2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.commands.EditCommand;
24 import jalview.commands.EditCommand.Action;
25 import jalview.datamodel.ColumnSelection;
26 import jalview.datamodel.SearchResults;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceGroup;
30 import jalview.datamodel.SequenceI;
31 import jalview.schemes.ResidueProperties;
32 import jalview.structure.SelectionSource;
33 import jalview.structure.SequenceListener;
34 import jalview.structure.StructureSelectionManager;
35 import jalview.structure.VamsasSource;
36 import jalview.util.MessageManager;
38 import java.awt.BorderLayout;
40 import java.awt.FontMetrics;
41 import java.awt.Panel;
42 import java.awt.Point;
43 import java.awt.event.InputEvent;
44 import java.awt.event.MouseEvent;
45 import java.awt.event.MouseListener;
46 import java.awt.event.MouseMotionListener;
47 import java.util.Vector;
49 public class SeqPanel extends Panel implements MouseMotionListener,
50 MouseListener, SequenceListener
53 public SeqCanvas seqCanvas;
55 public AlignmentPanel ap;
57 protected int lastres;
59 protected int startseq;
61 protected AlignViewport av;
63 // if character is inserted or deleted, we will need to recalculate the
65 boolean seqEditOccurred = false;
67 ScrollThread scrollThread = null;
69 boolean mouseDragging = false;
71 boolean editingSeqs = false;
73 boolean groupEditing = false;
77 boolean changeEndSeq = false;
79 boolean changeStartSeq = false;
81 boolean changeEndRes = false;
83 boolean changeStartRes = false;
85 SequenceGroup stretchGroup = null;
87 StringBuffer keyboardNo1;
89 StringBuffer keyboardNo2;
91 boolean mouseWheelPressed = false;
95 EditCommand editCommand;
97 StructureSelectionManager ssm;
99 public SeqPanel(AlignViewport avp, AlignmentPanel p)
103 seqCanvas = new SeqCanvas(avp);
104 setLayout(new BorderLayout());
109 seqCanvas.addMouseMotionListener(this);
110 seqCanvas.addMouseListener(this);
111 ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
112 ssm.addStructureViewerListener(this);
119 if (editCommand != null && editCommand.getSize() > 0)
121 ap.alignFrame.addHistoryItem(editCommand);
122 av.firePropertyChange("alignment", null, av.getAlignment()
129 groupEditing = false;
137 seqCanvas.cursorY = getKeyboardNo1() - 1;
141 void setCursorColumn()
143 seqCanvas.cursorX = getKeyboardNo1() - 1;
147 void setCursorRowAndColumn()
149 if (keyboardNo2 == null)
151 keyboardNo2 = new StringBuffer();
155 seqCanvas.cursorX = getKeyboardNo1() - 1;
156 seqCanvas.cursorY = getKeyboardNo2() - 1;
161 void setCursorPosition()
163 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
165 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
169 void moveCursor(int dx, int dy)
171 seqCanvas.cursorX += dx;
172 seqCanvas.cursorY += dy;
173 if (av.hasHiddenColumns()
174 && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
176 int original = seqCanvas.cursorX - dx;
177 int maxWidth = av.getAlignment().getWidth();
179 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
180 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
182 seqCanvas.cursorX += dx;
185 if (seqCanvas.cursorX >= maxWidth
186 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
188 seqCanvas.cursorX = original;
194 void scrollToVisible()
196 if (seqCanvas.cursorX < 0)
198 seqCanvas.cursorX = 0;
200 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
202 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
205 if (seqCanvas.cursorY < 0)
207 seqCanvas.cursorY = 0;
209 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
211 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
215 if (av.getWrapAlignment())
217 ap.scrollToWrappedVisible(seqCanvas.cursorX);
221 while (seqCanvas.cursorY < av.startSeq)
225 while (seqCanvas.cursorY + 1 > av.endSeq)
229 while (seqCanvas.cursorX < av.getColumnSelection()
230 .adjustForHiddenColumns(av.startRes))
233 if (!ap.scrollRight(false))
238 while (seqCanvas.cursorX > av.getColumnSelection()
239 .adjustForHiddenColumns(av.endRes))
241 if (!ap.scrollRight(true))
247 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
248 seqCanvas.cursorX, seqCanvas.cursorY);
253 void setSelectionAreaAtCursor(boolean topLeft)
255 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
257 if (av.getSelectionGroup() != null)
259 SequenceGroup sg = av.getSelectionGroup();
260 // Find the top and bottom of this group
261 int min = av.getAlignment().getHeight(), max = 0;
262 for (int i = 0; i < sg.getSize(); i++)
