2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.api.AlignViewportI;
24 import jalview.commands.EditCommand;
25 import jalview.commands.EditCommand.Action;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.ColumnSelection;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SearchResultMatchI;
30 import jalview.datamodel.SearchResults;
31 import jalview.datamodel.SearchResultsI;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.schemes.ResidueProperties;
37 import jalview.structure.SelectionListener;
38 import jalview.structure.SelectionSource;
39 import jalview.structure.SequenceListener;
40 import jalview.structure.StructureSelectionManager;
41 import jalview.structure.VamsasSource;
42 import jalview.util.Comparison;
43 import jalview.util.MappingUtils;
44 import jalview.util.MessageManager;
45 import jalview.viewmodel.AlignmentViewport;
46 import jalview.viewmodel.ViewportRanges;
48 import java.awt.BorderLayout;
50 import java.awt.FontMetrics;
51 import java.awt.Panel;
52 import java.awt.Point;
53 import java.awt.event.InputEvent;
54 import java.awt.event.MouseEvent;
55 import java.awt.event.MouseListener;
56 import java.awt.event.MouseMotionListener;
57 import java.util.ArrayList;
58 import java.util.Collections;
59 import java.util.List;
60 import java.util.ListIterator;
61 import java.util.Vector;
63 public class SeqPanel extends Panel implements MouseMotionListener,
64 MouseListener, SequenceListener, SelectionListener
67 public SeqCanvas seqCanvas;
69 public AlignmentPanel ap;
71 protected int lastres;
73 protected int startseq;
75 protected AlignViewport av;
77 // if character is inserted or deleted, we will need to recalculate the
79 boolean seqEditOccurred = false;
81 ScrollThread scrollThread = null;
83 boolean mouseDragging = false;
85 boolean editingSeqs = false;
87 boolean groupEditing = false;
91 boolean changeEndSeq = false;
93 boolean changeStartSeq = false;
95 boolean changeEndRes = false;
97 boolean changeStartRes = false;
99 SequenceGroup stretchGroup = null;
101 StringBuffer keyboardNo1;
103 StringBuffer keyboardNo2;
105 boolean mouseWheelPressed = false;
107 Point lastMousePress;
109 EditCommand editCommand;
111 StructureSelectionManager ssm;
113 public SeqPanel(AlignViewport avp, AlignmentPanel p)
117 seqCanvas = new SeqCanvas(avp);
118 setLayout(new BorderLayout());
123 seqCanvas.addMouseMotionListener(this);
124 seqCanvas.addMouseListener(this);
125 ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
126 ssm.addStructureViewerListener(this);
127 ssm.addSelectionListener(this);
134 if (editCommand != null && editCommand.getSize() > 0)
136 ap.alignFrame.addHistoryItem(editCommand);
137 av.firePropertyChange("alignment", null,
138 av.getAlignment().getSequences());
144 groupEditing = false;
152 seqCanvas.cursorY = getKeyboardNo1() - 1;
156 void setCursorColumn()
158 seqCanvas.cursorX = getKeyboardNo1() - 1;
162 void setCursorRowAndColumn()
164 if (keyboardNo2 == null)
166 keyboardNo2 = new StringBuffer();
170 seqCanvas.cursorX = getKeyboardNo1() - 1;
171 seqCanvas.cursorY = getKeyboardNo2() - 1;
176 void setCursorPosition()
178 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
180 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
184 void moveCursor(int dx, int dy)
186 seqCanvas.cursorX += dx;
187 seqCanvas.cursorY += dy;
188 if (av.hasHiddenColumns() && !av.getAlignment().getHiddenColumns()
189 .isVisible(seqCanvas.cursorX))
191 int original = seqCanvas.cursorX - dx;
192 int maxWidth = av.getAlignment().getWidth();
194 while (!av.getAlignment().getHiddenColumns()
195 .isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth
196 && seqCanvas.cursorX > 0)
198 seqCanvas.cursorX += dx;
201 if (seqCanvas.cursorX >= maxWidth || !av.getAlignment()
