1847 if (mouseDragging && (evt.getY() >= getHeight())
1848 && (av.alignment.getHeight() > av.getEndSeq()))
1850 running = ap.scrollUp(false);
1853 if (mouseDragging && (evt.getX() < 0))
1855 running = ap.scrollRight(false);
1857 else if (mouseDragging && (evt.getX() >= getWidth()))
1859 running = ap.scrollRight(true);
1866 } catch (Exception ex)
1874 * modify current selection according to a received message.
1876 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1877 SelectionSource source)
1879 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1880 // handles selection messages...
1881 // TODO: extend config options to allow user to control if selections may be
1882 // shared between viewports.
1884 || !av.followSelection
1885 || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
1886 || (source instanceof AlignViewport && ((AlignViewport) source)
1887 .getSequenceSetId().equals(av.getSequenceSetId())))
1891 // do we want to thread this ? (contention with seqsel and colsel locks, I
1893 // rules are: colsel is copied if there is a real intersection between
1894 // sequence selection
1895 boolean repaint = false, copycolsel = true;
1896 // if (!av.isSelectionGroupChanged(false))
1898 SequenceGroup sgroup = null;
1899 if (seqsel != null && seqsel.getSize()>0)
1901 if (av.alignment == null)
1903 jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
1904 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1905 + " 's alignment is NULL! returning immediatly.");
1908 sgroup = seqsel.intersect(av.alignment,
1909 (av.hasHiddenRows) ? av.hiddenRepSequences : null);
1910 if ((sgroup == null || sgroup.getSize() == 0)
1911 || (colsel == null || colsel.size() == 0))
1913 // don't copy columns if the region didn't intersect.
1917 if (sgroup != null && sgroup.getSize() > 0)
1919 av.setSelectionGroup(sgroup);
1923 av.setSelectionGroup(null);
1925 av.isSelectionGroupChanged(true);
1930 // the current selection is unset or from a previous message
1931 // so import the new colsel.
1932 if (colsel == null || colsel.size() == 0)
1934 if (av.colSel != null)
1942 // TODO: shift colSel according to the intersecting sequences
1943 if (av.colSel == null)
1945 av.colSel = new ColumnSelection(colsel);
1949 av.colSel.setElementsFrom(colsel);
1952 av.isColSelChanged(true);
1955 if (copycolsel && av.hasHiddenColumns
1956 && (av.colSel == null || av.colSel.getHiddenColumns() == null))
1958 System.err.println("Bad things");
1962 // probably finessing with multiple redraws here
1963 PaintRefresher.Refresh(this, av.getSequenceSetId());
1964 // ap.paintAlignment(false);