264 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
279 sg.setStartRes(seqCanvas.cursorX);
280 if (sg.getEndRes() < seqCanvas.cursorX)
282 sg.setEndRes(seqCanvas.cursorX);
285 min = seqCanvas.cursorY;
289 sg.setEndRes(seqCanvas.cursorX);
290 if (sg.getStartRes() > seqCanvas.cursorX)
292 sg.setStartRes(seqCanvas.cursorX);
295 max = seqCanvas.cursorY + 1;
300 // Only the user can do this
301 av.setSelectionGroup(null);
305 // Now add any sequences between min and max
307 for (int i = min; i < max; i++)
309 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
314 if (av.getSelectionGroup() == null)
316 SequenceGroup sg = new SequenceGroup();
317 sg.setStartRes(seqCanvas.cursorX);
318 sg.setEndRes(seqCanvas.cursorX);
319 sg.addSequence(sequence, false);
320 av.setSelectionGroup(sg);
322 ap.paintAlignment(false);
326 void insertGapAtCursor(boolean group)
328 groupEditing = group;
329 startseq = seqCanvas.cursorY;
330 lastres = seqCanvas.cursorX;
331 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
335 void deleteGapAtCursor(boolean group)
337 groupEditing = group;
338 startseq = seqCanvas.cursorY;
339 lastres = seqCanvas.cursorX + getKeyboardNo1();
340 editSequence(false, seqCanvas.cursorX);
344 void numberPressed(char value)
346 if (keyboardNo1 == null)
348 keyboardNo1 = new StringBuffer();
351 if (keyboardNo2 != null)
353 keyboardNo2.append(value);
357 keyboardNo1.append(value);
365 if (keyboardNo1 != null)
367 int value = Integer.parseInt(keyboardNo1.toString());
371 } catch (Exception x)
382 if (keyboardNo2 != null)
384 int value = Integer.parseInt(keyboardNo2.toString());
388 } catch (Exception x)
395 void setStatusMessage(SequenceI sequence, int res, int seq)
397 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
398 + sequence.getName());
401 if (av.getAlignment().isNucleotide())
403 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
407 text.append(" Nucleotide: ");
412 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
415 text.append(" Residue: ");
424 text.append(obj + " (" + sequence.findPosition(res) + ")");
428 ap.alignFrame.statusBar.setText(text.toString());
432 public void mousePressed(MouseEvent evt)
434 lastMousePress = evt.getPoint();
436 // For now, ignore the mouseWheel font resizing on Macs
437 // As the Button2_mask always seems to be true
438 if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
441 mouseWheelPressed = true;
445 if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
447 if (evt.isControlDown() || evt.isAltDown())
455 doMousePressedDefineMode(evt);
459 int seq = findSeq(evt);
460 int res = findRes(evt);
462 if (seq < 0 || res < 0)
467 if ((seq < av.getAlignment().getHeight())
468 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
482 public void mouseClicked(MouseEvent evt)
484 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
485 if (evt.getClickCount() > 1)
487 if (av.getSelectionGroup() != null
488 && av.getSelectionGroup().getSize() == 1
489 && av.getSelectionGroup().getEndRes()
490 - av.getSelectionGroup().getStartRes() < 2)
492 av.setSelectionGroup(null);
495 SequenceFeature[] features = findFeaturesAtRes(sequence,
496 sequence.findPosition(findRes(evt)));
498 if (features != null && features.length > 0)
500 SearchResults highlight = new SearchResults();
501 highlight.addResult(sequence, features[0].getBegin(),
502 features[0].getEnd());
503 seqCanvas.highlightSearchResults(highlight);
505 if (features != null && features.length > 0)
507 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
508 { sequence }, features, false, ap);
510 seqCanvas.highlightSearchResults(null);
515 public void mouseReleased(MouseEvent evt)
517 mouseDragging = false;
518 mouseWheelPressed = false;
519 ap.paintAlignment(true);
523 doMouseReleasedDefineMode(evt);
531 int startWrapBlock = -1;
533 int wrappedBlock = -1;
535 int findRes(MouseEvent evt)
540 if (av.getWrapAlignment())
543 int hgap = av.getCharHeight();
544 if (av.getScaleAboveWrapped())
546 hgap += av.getCharHeight();
549 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
551 + seqCanvas.getAnnotationHeight();
555 x -= seqCanvas.LABEL_WEST;
557 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
563 wrappedBlock = y / cHeight;
564 wrappedBlock += av.getStartRes() / cwidth;
566 res = wrappedBlock * cwidth + x / av.getCharWidth();
571 res = (x / av.getCharWidth()) + av.getStartRes();
574 if (av.hasHiddenColumns())
576 res = av.getColumnSelection().adjustForHiddenColumns(res);
583 int findSeq(MouseEvent evt)