202 .getHiddenColumns().isVisible(seqCanvas.cursorX))
204 seqCanvas.cursorX = original;
210 void scrollToVisible()
212 if (seqCanvas.cursorX < 0)
214 seqCanvas.cursorX = 0;
216 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
218 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
221 if (seqCanvas.cursorY < 0)
223 seqCanvas.cursorY = 0;
225 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
227 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
231 if (av.getWrapAlignment())
233 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
237 ViewportRanges ranges = av.getRanges();
238 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
239 while (seqCanvas.cursorY < ranges.getStartSeq())
241 ranges.scrollUp(true);
243 while (seqCanvas.cursorY > ranges.getEndSeq())
245 ranges.scrollUp(false);
247 while (seqCanvas.cursorX < hidden
248 .adjustForHiddenColumns(ranges.getStartRes()))
251 if (!ranges.scrollRight(false))
256 while (seqCanvas.cursorX > hidden
257 .adjustForHiddenColumns(ranges.getEndRes()))
259 if (!ranges.scrollRight(true))
265 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
266 seqCanvas.cursorX, seqCanvas.cursorY);
271 void setSelectionAreaAtCursor(boolean topLeft)
273 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
275 if (av.getSelectionGroup() != null)
277 SequenceGroup sg = av.getSelectionGroup();
278 // Find the top and bottom of this group
279 int min = av.getAlignment().getHeight(), max = 0;
280 for (int i = 0; i < sg.getSize(); i++)
282 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
297 sg.setStartRes(seqCanvas.cursorX);
298 if (sg.getEndRes() < seqCanvas.cursorX)
300 sg.setEndRes(seqCanvas.cursorX);
303 min = seqCanvas.cursorY;
307 sg.setEndRes(seqCanvas.cursorX);
308 if (sg.getStartRes() > seqCanvas.cursorX)
310 sg.setStartRes(seqCanvas.cursorX);
313 max = seqCanvas.cursorY + 1;
318 // Only the user can do this
319 av.setSelectionGroup(null);
323 // Now add any sequences between min and max
325 for (int i = min; i < max; i++)
327 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
332 if (av.getSelectionGroup() == null)
334 SequenceGroup sg = new SequenceGroup();
335 sg.setStartRes(seqCanvas.cursorX);
336 sg.setEndRes(seqCanvas.cursorX);
337 sg.addSequence(sequence, false);
338 av.setSelectionGroup(sg);
340 ap.paintAlignment(false);
344 void insertGapAtCursor(boolean group)
346 groupEditing = group;
347 startseq = seqCanvas.cursorY;
348 lastres = seqCanvas.cursorX;
349 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
353 void deleteGapAtCursor(boolean group)
355 groupEditing = group;
356 startseq = seqCanvas.cursorY;
357 lastres = seqCanvas.cursorX + getKeyboardNo1();
358 editSequence(false, seqCanvas.cursorX);
362 void numberPressed(char value)
364 if (keyboardNo1 == null)
366 keyboardNo1 = new StringBuffer();
369 if (keyboardNo2 != null)
371 keyboardNo2.append(value);
375 keyboardNo1.append(value);
383 if (keyboardNo1 != null)
385 int value = Integer.parseInt(keyboardNo1.toString());
389 } catch (Exception x)
400 if (keyboardNo2 != null)
402 int value = Integer.parseInt(keyboardNo2.toString());
406 } catch (Exception x)
414 * Set status message in alignment panel
417 * aligned sequence object
421 * index of sequence in alignment
422 * @return position of column in sequence or -1 if at gap
424 void setStatusMessage(SequenceI sequence, int column, int seq)
426 // TODO remove duplication of identical gui method
427 StringBuilder text = new StringBuilder(32);
428 String seqno = seq == -1 ? "" : " " + (seq + 1);
429 text.append("Sequence" + seqno + " ID: " + sequence.getName());
431 String residue = null;
433 * Try to translate the display character to residue name (null for gap).
