2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.appletgui;
24 import java.awt.event.*;
26 import jalview.commands.*;
27 import jalview.datamodel.*;
28 import jalview.schemes.*;
29 import jalview.structure.SequenceListener;
30 import jalview.structure.StructureSelectionManager;
32 public class SeqPanel extends Panel implements MouseMotionListener,
33 MouseListener, SequenceListener
36 public SeqCanvas seqCanvas;
38 public AlignmentPanel ap;
40 protected int lastres;
42 protected int startseq;
44 protected AlignViewport av;
46 // if character is inserted or deleted, we will need to recalculate the
48 boolean seqEditOccurred = false;
50 ScrollThread scrollThread = null;
52 boolean mouseDragging = false;
54 boolean editingSeqs = false;
56 boolean groupEditing = false;
60 boolean changeEndSeq = false;
62 boolean changeStartSeq = false;
64 boolean changeEndRes = false;
66 boolean changeStartRes = false;
68 SequenceGroup stretchGroup = null;
70 StringBuffer keyboardNo1;
72 StringBuffer keyboardNo2;
74 boolean mouseWheelPressed = false;
78 EditCommand editCommand;
80 StructureSelectionManager ssm;
82 public SeqPanel(AlignViewport avp, AlignmentPanel p)
86 seqCanvas = new SeqCanvas(avp);
87 setLayout(new BorderLayout());
92 seqCanvas.addMouseMotionListener(this);
93 seqCanvas.addMouseListener(this);
94 ssm = StructureSelectionManager.getStructureSelectionManager();
95 ssm.addStructureViewerListener(this);
102 if (editCommand != null && editCommand.getSize() > 0)
104 ap.alignFrame.addHistoryItem(editCommand);
105 av.firePropertyChange("alignment", null, av.getAlignment()
112 groupEditing = false;
120 seqCanvas.cursorY = getKeyboardNo1() - 1;
124 void setCursorColumn()
126 seqCanvas.cursorX = getKeyboardNo1() - 1;
130 void setCursorRowAndColumn()
132 if (keyboardNo2 == null)
134 keyboardNo2 = new StringBuffer();
138 seqCanvas.cursorX = getKeyboardNo1() - 1;
139 seqCanvas.cursorY = getKeyboardNo2() - 1;
144 void setCursorPosition()
146 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
149 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
153 void moveCursor(int dx, int dy)
155 seqCanvas.cursorX += dx;
156 seqCanvas.cursorY += dy;
157 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
159 int original = seqCanvas.cursorX - dx;
160 int maxWidth = av.alignment.getWidth();
162 while (!av.colSel.isVisible(seqCanvas.cursorX)
163 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
165 seqCanvas.cursorX += dx;
168 if (seqCanvas.cursorX >= maxWidth
169 || !av.colSel.isVisible(seqCanvas.cursorX))
171 seqCanvas.cursorX = original;
177 void scrollToVisible()
179 if (seqCanvas.cursorX < 0)
181 seqCanvas.cursorX = 0;
183 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
185 seqCanvas.cursorX = av.alignment.getWidth() - 1;
188 if (seqCanvas.cursorY < 0)
190 seqCanvas.cursorY = 0;
192 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
194 seqCanvas.cursorY = av.alignment.getHeight() - 1;
198 if (av.wrapAlignment)
200 ap.scrollToWrappedVisible(seqCanvas.cursorX);
204 while (seqCanvas.cursorY < av.startSeq)
208 while (seqCanvas.cursorY + 1 > av.endSeq)
212 while (seqCanvas.cursorX < av.colSel
213 .adjustForHiddenColumns(av.startRes))
216 if (!ap.scrollRight(false))
221 while (seqCanvas.cursorX > av.colSel
222 .adjustForHiddenColumns(av.endRes))
224 if (!ap.scrollRight(true))
230 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
231 seqCanvas.cursorX, seqCanvas.cursorY);
236 void setSelectionAreaAtCursor(boolean topLeft)
238 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
241 if (av.getSelectionGroup() != null)
243 SequenceGroup sg = av.selectionGroup;
244 // Find the top and bottom of this group
245 int min = av.alignment.getHeight(), max = 0;
246 for (int i = 0; i < sg.getSize(); i++)
248 int index = av.alignment.findIndex(sg.getSequenceAt(i));
263 sg.setStartRes(seqCanvas.cursorX);
264 if (sg.getEndRes() < seqCanvas.cursorX)
266 sg.setEndRes(seqCanvas.cursorX);
269 min = seqCanvas.cursorY;
273 sg.setEndRes(seqCanvas.cursorX);
274 if (sg.getStartRes() > seqCanvas.cursorX)
276 sg.setStartRes(seqCanvas.cursorX);
279 max = seqCanvas.cursorY + 1;