585 final int sqnum = findAlRow(evt);
586 return (sqnum < 0) ? 0 : sqnum;
592 * @return row in alignment that was selected (or -1 for column selection)
594 private int findAlRow(MouseEvent evt)
599 if (av.getWrapAlignment())
601 int hgap = av.getCharHeight();
602 if (av.getScaleAboveWrapped())
604 hgap += av.getCharHeight();
607 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
609 + seqCanvas.getAnnotationHeight();
613 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
622 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
623 .getAlignment().getHeight() - 1);
633 public void doMousePressed(MouseEvent evt)
636 int seq = findSeq(evt);
637 int res = findRes(evt);
639 if (seq < av.getAlignment().getHeight()
640 && res < av.getAlignment().getSequenceAt(seq).getLength())
642 // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
643 // Find the residue's position in the sequence (res is the position
660 public void mouseOverSequence(SequenceI sequence, int index, int pos)
662 String tmp = sequence.hashCode() + index + "";
663 if (lastMessage == null || !lastMessage.equals(tmp))
665 ssm.mouseOverSequence(sequence, index, pos, av);
671 public void highlightSequence(SearchResults results)
673 if (av.followHighlight)
675 if (ap.scrollToPosition(results, true))
677 ap.alignFrame.repaint();
680 seqCanvas.highlightSearchResults(results);
685 public VamsasSource getVamsasSource()
687 return this.ap == null ? null : this.ap.av;
690 public void updateColours(SequenceI seq, int index)
692 System.out.println("update the seqPanel colours");
696 public void mouseMoved(MouseEvent evt)
698 int res = findRes(evt);
699 int seq = findSeq(evt);
701 if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
710 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
711 if (res > sequence.getLength())
720 int respos = sequence.findPosition(res);
723 mouseOverSequence(sequence, res, respos);
726 StringBuilder text = new StringBuilder();
727 text.append("Sequence ").append(Integer.toString(seq + 1))
728 .append(" ID: ").append(sequence.getName());
731 final String ch = String.valueOf(sequence.getCharAt(res));
732 if (av.getAlignment().isNucleotide())
734 obj = ResidueProperties.nucleotideName.get(ch);
737 text.append(" Nucleotide: ").append(obj);
742 obj = "X".equalsIgnoreCase(ch) ? "STOP"
743 : ResidueProperties.aa2Triplet.get(ch);
746 text.append(" Residue: ").append(obj);
752 text.append(" (").append(Integer.toString(respos)).append(")");
755 ap.alignFrame.statusBar.setText(text.toString());
757 StringBuilder tooltipText = new StringBuilder();
758 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
761 for (int g = 0; g < groups.length; g++)
763 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
765 if (!groups[g].getName().startsWith("JTreeGroup")
766 && !groups[g].getName().startsWith("JGroup"))
768 tooltipText.append(groups[g].getName()).append(" ");
770 if (groups[g].getDescription() != null)
772 tooltipText.append(groups[g].getDescription());
774 tooltipText.append("\n");
779 // use aa to see if the mouse pointer is on a
780 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
781 sequence.findPosition(res));
784 while (index < allFeatures.length)
786 SequenceFeature sf = allFeatures[index];
788 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
790 if (sf.getDescription() != null)
792 tooltipText.append(" " + sf.getDescription());
795 if (sf.getValue("status") != null)
797 String status = sf.getValue("status").toString();
798 if (status.length() > 0)
800 tooltipText.append(" (" + sf.getValue("status") + ")");
803 tooltipText.append("\n");
810 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
814 tooltip.setTip(tooltipText.toString());
818 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
820 Vector tmp = new Vector();
821 SequenceFeature[] features = sequence.getSequenceFeatures();
822 if (features != null)
824 for (int i = 0; i < features.length; i++)
826 if (av.getFeaturesDisplayed() == null
827 || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
832 if (features[i].featureGroup != null
833 && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
838 if ((features[i].getBegin() <= res)
839 && (features[i].getEnd() >= res))
841 tmp.addElement(features[i]);
846 features = new SequenceFeature[tmp.size()];
847 tmp.copyInto(features);
854 public void mouseDragged(MouseEvent evt)
856 if (mouseWheelPressed)
858 int oldWidth = av.getCharWidth();
860 // Which is bigger, left-right or up-down?