435 final String displayChar = String.valueOf(sequence.getCharAt(column));
436 if (av.getAlignment().isNucleotide())
438 residue = ResidueProperties.nucleotideName.get(displayChar);
441 text.append(" Nucleotide: ").append(residue);
446 residue = "X".equalsIgnoreCase(displayChar) ? "X"
447 : ("*".equals(displayChar) ? "STOP"
448 : ResidueProperties.aa2Triplet.get(displayChar));
451 text.append(" Residue: ").append(residue);
458 pos = sequence.findPosition(column);
459 text.append(" (").append(Integer.toString(pos)).append(")");
462 ap.alignFrame.statusBar.setText(text.toString());
466 * Set the status bar message to highlight the first matched position in
470 * @return true if results were matched, false if not
472 private boolean setStatusMessage(SearchResultsI results)
474 AlignmentI al = this.av.getAlignment();
475 int sequenceIndex = al.findIndex(results);
476 if (sequenceIndex == -1)
480 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
481 for (SearchResultMatchI m : results.getResults())
483 SequenceI seq = m.getSequence();
484 if (seq.getDatasetSequence() != null)
486 seq = seq.getDatasetSequence();
492 * Convert position in sequence (base 1) to sequence character array
495 int start = m.getStart() - m.getSequence().getStart();
496 setStatusMessage(seq, start, sequenceIndex);
504 public void mousePressed(MouseEvent evt)
506 lastMousePress = evt.getPoint();
508 // For now, ignore the mouseWheel font resizing on Macs
509 // As the Button2_mask always seems to be true
510 if ((evt.getModifiers()
511 & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
514 mouseWheelPressed = true;
518 if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
520 if (evt.isControlDown() || evt.isAltDown())
528 doMousePressedDefineMode(evt);
532 int seq = findSeq(evt);
533 int res = findRes(evt);
535 if (seq < 0 || res < 0)
540 if ((seq < av.getAlignment().getHeight())
541 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
556 public void mouseClicked(MouseEvent evt)
558 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
559 if (evt.getClickCount() > 1)
561 if (av.getSelectionGroup() != null
562 && av.getSelectionGroup().getSize() == 1
563 && av.getSelectionGroup().getEndRes()
564 - av.getSelectionGroup().getStartRes() < 2)
566 av.setSelectionGroup(null);
569 int column = findRes(evt);
570 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
571 List<SequenceFeature> features = findFeaturesAtRes(sequence,
572 sequence.findPosition(column));
575 removeAdjacentFeatures(features, column + 1, sequence);
578 if (!features.isEmpty())
580 SearchResultsI highlight = new SearchResults();
581 highlight.addResult(sequence, features.get(0).getBegin(),
582 features.get(0).getEnd());
583 seqCanvas.highlightSearchResults(highlight);
584 seqCanvas.getFeatureRenderer().amendFeatures(
585 Collections.singletonList(sequence), features, false, ap);
587 seqCanvas.highlightSearchResults(null);
593 public void mouseReleased(MouseEvent evt)
595 boolean didDrag = mouseDragging; // did we come here after a drag
596 mouseDragging = false;
597 mouseWheelPressed = false;
601 doMouseReleasedDefineMode(evt, didDrag);
609 int startWrapBlock = -1;
611 int wrappedBlock = -1;
613 int findRes(MouseEvent evt)
618 int startRes = av.getRanges().getStartRes();
619 if (av.getWrapAlignment())
622 int hgap = av.getCharHeight();
623 if (av.getScaleAboveWrapped())
625 hgap += av.getCharHeight();
628 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
629 + hgap + seqCanvas.getAnnotationHeight();
633 x = Math.max(0, x - seqCanvas.LABEL_WEST);
635 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
641 wrappedBlock = y / cHeight;
642 wrappedBlock += startRes / cwidth;
643 int startOffset = startRes % cwidth; // in case start is scrolled right
645 res = wrappedBlock * cwidth + startOffset
646 + +Math.min(cwidth - 1, x / av.getCharWidth());
650 res = (x / av.getCharWidth()) + startRes;
653 if (av.hasHiddenColumns())
655 res = av.getAlignment().getHiddenColumns()
656 .adjustForHiddenColumns(res);
663 int findSeq(MouseEvent evt)
665 final int sqnum = findAlRow(evt);
666 return (sqnum < 0) ? 0 : sqnum;
672 * @return row in alignment that was selected (or -1 for column selection)
674 private int findAlRow(MouseEvent evt)
679 if (av.getWrapAlignment())
681 int hgap = av.getCharHeight();
682 if (av.getScaleAboveWrapped())
684 hgap += av.getCharHeight();
687 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
688 + hgap + seqCanvas.getAnnotationHeight();
692 seq = Math.min((y % cHeight) / av.getCharHeight(),
693 av.getAlignment().getHeight() - 1);
702 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
703 av.getAlignment().getHeight() - 1);
713 public void doMousePressed(MouseEvent evt)
716 int seq = findSeq(evt);
717 int res = findRes(evt);
719 if (seq < av.getAlignment().getHeight()
720 && res < av.getAlignment().getSequenceAt(seq).getLength())
722 // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
723 // Find the residue's position in the sequence (res is the position
741 public void mouseOverSequence(SequenceI sequence, int index, int pos)
743 String tmp = sequence.hashCode() + index + "";
744 if (lastMessage == null || !lastMessage.equals(tmp))