284 // Only the user can do this
285 av.setSelectionGroup(null);
289 // Now add any sequences between min and max
290 sg.getSequences(null).removeAllElements();
291 for (int i = min; i < max; i++)
293 sg.addSequence(av.alignment.getSequenceAt(i), false);
298 if (av.getSelectionGroup() == null)
300 SequenceGroup sg = new SequenceGroup();
301 sg.setStartRes(seqCanvas.cursorX);
302 sg.setEndRes(seqCanvas.cursorX);
303 sg.addSequence(sequence, false);
304 av.setSelectionGroup(sg);
307 ap.paintAlignment(false);
310 void insertGapAtCursor(boolean group)
312 groupEditing = group;
313 startseq = seqCanvas.cursorY;
314 lastres = seqCanvas.cursorX;
315 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
319 void deleteGapAtCursor(boolean group)
321 groupEditing = group;
322 startseq = seqCanvas.cursorY;
323 lastres = seqCanvas.cursorX + getKeyboardNo1();
324 editSequence(false, seqCanvas.cursorX);
328 void numberPressed(char value)
330 if (keyboardNo1 == null)
332 keyboardNo1 = new StringBuffer();
335 if (keyboardNo2 != null)
337 keyboardNo2.append(value);
341 keyboardNo1.append(value);
347 if (keyboardNo1 == null)
351 int value = Integer.parseInt(keyboardNo1.toString());
359 if (keyboardNo2 == null)
363 int value = Integer.parseInt(keyboardNo2.toString());
369 void setStatusMessage(SequenceI sequence, int res, int seq)
371 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
372 + sequence.getName());
375 if (av.alignment.isNucleotide())
377 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
381 text.append(" Nucleotide: ");
386 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
389 text.append(" Residue: ");
398 text.append(obj + " (" + sequence.findPosition(res) + ")");
402 ap.alignFrame.statusBar.setText(text.toString());
406 public void mousePressed(MouseEvent evt)
408 lastMousePress = evt.getPoint();
410 // For now, ignore the mouseWheel font resizing on Macs
411 // As the Button2_mask always seems to be true
412 if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
415 mouseWheelPressed = true;
419 if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
421 if (evt.isControlDown() || evt.isAltDown())
429 doMousePressedDefineMode(evt);
433 int seq = findSeq(evt);
434 int res = findRes(evt);
436 if (seq < 0 || res < 0)
441 if ((seq < av.getAlignment().getHeight())
442 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
456 public void mouseClicked(MouseEvent evt)
458 SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
459 if (evt.getClickCount() > 1)
461 if (av.getSelectionGroup().getSize() == 1
462 && av.getSelectionGroup().getEndRes()
463 - av.getSelectionGroup().getStartRes() < 2)
465 av.setSelectionGroup(null);
468 SequenceFeature[] features = findFeaturesAtRes(sequence, sequence
469 .findPosition(findRes(evt)));
471 if (features != null && features.length > 0)
473 SearchResults highlight = new SearchResults();
474 highlight.addResult(sequence, features[0].getBegin(), features[0]
476 seqCanvas.highlightSearchResults(highlight);
478 if (features != null && features.length > 0)
480 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
481 { sequence }, features, false, ap);
483 seqCanvas.highlightSearchResults(null);
488 public void mouseReleased(MouseEvent evt)
490 mouseDragging = false;
491 mouseWheelPressed = false;
492 ap.paintAlignment(true);
496 doMouseReleasedDefineMode(evt);
504 int startWrapBlock = -1;
506 int wrappedBlock = -1;
508 int findRes(MouseEvent evt)
513 if (av.wrapAlignment)
516 int hgap = av.charHeight;
517 if (av.scaleAboveWrapped)
519 hgap += av.charHeight;
522 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
523 + seqCanvas.getAnnotationHeight();
527 x -= seqCanvas.LABEL_WEST;
529 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
535 wrappedBlock = y / cHeight;
536 wrappedBlock += av.getStartRes() / cwidth;
538 res = wrappedBlock * cwidth + x / av.getCharWidth();
543 res = (x / av.getCharWidth()) + av.getStartRes();
546 if (av.hasHiddenColumns)
548 res = av.getColumnSelection().adjustForHiddenColumns(res);
555 int findSeq(MouseEvent evt)
557 final int sqnum = findAlRow(evt);