861 if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
864 int fontSize = av.font.getSize();
866 if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
870 else if (evt.getY() > lastMousePress.y)
880 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
881 av.setCharWidth(oldWidth);
885 if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
887 av.setCharWidth(av.getCharWidth() - 1);
889 else if (evt.getX() > lastMousePress.x)
891 av.setCharWidth(av.getCharWidth() + 1);
894 if (av.getCharWidth() < 1)
902 FontMetrics fm = getFontMetrics(av.getFont());
903 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
905 lastMousePress = evt.getPoint();
907 ap.paintAlignment(false);
908 ap.annotationPanel.image = null;
914 doMouseDraggedDefineMode(evt);
918 int res = findRes(evt);
925 if ((lastres == -1) || (lastres == res))
930 if ((res < av.getAlignment().getWidth()) && (res < lastres))
932 // dragLeft, delete gap
933 editSequence(false, res);
937 editSequence(true, res);
940 mouseDragging = true;
941 if (scrollThread != null)
943 scrollThread.setEvent(evt);
948 synchronized void editSequence(boolean insertGap, int startres)
952 boolean fixedColumns = false;
953 SequenceGroup sg = av.getSelectionGroup();
955 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
957 if (!groupEditing && av.hasHiddenRows())
959 if (av.isHiddenRepSequence(seq))
961 sg = av.getRepresentedSequences(seq);
966 StringBuffer message = new StringBuffer();
969 message.append(MessageManager.getString("action.edit_group")).append(
971 if (editCommand == null)
973 editCommand = new EditCommand(
974 MessageManager.getString("action.edit_group"));
979 message.append(MessageManager.getString("label.edit_sequence"))
980 .append(" " + seq.getName());
981 String label = seq.getName();
982 if (label.length() > 10)
984 label = label.substring(0, 10);
986 if (editCommand == null)
988 editCommand = new EditCommand(MessageManager.formatMessage(
989 "label.edit_params", new String[]
996 message.append(" insert ");
1000 message.append(" delete ");
1003 message.append(Math.abs(startres - lastres) + " gaps.");
1004 ap.alignFrame.statusBar.setText(message.toString());
1006 // Are we editing within a selection group?
1008 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1011 fixedColumns = true;
1013 // sg might be null as the user may only see 1 sequence,
1014 // but the sequence represents a group
1017 if (!av.isHiddenRepSequence(seq))
1023 sg = av.getRepresentedSequences(seq);
1026 fixedLeft = sg.getStartRes();
1027 fixedRight = sg.getEndRes();
1029 if ((startres < fixedLeft && lastres >= fixedLeft)
1030 || (startres >= fixedLeft && lastres < fixedLeft)
1031 || (startres > fixedRight && lastres <= fixedRight)
1032 || (startres <= fixedRight && lastres > fixedRight))
1038 if (fixedLeft > startres)
1040 fixedRight = fixedLeft - 1;
1043 else if (fixedRight < startres)
1045 fixedLeft = fixedRight;
1050 if (av.hasHiddenColumns())
1052 fixedColumns = true;
1053 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1054 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1056 if ((insertGap && startres > y1 && lastres < y1)
1057 || (!insertGap && startres < y2 && lastres > y2))
1063 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1064 // Selection spans a hidden region
1065 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1073 fixedRight = y2 - 1;
1080 SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
1081 .toArray(new SequenceI[0]);
1086 // If the user has selected the whole sequence, and is dragging to
1087 // the right, we can still extend the alignment and selectionGroup
1088 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1089 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1091 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1092 fixedRight = sg.getEndRes();
1095 // Is it valid with fixed columns??