746 ssm.mouseOverSequence(sequence, index, pos, av);
753 public void highlightSequence(SearchResultsI results)
755 if (av.isFollowHighlight())
757 // don't allow highlight of protein/cDNA to also scroll a complementary
758 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
759 // over residue to change abruptly, causing highlighted residue in panel 2
760 // to change, causing a scroll in panel 1 etc)
761 ap.setToScrollComplementPanel(false);
762 if (ap.scrollToPosition(results, true))
764 ap.alignFrame.repaint();
766 ap.setToScrollComplementPanel(true);
768 setStatusMessage(results);
769 seqCanvas.highlightSearchResults(results);
774 public VamsasSource getVamsasSource()
776 return this.ap == null ? null : this.ap.av;
780 public void updateColours(SequenceI seq, int index)
782 System.out.println("update the seqPanel colours");
787 public void mouseMoved(MouseEvent evt)
789 final int column = findRes(evt);
790 int seq = findSeq(evt);
792 if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
801 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
802 if (column > sequence.getLength())
811 final char ch = sequence.getCharAt(column);
812 boolean isGapped = Comparison.isGap(ch);
813 // find residue at column (or nearest if at a gap)
814 int respos = sequence.findPosition(column);
816 if (ssm != null && !isGapped)
818 mouseOverSequence(sequence, column, respos);
821 StringBuilder text = new StringBuilder();
822 text.append("Sequence ").append(Integer.toString(seq + 1))
823 .append(" ID: ").append(sequence.getName());
827 if (av.getAlignment().isNucleotide())
829 String base = ResidueProperties.nucleotideName.get(ch);
830 text.append(" Nucleotide: ").append(base == null ? ch : base);
834 String residue = (ch == 'x' || ch == 'X') ? "X"
835 : ResidueProperties.aa2Triplet.get(String.valueOf(ch));
836 text.append(" Residue: ").append(residue == null ? ch : residue);
838 text.append(" (").append(Integer.toString(respos)).append(")");
841 ap.alignFrame.statusBar.setText(text.toString());
843 StringBuilder tooltipText = new StringBuilder();
844 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
847 for (int g = 0; g < groups.length; g++)
849 if (groups[g].getStartRes() <= column
850 && groups[g].getEndRes() >= column)
852 if (!groups[g].getName().startsWith("JTreeGroup")
853 && !groups[g].getName().startsWith("JGroup"))
855 tooltipText.append(groups[g].getName()).append(" ");
857 if (groups[g].getDescription() != null)
859 tooltipText.append(groups[g].getDescription());
861 tooltipText.append("\n");
867 * add feature details to tooltip, including any that straddle
870 if (av.isShowSequenceFeatures())
872 List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
873 sequence.findPosition(column));
876 removeAdjacentFeatures(allFeatures, column + 1, sequence);
878 for (SequenceFeature sf : allFeatures)
880 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
882 if (sf.getDescription() != null)
884 tooltipText.append(" " + sf.getDescription());
887 if (sf.getValue("status") != null)
889 String status = sf.getValue("status").toString();
890 if (status.length() > 0)
892 tooltipText.append(" (" + sf.getValue("status") + ")");
895 tooltipText.append("\n");
901 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
905 tooltip.setTip(tooltipText.toString());
910 * Removes from the list of features any that start after, or end before, the
911 * given column position. This allows us to retain only those features
912 * adjacent to a gapped position that straddle the position. Contact features
913 * that 'straddle' the position are also removed, since they are not 'at' the
918 * alignment column (1..)
921 protected void removeAdjacentFeatures(List<SequenceFeature> features,
922 int column, SequenceI sequence)
924 // TODO should this be an AlignViewController method (shared by gui)?
925 ListIterator<SequenceFeature> it = features.listIterator();
928 SequenceFeature sf = it.next();
929 if (sf.isContactFeature()
930 || sequence.findIndex(sf.getBegin()) > column
931 || sequence.findIndex(sf.getEnd()) < column)
938 List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
940 List<SequenceFeature> result = new ArrayList<>();
941 SequenceFeature[] features = sequence.getSequenceFeatures();
942 if (features != null)
944 for (int i = 0; i < features.length; i++)
946 if (av.getFeaturesDisplayed() == null || !av.getFeaturesDisplayed()
947 .isVisible(features[i].getType()))
952 if (features[i].featureGroup != null && !seqCanvas.fr
953 .checkGroupVisibility(features[i].featureGroup, false))
958 if ((features[i].getBegin() <= res)
959 && (features[i].getEnd() >= res))
961 result.add(features[i]);
972 * set when the current UI interaction has resulted in a change that requires
973 * overview shading to be recalculated. this could be changed to something
974 * more expressive that indicates what actually has changed, so selective
975 * redraws can be applied
977 private boolean needOverviewUpdate; // TODO: refactor to avcontroller
980 public void mouseDragged(MouseEvent evt)
982 if (mouseWheelPressed)
984 int oldWidth = av.getCharWidth();
986 // Which is bigger, left-right or up-down?