558 return (sqnum < 0) ? 0 : sqnum;
564 * @return row in alignment that was selected (or -1 for column selection)
566 private int findAlRow(MouseEvent evt)
571 if (av.wrapAlignment)
573 int hgap = av.charHeight;
574 if (av.scaleAboveWrapped)
576 hgap += av.charHeight;
579 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
580 + seqCanvas.getAnnotationHeight();
584 seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
593 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
594 av.alignment.getHeight() - 1);
604 public void doMousePressed(MouseEvent evt)
607 int seq = findSeq(evt);
608 int res = findRes(evt);
610 if (seq < av.getAlignment().getHeight()
611 && res < av.getAlignment().getSequenceAt(seq).getLength())
613 // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
614 // Find the residue's position in the sequence (res is the position
631 public void mouseOverSequence(SequenceI sequence, int index, int pos)
633 String tmp = sequence.hashCode() + index + "";
634 if (lastMessage == null || !lastMessage.equals(tmp))
635 ssm.mouseOverSequence(sequence, index, pos);
640 public void highlightSequence(SearchResults results)
642 seqCanvas.highlightSearchResults(results);
645 public void updateColours(SequenceI seq, int index)
647 System.out.println("update the seqPanel colours");
651 public void mouseMoved(MouseEvent evt)
653 int res = findRes(evt);
654 int seq = findSeq(evt);
656 if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
665 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
666 if (res > sequence.getLength())
675 int respos = sequence.findPosition(res);
677 mouseOverSequence(sequence, res, respos);
679 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
680 + sequence.getName());
683 if (av.alignment.isNucleotide())
685 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
689 text.append(" Nucleotide: ");
694 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
697 text.append(" Residue: ");
705 text.append(obj + " (" + respos + ")");
709 ap.alignFrame.statusBar.setText(text.toString());
711 StringBuffer tooltipText = new StringBuffer();
712 SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
715 for (int g = 0; g < groups.length; g++)
717 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
719 if (!groups[g].getName().startsWith("JTreeGroup")
720 && !groups[g].getName().startsWith("JGroup"))
722 tooltipText.append(groups[g].getName() + " ");
724 if (groups[g].getDescription() != null)
726 tooltipText.append(groups[g].getDescription());
728 tooltipText.append("\n");
733 // use aa to see if the mouse pointer is on a
734 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence
738 while (index < allFeatures.length)
740 SequenceFeature sf = allFeatures[index];
742 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
744 if (sf.getDescription() != null)
746 tooltipText.append(" " + sf.getDescription());
749 if (sf.getValue("status") != null)
751 String status = sf.getValue("status").toString();
752 if (status.length() > 0)
754 tooltipText.append(" (" + sf.getValue("status") + ")");
757 tooltipText.append("\n");
764 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
768 tooltip.setTip(tooltipText.toString());
772 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
774 Vector tmp = new Vector();
775 SequenceFeature[] features = sequence.getSequenceFeatures();
776 if (features != null)
778 for (int i = 0; i < features.length; i++)
780 if (av.featuresDisplayed == null
781 || !av.featuresDisplayed.containsKey(features[i].getType()))
786 if (features[i].featureGroup != null
787 && seqCanvas.fr.featureGroups != null
788 && seqCanvas.fr.featureGroups
789 .containsKey(features[i].featureGroup)
790 && !((Boolean) seqCanvas.fr.featureGroups
791 .get(features[i].featureGroup)).booleanValue())
794 if ((features[i].getBegin() <= res)
795 && (features[i].getEnd() >= res))
797 tmp.addElement(features[i]);
802 features = new SequenceFeature[tmp.size()];
803 tmp.copyInto(features);
810 public void mouseDragged(MouseEvent evt)
812 if (mouseWheelPressed)
814 int oldWidth = av.charWidth;
816 // Which is bigger, left-right or up-down?