1096 // Find the next gap before the end
1097 // of the visible region boundary
1098 boolean blank = false;
1099 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1103 for (SequenceI gs : groupSeqs)
1105 for (int j = 0; j < startres - lastres; j++)
1107 if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
1123 if (sg.getSize() == av.getAlignment().getHeight())
1125 if ((av.hasHiddenColumns() && startres < av
1126 .getColumnSelection().getHiddenBoundaryRight(startres)))
1132 int alWidth = av.getAlignment().getWidth();
1133 if (av.hasHiddenRows())
1135 int hwidth = av.getAlignment().getHiddenSequences()
1137 if (hwidth > alWidth)
1142 // We can still insert gaps if the selectionGroup
1143 // contains all the sequences
1144 sg.setEndRes(sg.getEndRes() + startres - lastres);
1145 fixedRight = alWidth + startres - lastres;
1156 else if (!insertGap)
1158 // / Are we able to delete?
1159 // ie are all columns blank?
1161 for (SequenceI gs : groupSeqs)
1163 for (int j = startres; j < lastres; j++)
1165 if (gs.getLength() <= j)
1170 if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
1172 // Not a gap, block edit not valid
1182 // dragging to the right
1183 if (fixedColumns && fixedRight != -1)
1185 for (int j = lastres; j < startres; j++)
1187 insertChar(j, groupSeqs, fixedRight);
1192 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1193 startres - lastres, av.getAlignment(), true);
1198 // dragging to the left
1199 if (fixedColumns && fixedRight != -1)
1201 for (int j = lastres; j > startres; j--)
1203 deleteChar(startres, groupSeqs, fixedRight);
1208 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1209 lastres - startres, av.getAlignment(), true);
1215 // ///Editing a single sequence///////////
1219 // dragging to the right
1220 if (fixedColumns && fixedRight != -1)
1222 for (int j = lastres; j < startres; j++)
1224 insertChar(j, new SequenceI[]
1225 { seq }, fixedRight);
1230 editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
1231 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1236 // dragging to the left
1237 if (fixedColumns && fixedRight != -1)
1239 for (int j = lastres; j > startres; j--)
1241 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1246 deleteChar(startres, new SequenceI[]
1247 { seq }, fixedRight);
1252 // could be a keyboard edit trying to delete none gaps
1254 for (int m = startres; m < lastres; m++)
1256 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1265 editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
1266 { seq }, startres, max, av.getAlignment(), true);
1273 seqCanvas.repaint();
1276 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1278 int blankColumn = fixedColumn;
1279 for (int s = 0; s < seq.length; s++)
1281 // Find the next gap before the end of the visible region boundary
1282 // If lastCol > j, theres a boundary after the gap insertion
1284 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1286 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1288 // Theres a space, so break and insert the gap
1293 if (blankColumn <= j)
1295 blankColumn = fixedColumn;
1301 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
1302 av.getAlignment(), true);
1304 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
1309 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1312 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
1315 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
1316 av.getAlignment(), true);
1319 // ////////////////////////////////////////
1320 // ///Everything below this is for defining the boundary of the rubberband
1321 // ////////////////////////////////////////
1322 public void doMousePressedDefineMode(MouseEvent evt)
1324 if (scrollThread != null)
1326 scrollThread.running = false;
1327 scrollThread = null;
1330 int res = findRes(evt);
1331 int seq = findSeq(evt);