987 if (Math.abs(evt.getY() - lastMousePress.y) > Math
988 .abs(evt.getX() - lastMousePress.x))
990 int fontSize = av.font.getSize();
992 if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
996 else if (evt.getY() > lastMousePress.y)
1007 new Font(av.font.getName(), av.font.getStyle(), fontSize),
1009 av.setCharWidth(oldWidth);
1013 if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
1015 av.setCharWidth(av.getCharWidth() - 1);
1017 else if (evt.getX() > lastMousePress.x)
1019 av.setCharWidth(av.getCharWidth() + 1);
1022 if (av.getCharWidth() < 1)
1030 FontMetrics fm = getFontMetrics(av.getFont());
1031 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1033 lastMousePress = evt.getPoint();
1035 ap.paintAlignment(false);
1036 ap.annotationPanel.image = null;
1042 doMouseDraggedDefineMode(evt);
1046 int res = findRes(evt);
1053 if ((lastres == -1) || (lastres == res))
1058 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1060 // dragLeft, delete gap
1061 editSequence(false, res);
1065 editSequence(true, res);
1068 mouseDragging = true;
1069 if (scrollThread != null)
1071 scrollThread.setEvent(evt);
1076 synchronized void editSequence(boolean insertGap, int startres)
1079 int fixedRight = -1;
1080 boolean fixedColumns = false;
1081 SequenceGroup sg = av.getSelectionGroup();
1083 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1085 if (!groupEditing && av.hasHiddenRows())
1087 if (av.isHiddenRepSequence(seq))
1089 sg = av.getRepresentedSequences(seq);
1090 groupEditing = true;
1094 StringBuffer message = new StringBuffer();
1097 message.append(MessageManager.getString("action.edit_group"))
1099 if (editCommand == null)
1101 editCommand = new EditCommand(
1102 MessageManager.getString("action.edit_group"));
1107 message.append(MessageManager.getString("label.edit_sequence"))
1108 .append(" " + seq.getName());
1109 String label = seq.getName();
1110 if (label.length() > 10)
1112 label = label.substring(0, 10);
1114 if (editCommand == null)
1116 editCommand = new EditCommand(MessageManager
1117 .formatMessage("label.edit_params", new String[]
1124 message.append(" insert ");
1128 message.append(" delete ");
1131 message.append(Math.abs(startres - lastres) + " gaps.");
1132 ap.alignFrame.statusBar.setText(message.toString());
1134 // Are we editing within a selection group?
1135 if (groupEditing || (sg != null
1136 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1138 fixedColumns = true;
1140 // sg might be null as the user may only see 1 sequence,
1141 // but the sequence represents a group
1144 if (!av.isHiddenRepSequence(seq))
1150 sg = av.getRepresentedSequences(seq);
1153 fixedLeft = sg.getStartRes();
1154 fixedRight = sg.getEndRes();
1156 if ((startres < fixedLeft && lastres >= fixedLeft)
1157 || (startres >= fixedLeft && lastres < fixedLeft)
1158 || (startres > fixedRight && lastres <= fixedRight)
1159 || (startres <= fixedRight && lastres > fixedRight))
1165 if (fixedLeft > startres)
1167 fixedRight = fixedLeft - 1;
1170 else if (fixedRight < startres)
1172 fixedLeft = fixedRight;
1177 if (av.hasHiddenColumns())
1179 fixedColumns = true;
1180 int y1 = av.getAlignment().getHiddenColumns()
1181 .getHiddenBoundaryLeft(startres);
1182 int y2 = av.getAlignment().getHiddenColumns()
1183 .getHiddenBoundaryRight(startres);
1185 if ((insertGap && startres > y1 && lastres < y1)
1186 || (!insertGap && startres < y2 && lastres > y2))
1192 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1193 // Selection spans a hidden region
1194 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1202 fixedRight = y2 - 1;
1209 SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
1210 .toArray(new SequenceI[0]);
1215 // If the user has selected the whole sequence, and is dragging to
1216 // the right, we can still extend the alignment and selectionGroup
1217 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1218 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1220 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1221 fixedRight = sg.getEndRes();
1224 // Is it valid with fixed columns??