817 if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
820 int fontSize = av.font.getSize();
822 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
826 else if (evt.getY() > lastMousePress.y)
837 .setFont(new Font(av.font.getName(), av.font.getStyle(),
839 av.charWidth = oldWidth;
843 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
847 else if (evt.getX() > lastMousePress.x)
852 if (av.charWidth < 1)
860 FontMetrics fm = getFontMetrics(av.getFont());
861 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
863 lastMousePress = evt.getPoint();
865 ap.paintAlignment(false);
866 ap.annotationPanel.image = null;
872 doMouseDraggedDefineMode(evt);
876 int res = findRes(evt);
883 if ((lastres == -1) || (lastres == res))
888 if ((res < av.getAlignment().getWidth()) && (res < lastres))
890 // dragLeft, delete gap
891 editSequence(false, res);
895 editSequence(true, res);
898 mouseDragging = true;
899 if (scrollThread != null)
901 scrollThread.setEvent(evt);
906 synchronized void editSequence(boolean insertGap, int startres)
910 boolean fixedColumns = false;
911 SequenceGroup sg = av.getSelectionGroup();
913 SequenceI seq = av.alignment.getSequenceAt(startseq);
915 if (!groupEditing && av.hasHiddenRows)
917 if (av.hiddenRepSequences != null
918 && av.hiddenRepSequences.containsKey(seq))
920 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
925 StringBuffer message = new StringBuffer();
928 message.append("Edit group:");
929 if (editCommand == null)
931 editCommand = new EditCommand("Edit Group");
936 message.append("Edit sequence: " + seq.getName());
937 String label = seq.getName();
938 if (label.length() > 10)
940 label = label.substring(0, 10);
942 if (editCommand == null)
944 editCommand = new EditCommand("Edit " + label);
950 message.append(" insert ");
954 message.append(" delete ");
957 message.append(Math.abs(startres - lastres) + " gaps.");
958 ap.alignFrame.statusBar.setText(message.toString());
960 // Are we editing within a selection group?
962 || (sg != null && sg.getSequences(av.hiddenRepSequences)
967 // sg might be null as the user may only see 1 sequence,
968 // but the sequence represents a group
971 if (av.hiddenRepSequences == null
972 || !av.hiddenRepSequences.containsKey(seq))
978 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
981 fixedLeft = sg.getStartRes();
982 fixedRight = sg.getEndRes();
984 if ((startres < fixedLeft && lastres >= fixedLeft)
985 || (startres >= fixedLeft && lastres < fixedLeft)
986 || (startres > fixedRight && lastres <= fixedRight)
987 || (startres <= fixedRight && lastres > fixedRight))
993 if (fixedLeft > startres)
995 fixedRight = fixedLeft - 1;
998 else if (fixedRight < startres)
1000 fixedLeft = fixedRight;
1005 if (av.hasHiddenColumns)
1007 fixedColumns = true;
1008 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1009 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1011 if ((insertGap && startres > y1 && lastres < y1)
1012 || (!insertGap && startres < y2 && lastres > y2))
1018 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1019 // Selection spans a hidden region
1020 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1028 fixedRight = y2 - 1;
1035 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
1036 int g, groupSize = vseqs.size();
1037 SequenceI[] groupSeqs = new SequenceI[groupSize];
1038 for (g = 0; g < groupSeqs.length; g++)
1040 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
1046 // If the user has selected the whole sequence, and is dragging to
1047 // the right, we can still extend the alignment and selectionGroup
1048 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1049 && sg.getEndRes() == av.alignment.getWidth() - 1)
1051 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
1052 fixedRight = sg.getEndRes();
1055 // Is it valid with fixed columns??
1056 // Find the next gap before the end
1057 // of the visible region boundary
1058 boolean blank = false;
1059 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1063 for (g = 0; g < groupSize; g++)
1065 for (int j = 0; j < startres - lastres; j++)
1067 if (!jalview.util.Comparison.isGap(groupSeqs[g]
1068 .getCharAt(fixedRight - j)))
1083 if (sg.getSize() == av.alignment.getHeight())
1085 if ((av.hasHiddenColumns && startres < av.getColumnSelection()
1086 .getHiddenBoundaryRight(startres)))
1092 int alWidth = av.alignment.getWidth();
1093 if (av.hasHiddenRows)
1095 int hwidth = av.alignment.getHiddenSequences().getWidth();
1096 if (hwidth > alWidth)
1101 // We can still insert gaps if the selectionGroup
1102 // contains all the sequences
1103 sg.setEndRes(sg.getEndRes() + startres - lastres);
1104 fixedRight = alWidth + startres - lastres;
1115 else if (!insertGap)
1117 // / Are we able to delete?