1333 startWrapBlock = wrappedBlock;
1340 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1342 if (sequence == null || res > sequence.getLength())
1347 stretchGroup = av.getSelectionGroup();
1349 if (stretchGroup == null)
1351 stretchGroup = av.getAlignment().findGroup(sequence);
1352 if (stretchGroup != null && res > stretchGroup.getStartRes()
1353 && res < stretchGroup.getEndRes())
1355 av.setSelectionGroup(stretchGroup);
1359 stretchGroup = null;
1363 else if (!stretchGroup.getSequences(null).contains(sequence)
1364 || stretchGroup.getStartRes() > res
1365 || stretchGroup.getEndRes() < res)
1367 stretchGroup = null;
1369 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1371 if (allGroups != null)
1373 for (int i = 0; i < allGroups.length; i++)
1375 if (allGroups[i].getStartRes() <= res
1376 && allGroups[i].getEndRes() >= res)
1378 stretchGroup = allGroups[i];
1383 av.setSelectionGroup(stretchGroup);
1386 // DETECT RIGHT MOUSE BUTTON IN AWT
1387 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
1389 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
1390 sequence.findPosition(res));
1392 Vector links = null;
1393 if (allFeatures != null)
1395 for (int i = 0; i < allFeatures.length; i++)
1397 if (allFeatures[i].links != null)
1401 links = new Vector();
1403 for (int j = 0; j < allFeatures[i].links.size(); j++)
1405 links.addElement(allFeatures[i].links.elementAt(j));
1410 APopupMenu popup = new APopupMenu(ap, null, links);
1412 popup.show(this, evt.getX(), evt.getY());
1418 seqCanvas.cursorX = findRes(evt);
1419 seqCanvas.cursorY = findSeq(evt);
1420 seqCanvas.repaint();
1424 // Only if left mouse button do we want to change group sizes
1426 if (stretchGroup == null)
1428 // define a new group here
1429 SequenceGroup sg = new SequenceGroup();
1430 sg.setStartRes(res);
1432 sg.addSequence(sequence, false);
1433 av.setSelectionGroup(sg);
1436 if (av.getConservationSelected())
1438 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1441 if (av.getAbovePIDThreshold())
1443 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1450 public void doMouseReleasedDefineMode(MouseEvent evt)
1452 if (stretchGroup == null)
1457 stretchGroup.recalcConservation(); // always do this - annotation has own
1459 if (stretchGroup.cs != null)
1461 stretchGroup.cs.alignmentChanged(stretchGroup,
1462 av.getHiddenRepSequences());
1464 if (stretchGroup.cs.conservationApplied())
1466 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1467 stretchGroup.getName());
1471 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1472 stretchGroup.getName());
1475 changeEndRes = false;
1476 changeStartRes = false;
1477 stretchGroup = null;
1478 PaintRefresher.Refresh(ap, av.getSequenceSetId());
1479 ap.paintAlignment(true);
1483 public void doMouseDraggedDefineMode(MouseEvent evt)
1485 int res = findRes(evt);
1486 int y = findSeq(evt);
1488 if (wrappedBlock != startWrapBlock)
1493 if (stretchGroup == null)
1498 mouseDragging = true;
1500 if (y > av.getAlignment().getHeight())
1502 y = av.getAlignment().getHeight() - 1;
1505 if (res >= av.getAlignment().getWidth())
1507 res = av.getAlignment().getWidth() - 1;
1510 if (stretchGroup.getEndRes() == res)
1512 // Edit end res position of selected group
1513 changeEndRes = true;
1515 else if (stretchGroup.getStartRes() == res)
1517 // Edit start res position of selected group
1518 changeStartRes = true;
1528 if (res > (stretchGroup.getStartRes() - 1))
1530 stretchGroup.setEndRes(res);
1533 else if (changeStartRes)
1535 if (res < (stretchGroup.getEndRes() + 1))
1537 stretchGroup.setStartRes(res);
1541 int dragDirection = 0;
1547 else if (y < oldSeq)
1552 while ((y != oldSeq) && (oldSeq > -1)
1553 && (y < av.getAlignment().getHeight()))
1555 // This routine ensures we don't skip any sequences, as the
1556 // selection is quite slow.