1225 // Find the next gap before the end
1226 // of the visible region boundary
1227 boolean blank = false;
1228 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1232 for (SequenceI gs : groupSeqs)
1234 for (int j = 0; j < startres - lastres; j++)
1236 if (!jalview.util.Comparison
1237 .isGap(gs.getCharAt(fixedRight - j)))
1252 if (sg.getSize() == av.getAlignment().getHeight())
1254 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1255 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1261 int alWidth = av.getAlignment().getWidth();
1262 if (av.hasHiddenRows())
1264 int hwidth = av.getAlignment().getHiddenSequences()
1266 if (hwidth > alWidth)
1271 // We can still insert gaps if the selectionGroup
1272 // contains all the sequences
1273 sg.setEndRes(sg.getEndRes() + startres - lastres);
1274 fixedRight = alWidth + startres - lastres;
1285 else if (!insertGap)
1287 // / Are we able to delete?
1288 // ie are all columns blank?
1290 for (SequenceI gs : groupSeqs)
1292 for (int j = startres; j < lastres; j++)
1294 if (gs.getLength() <= j)
1299 if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
1301 // Not a gap, block edit not valid
1311 // dragging to the right
1312 if (fixedColumns && fixedRight != -1)
1314 for (int j = lastres; j < startres; j++)
1316 insertChar(j, groupSeqs, fixedRight);
1321 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1322 startres - lastres, av.getAlignment(), true);
1327 // dragging to the left
1328 if (fixedColumns && fixedRight != -1)
1330 for (int j = lastres; j > startres; j--)
1332 deleteChar(startres, groupSeqs, fixedRight);
1337 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1338 lastres - startres, av.getAlignment(), true);
1344 // ///Editing a single sequence///////////
1348 // dragging to the right
1349 if (fixedColumns && fixedRight != -1)
1351 for (int j = lastres; j < startres; j++)
1353 insertChar(j, new SequenceI[] { seq }, fixedRight);
1358 editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] { seq },
1359 lastres, startres - lastres, av.getAlignment(), true);
1364 // dragging to the left
1365 if (fixedColumns && fixedRight != -1)
1367 for (int j = lastres; j > startres; j--)
1369 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1374 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1379 // could be a keyboard edit trying to delete none gaps
1381 for (int m = startres; m < lastres; m++)
1383 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1392 editCommand.appendEdit(Action.DELETE_GAP,
1394 { seq }, startres, max, av.getAlignment(), true);
1401 seqCanvas.repaint();
1404 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1406 int blankColumn = fixedColumn;
1407 for (int s = 0; s < seq.length; s++)
1409 // Find the next gap before the end of the visible region boundary
1410 // If lastCol > j, theres a boundary after the gap insertion
1412 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1414 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1416 // Theres a space, so break and insert the gap
1421 if (blankColumn <= j)
1423 blankColumn = fixedColumn;
1429 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
1430 av.getAlignment(), true);
1432 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
1437 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1440 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
1443 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
1444 av.getAlignment(), true);
1447 // ////////////////////////////////////////
1448 // ///Everything below this is for defining the boundary of the rubberband
1449 // ////////////////////////////////////////
1450 public void doMousePressedDefineMode(MouseEvent evt)
1452 if (scrollThread != null)
1454 scrollThread.threadRunning = false;
1455 scrollThread = null;
1458 int res = findRes(evt);
1459 int seq = findSeq(evt);
1461 startWrapBlock = wrappedBlock;
1468 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1470 if (sequence == null || res > sequence.getLength())
1475 stretchGroup = av.getSelectionGroup();
1477 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1479 stretchGroup = av.getAlignment().findGroup(sequence, res);
1480 if (stretchGroup != null)
1482 // only update the current selection if the popup menu has a group to
1484 av.setSelectionGroup(stretchGroup);
1488 // DETECT RIGHT MOUSE BUTTON IN AWT
1489 if ((evt.getModifiers()
1490 & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
1492 List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
1493 sequence.findPosition(res));
1495 Vector<String> links = null;
1496 for (SequenceFeature sf : allFeatures)
1498 if (sf.links != null)
1502 links = new Vector<>();
1504 for (int j = 0; j < sf.links.size(); j++)
1506 links.addElement(sf.links.elementAt(j));
1510 APopupMenu popup = new APopupMenu(ap, null, links);
1512 popup.show(this, evt.getX(), evt.getY());
1518 seqCanvas.cursorX = findRes(evt);
1519 seqCanvas.cursorY = findSeq(evt);
1520 seqCanvas.repaint();