1118 // ie are all columns blank?
1120 for (g = 0; g < groupSize; g++)
1122 for (int j = startres; j < lastres; j++)
1124 if (groupSeqs[g].getLength() <= j)
1129 if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
1131 // Not a gap, block edit not valid
1141 // dragging to the right
1142 if (fixedColumns && fixedRight != -1)
1144 for (int j = lastres; j < startres; j++)
1146 insertChar(j, groupSeqs, fixedRight);
1151 editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
1152 startres, startres - lastres, av.alignment, true);
1157 // dragging to the left
1158 if (fixedColumns && fixedRight != -1)
1160 for (int j = lastres; j > startres; j--)
1162 deleteChar(startres, groupSeqs, fixedRight);
1167 editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
1168 startres, lastres - startres, av.alignment, true);
1174 // ///Editing a single sequence///////////
1178 // dragging to the right
1179 if (fixedColumns && fixedRight != -1)
1181 for (int j = lastres; j < startres; j++)
1183 insertChar(j, new SequenceI[]
1184 { seq }, fixedRight);
1189 editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
1190 { seq }, lastres, startres - lastres, av.alignment, true);
1195 // dragging to the left
1196 if (fixedColumns && fixedRight != -1)
1198 for (int j = lastres; j > startres; j--)
1200 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1205 deleteChar(startres, new SequenceI[]
1206 { seq }, fixedRight);
1211 // could be a keyboard edit trying to delete none gaps
1213 for (int m = startres; m < lastres; m++)
1215 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1224 editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
1225 { seq }, startres, max, av.alignment, true);
1232 seqCanvas.repaint();
1235 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1237 int blankColumn = fixedColumn;
1238 for (int s = 0; s < seq.length; s++)
1240 // Find the next gap before the end of the visible region boundary
1241 // If lastCol > j, theres a boundary after the gap insertion
1243 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1245 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1247 // Theres a space, so break and insert the gap
1252 if (blankColumn <= j)
1254 blankColumn = fixedColumn;
1260 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
1261 av.alignment, true);
1263 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
1268 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1271 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
1274 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
1275 av.alignment, true);
1278 // ////////////////////////////////////////
1279 // ///Everything below this is for defining the boundary of the rubberband
1280 // ////////////////////////////////////////
1281 public void doMousePressedDefineMode(MouseEvent evt)
1283 if (scrollThread != null)
1285 scrollThread.running = false;
1286 scrollThread = null;
1289 int res = findRes(evt);
1290 int seq = findSeq(evt);
1292 startWrapBlock = wrappedBlock;
1299 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
1301 if (sequence == null || res > sequence.getLength())
1306 stretchGroup = av.getSelectionGroup();
1308 if (stretchGroup == null)
1310 stretchGroup = av.alignment.findGroup(sequence);
1311 if (stretchGroup != null && res > stretchGroup.getStartRes()
1312 && res < stretchGroup.getEndRes())
1314 av.setSelectionGroup(stretchGroup);
1318 stretchGroup = null;
1322 else if (!stretchGroup.getSequences(null).contains(sequence)
1323 || stretchGroup.getStartRes() > res
1324 || stretchGroup.getEndRes() < res)
1326 stretchGroup = null;
1328 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
1330 if (allGroups != null)
1332 for (int i = 0; i < allGroups.length; i++)
1334 if (allGroups[i].getStartRes() <= res
1335 && allGroups[i].getEndRes() >= res)
1337 stretchGroup = allGroups[i];
1342 av.setSelectionGroup(stretchGroup);
1345 // DETECT RIGHT MOUSE BUTTON IN AWT
1346 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
1348 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence
1349 .findPosition(res));
1351 Vector links = null;
1352 if (allFeatures != null)
1354 for (int i = 0; i < allFeatures.length; i++)
1356 if (allFeatures[i].links != null)
1360 links = new Vector();
1362 for (int j = 0; j < allFeatures[i].links.size(); j++)
1364 links.addElement(allFeatures[i].links.elementAt(j));