1557 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1559 oldSeq += dragDirection;
1566 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1568 if (stretchGroup.getSequences(null).contains(nextSeq))
1570 stretchGroup.deleteSequence(seq, false);
1576 stretchGroup.addSequence(seq, false);
1579 stretchGroup.addSequence(nextSeq, false);
1588 if (res > av.endRes || res < av.startRes || y < av.startSeq
1594 if (scrollThread != null)
1596 scrollThread.setEvent(evt);
1599 seqCanvas.repaint();
1602 public void mouseEntered(MouseEvent e)
1609 if (scrollThread != null)
1611 scrollThread.running = false;
1612 scrollThread = null;
1616 public void mouseExited(MouseEvent e)
1618 if (av.getWrapAlignment())
1623 if (mouseDragging && scrollThread == null)
1625 scrollThread = new ScrollThread();
1629 void scrollCanvas(MouseEvent evt)
1633 if (scrollThread != null)
1635 scrollThread.running = false;
1636 scrollThread = null;
1638 mouseDragging = false;
1642 if (scrollThread == null)
1644 scrollThread = new ScrollThread();
1647 mouseDragging = true;
1648 scrollThread.setEvent(evt);
1653 // this class allows scrolling off the bottom of the visible alignment
1654 class ScrollThread extends Thread
1658 boolean running = false;
1660 public ScrollThread()
1665 public void setEvent(MouseEvent e)
1670 public void stopScrolling()
1684 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
1686 running = ap.scrollUp(true);
1689 if (mouseDragging && evt.getY() >= getSize().height
1690 && av.getAlignment().getHeight() > av.getEndSeq())
1692 running = ap.scrollUp(false);
1695 if (mouseDragging && evt.getX() < 0)
1697 running = ap.scrollRight(false);
1700 else if (mouseDragging && evt.getX() >= getSize().width)
1702 running = ap.scrollRight(true);
1709 } catch (Exception ex)
1717 * modify current selection according to a received message.
1719 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1720 SelectionSource source)
1722 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1723 // handles selection messages...
1724 // TODO: extend config options to allow user to control if selections may be
1725 // shared between viewports.
1727 && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source)
1728 .getSequenceSetId().equals(av.getSequenceSetId()))))
1732 // do we want to thread this ? (contention with seqsel and colsel locks, I
1734 // rules are: colsel is copied if there is a real intersection between
1735 // sequence selection
1736 boolean repaint = false, copycolsel = true;
1737 if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
1739 SequenceGroup sgroup = null;
1740 if (seqsel != null && seqsel.getSize() > 0)
1742 if (av.getAlignment() == null)
1745 .println("Selection message: alignviewport av SeqSetId="
1746 + av.getSequenceSetId() + " ViewId="
1748 + " 's alignment is NULL! returning immediatly.");
1751 sgroup = seqsel.intersect(av.getAlignment(),
1752 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1753 if ((sgroup == null || sgroup.getSize() == 0)
1754 && (colsel == null || colsel.size() == 0))
1756 // don't copy columns if the region didn't intersect.
1760 if (sgroup != null && sgroup.getSize() > 0)
1762 av.setSelectionGroup(sgroup);
1766 av.setSelectionGroup(null);
1768 repaint = av.isSelectionGroupChanged(true);
1771 && (av.getColumnSelection() == null || !av
1772 .isColSelChanged(true)))
1774 // the current selection is unset or from a previous message
1775 // so import the new colsel.
1776 if (colsel == null || colsel.size() == 0)
1778 if (av.getColumnSelection() != null)
1780 av.getColumnSelection().clear();
1785 // TODO: shift colSel according to the intersecting sequences
1786 if (av.getColumnSelection() == null)
1788 av.setColumnSelection(new ColumnSelection(colsel));
1792 av.getColumnSelection().setElementsFrom(colsel);
1795 repaint |= av.isColSelChanged(true);
1798 && av.hasHiddenColumns()
1799 && (av.getColumnSelection() == null || av.getColumnSelection()
1800 .getHiddenColumns() == null))
1802 System.err.println("Bad things");
1806 ap.scalePanelHolder.repaint();
1812 * scroll to the given row/column - or nearest visible location
1817 public void scrollTo(int row, int column)
1820 row = row < 0 ? ap.av.startSeq : row;
1821 column = column < 0 ? ap.av.startRes : column;
1822 ap.scrollTo(column, column, row, true, true);
1826 * scroll to the given row - or nearest visible location
1830 public void scrollToRow(int row)
1833 row = row < 0 ? ap.av.startSeq : row;
1834 ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
1838 * scroll to the given column - or nearest visible location
1842 public void scrollToColumn(int column)
1845 column = column < 0 ? ap.av.startRes : column;
1846 ap.scrollTo(column, column, ap.av.startSeq, true, true);