1524 // Only if left mouse button do we want to change group sizes
1526 if (stretchGroup == null)
1528 // define a new group here
1529 SequenceGroup sg = new SequenceGroup();
1530 sg.setStartRes(res);
1532 sg.addSequence(sequence, false);
1533 av.setSelectionGroup(sg);
1536 if (av.getConservationSelected())
1538 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1541 if (av.getAbovePIDThreshold())
1543 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1550 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1552 if (stretchGroup == null)
1556 // always do this - annotation has own state
1557 // but defer colourscheme update until hidden sequences are passed in
1558 boolean vischange = stretchGroup.recalcConservation(true);
1559 // here we rely on stretchGroup == av.getSelection()
1560 needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
1562 if (stretchGroup.cs != null)
1564 stretchGroup.cs.alignmentChanged(stretchGroup,
1565 av.getHiddenRepSequences());
1567 if (stretchGroup.cs.conservationApplied())
1569 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1570 stretchGroup.getName());
1572 if (stretchGroup.cs.getThreshold() > 0)
1574 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1575 stretchGroup.getName());
1578 PaintRefresher.Refresh(ap, av.getSequenceSetId());
1579 ap.paintAlignment(needOverviewUpdate);
1580 needOverviewUpdate = false;
1581 changeEndRes = false;
1582 changeStartRes = false;
1583 stretchGroup = null;
1587 public void doMouseDraggedDefineMode(MouseEvent evt)
1589 int res = findRes(evt);
1590 int y = findSeq(evt);
1592 if (wrappedBlock != startWrapBlock)
1597 if (stretchGroup == null)
1602 mouseDragging = true;
1604 if (y > av.getAlignment().getHeight())
1606 y = av.getAlignment().getHeight() - 1;
1609 if (res >= av.getAlignment().getWidth())
1611 res = av.getAlignment().getWidth() - 1;
1614 if (stretchGroup.getEndRes() == res)
1616 // Edit end res position of selected group
1617 changeEndRes = true;
1619 else if (stretchGroup.getStartRes() == res)
1621 // Edit start res position of selected group
1622 changeStartRes = true;
1632 if (res > (stretchGroup.getStartRes() - 1))
1634 stretchGroup.setEndRes(res);
1635 needOverviewUpdate |= av.isSelectionDefinedGroup();
1638 else if (changeStartRes)
1640 if (res < (stretchGroup.getEndRes() + 1))
1642 stretchGroup.setStartRes(res);
1643 needOverviewUpdate |= av.isSelectionDefinedGroup();
1647 int dragDirection = 0;
1653 else if (y < oldSeq)
1658 while ((y != oldSeq) && (oldSeq > -1)
1659 && (y < av.getAlignment().getHeight()))
1661 // This routine ensures we don't skip any sequences, as the
1662 // selection is quite slow.
1663 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1665 oldSeq += dragDirection;
1672 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1674 if (stretchGroup.getSequences(null).contains(nextSeq))
1676 stretchGroup.deleteSequence(seq, false);
1677 needOverviewUpdate |= av.isSelectionDefinedGroup();
1683 stretchGroup.addSequence(seq, false);
1686 stretchGroup.addSequence(nextSeq, false);
1687 needOverviewUpdate |= av.isSelectionDefinedGroup();
1696 if (res > av.getRanges().getEndRes()
1697 || res < av.getRanges().getStartRes()
1698 || y < av.getRanges().getStartSeq()
1699 || y > av.getRanges().getEndSeq())
1704 if ((scrollThread != null) && (scrollThread.isRunning()))
1706 scrollThread.setEvent(evt);
1709 seqCanvas.repaint();
1713 public void mouseEntered(MouseEvent e)
1720 if ((scrollThread != null) && (scrollThread.isRunning()))
1722 scrollThread.stopScrolling();
1723 scrollThread = null;
1728 public void mouseExited(MouseEvent e)
1730 if (av.getWrapAlignment())
1735 if (mouseDragging && scrollThread == null)
1737 scrollThread = new ScrollThread();
1741 void scrollCanvas(MouseEvent evt)
1745 if ((scrollThread != null) && (scrollThread.isRunning()))
1747 scrollThread.stopScrolling();
1748 scrollThread = null;
1750 mouseDragging = false;
1754 if (scrollThread == null)
1756 scrollThread = new ScrollThread();
1759 mouseDragging = true;
1760 scrollThread.setEvent(evt);
1765 // this class allows scrolling off the bottom of the visible alignment
1766 class ScrollThread extends Thread
1770 private volatile boolean threadRunning = true;
1772 public ScrollThread()
1777 public void setEvent(MouseEvent e)
1782 public void stopScrolling()
1784 threadRunning = false;
1787 public boolean isRunning()
1789 return threadRunning;
1795 while (threadRunning)
1801 if (mouseDragging && evt.getY() < 0
1802 && av.getRanges().getStartSeq() > 0)
1804 av.getRanges().scrollUp(true);
1807 if (mouseDragging && evt.getY() >= getSize().height && av
1808 .getAlignment().getHeight() > av.getRanges().getEndSeq())
1810 av.getRanges().scrollUp(false);
1813 if (mouseDragging && evt.getX() < 0)
1815 av.getRanges().scrollRight(false);
1818 else if (mouseDragging && evt.getX() >= getSize().width)
1820 av.getRanges().scrollRight(true);
1827 } catch (Exception ex)
1835 * modify current selection according to a received message.