1369 APopupMenu popup = new APopupMenu(ap, null, links);
1371 popup.show(this, evt.getX(), evt.getY());
1377 seqCanvas.cursorX = findRes(evt);
1378 seqCanvas.cursorY = findSeq(evt);
1379 seqCanvas.repaint();
1383 // Only if left mouse button do we want to change group sizes
1385 if (stretchGroup == null)
1387 // define a new group here
1388 SequenceGroup sg = new SequenceGroup();
1389 sg.setStartRes(res);
1391 sg.addSequence(sequence, false);
1392 av.setSelectionGroup(sg);
1395 if (av.getConservationSelected())
1397 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1400 if (av.getAbovePIDThreshold())
1402 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1409 public void doMouseReleasedDefineMode(MouseEvent evt)
1411 if (stretchGroup == null)
1416 if (stretchGroup.cs != null)
1418 if (stretchGroup.cs instanceof ClustalxColourScheme)
1420 ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
1421 .getSequences(av.hiddenRepSequences), stretchGroup
1425 if (stretchGroup.cs instanceof Blosum62ColourScheme
1426 || stretchGroup.cs instanceof PIDColourScheme
1427 || stretchGroup.cs.conservationApplied()
1428 || stretchGroup.cs.getThreshold() > 0)
1430 stretchGroup.recalcConservation();
1433 if (stretchGroup.cs.conservationApplied())
1435 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
1437 stretchGroup.recalcConservation();
1441 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
1445 changeEndRes = false;
1446 changeStartRes = false;
1447 stretchGroup = null;
1448 PaintRefresher.Refresh(ap, av.getSequenceSetId());
1449 ap.paintAlignment(true);
1452 public void doMouseDraggedDefineMode(MouseEvent evt)
1454 int res = findRes(evt);
1455 int y = findSeq(evt);
1457 if (wrappedBlock != startWrapBlock)
1462 if (stretchGroup == null)
1467 mouseDragging = true;
1469 if (y > av.alignment.getHeight())
1471 y = av.alignment.getHeight() - 1;
1474 if (res >= av.alignment.getWidth())
1476 res = av.alignment.getWidth() - 1;
1479 if (stretchGroup.getEndRes() == res)
1481 // Edit end res position of selected group
1482 changeEndRes = true;
1484 else if (stretchGroup.getStartRes() == res)
1486 // Edit start res position of selected group
1487 changeStartRes = true;
1497 if (res > (stretchGroup.getStartRes() - 1))
1499 stretchGroup.setEndRes(res);
1502 else if (changeStartRes)
1504 if (res < (stretchGroup.getEndRes() + 1))
1506 stretchGroup.setStartRes(res);
1510 int dragDirection = 0;
1516 else if (y < oldSeq)
1521 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
1523 // This routine ensures we don't skip any sequences, as the
1524 // selection is quite slow.
1525 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1527 oldSeq += dragDirection;
1534 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1536 if (stretchGroup.getSequences(null).contains(nextSeq))
1538 stretchGroup.deleteSequence(seq, false);
1544 stretchGroup.addSequence(seq, false);
1547 stretchGroup.addSequence(nextSeq, false);
1556 if (res > av.endRes || res < av.startRes || y < av.startSeq
1562 if (scrollThread != null)
1564 scrollThread.setEvent(evt);
1567 seqCanvas.repaint();
1570 public void mouseEntered(MouseEvent e)
1577 if (scrollThread != null)
1579 scrollThread.running = false;
1580 scrollThread = null;
1584 public void mouseExited(MouseEvent e)
1586 if (av.getWrapAlignment())
1591 if (mouseDragging && scrollThread == null)
1593 scrollThread = new ScrollThread();
1597 void scrollCanvas(MouseEvent evt)
1601 if (scrollThread != null)
1603 scrollThread.running = false;
1604 scrollThread = null;
1606 mouseDragging = false;
1610 if (scrollThread == null)
1612 scrollThread = new ScrollThread();
1615 mouseDragging = true;
1616 scrollThread.setEvent(evt);
1621 // this class allows scrolling off the bottom of the visible alignment
1622 class ScrollThread extends Thread
1626 boolean running = false;
1628 public ScrollThread()
1633 public void setEvent(MouseEvent e)
1638 public void stopScrolling()
1652 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
1654 running = ap.scrollUp(true);
1657 if (mouseDragging && evt.getY() >= getSize().height
1658 && av.alignment.getHeight() > av.getEndSeq())
1660 running = ap.scrollUp(false);
1663 if (mouseDragging && evt.getX() < 0)
1665 running = ap.scrollRight(false);
1668 else if (mouseDragging && evt.getX() >= getSize().width)
1670 running = ap.scrollRight(true);
1677 } catch (Exception ex)