1838 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1839 HiddenColumns hidden, SelectionSource source)
1841 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1842 // handles selection messages...
1843 // TODO: extend config options to allow user to control if selections may be
1844 // shared between viewports.
1845 if (av != null && (av == source || !av.followSelection
1846 || (source instanceof AlignViewport
1847 && ((AlignmentViewport) source).getSequenceSetId()
1848 .equals(av.getSequenceSetId()))))
1854 * Check for selection in a view of which this one is a dna/protein
1857 if (selectionFromTranslation(seqsel, colsel, hidden, source))
1862 // do we want to thread this ? (contention with seqsel and colsel locks, I
1865 * only copy colsel if there is a real intersection between
1866 * sequence selection and this panel's alignment
1868 boolean repaint = false;
1869 boolean copycolsel = false;
1870 if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
1872 SequenceGroup sgroup = null;
1873 if (seqsel != null && seqsel.getSize() > 0)
1875 if (av.getAlignment() == null)
1877 System.out.println("Selection message: alignviewport av SeqSetId="
1878 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1879 + " 's alignment is NULL! returning immediatly.");
1882 sgroup = seqsel.intersect(av.getAlignment(),
1883 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1884 if ((sgroup != null && sgroup.getSize() > 0))
1889 if (sgroup != null && sgroup.getSize() > 0)
1891 av.setSelectionGroup(sgroup);
1895 av.setSelectionGroup(null);
1897 repaint = av.isSelectionGroupChanged(true);
1899 if (copycolsel && (av.getColumnSelection() == null
1900 || !av.isColSelChanged(true)))
1902 // the current selection is unset or from a previous message
1903 // so import the new colsel.
1904 if (colsel == null || colsel.isEmpty())
1906 if (av.getColumnSelection() != null)
1908 av.getColumnSelection().clear();
1913 // TODO: shift colSel according to the intersecting sequences
1914 if (av.getColumnSelection() == null)
1916 av.setColumnSelection(new ColumnSelection(colsel));
1920 av.getColumnSelection().setElementsFrom(colsel,
1921 av.getAlignment().getHiddenColumns());
1924 repaint |= av.isColSelChanged(true);
1926 if (copycolsel && av.hasHiddenColumns()
1927 && (av.getColumnSelection() == null))
1929 System.err.println("Bad things");
1933 ap.scalePanelHolder.repaint();
1939 * scroll to the given row/column - or nearest visible location
1944 public void scrollTo(int row, int column)
1947 row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
1948 column = column < 0 ? ap.av.getRanges().getStartRes() : column;
1949 ap.scrollTo(column, column, row, true, true);
1953 * scroll to the given row - or nearest visible location
1957 public void scrollToRow(int row)
1960 row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
1961 ap.scrollTo(ap.av.getRanges().getStartRes(),
1962 ap.av.getRanges().getStartRes(), row, true, true);
1966 * scroll to the given column - or nearest visible location
1970 public void scrollToColumn(int column)
1973 column = column < 0 ? ap.av.getRanges().getStartRes() : column;
1974 ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
1979 * If this panel is a cdna/protein translation view of the selection source,
1980 * tries to map the source selection to a local one, and returns true. Else
1987 protected boolean selectionFromTranslation(SequenceGroup seqsel,
1988 ColumnSelection colsel, HiddenColumns hidden,
1989 SelectionSource source)
1991 if (!(source instanceof AlignViewportI))
1995 final AlignViewportI sourceAv = (AlignViewportI) source;
1996 if (sourceAv.getCodingComplement() != av
1997 && av.getCodingComplement() != sourceAv)
2003 * Map sequence selection
2005 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2006 av.setSelectionGroup(sg);
2007 av.isSelectionGroupChanged(true);
2010 * Map column selection
2012 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2014 ColumnSelection cs = new ColumnSelection();
2015 HiddenColumns hs = new HiddenColumns();
2016 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2017 av.setColumnSelection(cs);
2018 av.getAlignment().setHiddenColumns(hs);
2020 ap.scalePanelHolder.repaint();