2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import java.awt.event.*;
27 import jalview.commands.*;
28 import jalview.datamodel.*;
29 import jalview.schemes.*;
30 import jalview.structure.*;
36 * @version $Revision: 1.130 $
38 public class SeqPanel extends JPanel implements MouseListener,
39 MouseMotionListener, MouseWheelListener, SequenceListener,
44 public SeqCanvas seqCanvas;
47 public AlignmentPanel ap;
49 protected int lastres;
51 protected int startseq;
53 protected AlignViewport av;
55 ScrollThread scrollThread = null;
57 boolean mouseDragging = false;
59 boolean editingSeqs = false;
61 boolean groupEditing = false;
63 // ////////////////////////////////////////
64 // ///Everything below this is for defining the boundary of the rubberband
65 // ////////////////////////////////////////
68 boolean changeEndSeq = false;
70 boolean changeStartSeq = false;
72 boolean changeEndRes = false;
74 boolean changeStartRes = false;
76 SequenceGroup stretchGroup = null;
78 boolean remove = false;
82 boolean mouseWheelPressed = false;
84 StringBuffer keyboardNo1;
86 StringBuffer keyboardNo2;
88 java.net.URL linkImageURL;
90 StringBuffer tooltipText = new StringBuffer("<html>");
94 EditCommand editCommand;
96 StructureSelectionManager ssm;
99 * Creates a new SeqPanel object.
106 public SeqPanel(AlignViewport av, AlignmentPanel ap)
108 linkImageURL = getClass().getResource("/images/link.gif");
109 ToolTipManager.sharedInstance().registerComponent(this);
110 ToolTipManager.sharedInstance().setInitialDelay(0);
111 ToolTipManager.sharedInstance().setDismissDelay(10000);
113 setBackground(Color.white);
115 seqCanvas = new SeqCanvas(ap);
116 setLayout(new BorderLayout());
117 add(seqCanvas, BorderLayout.CENTER);
123 addMouseMotionListener(this);
124 addMouseListener(this);
125 addMouseWheelListener(this);
126 ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
127 ssm.addStructureViewerListener(this);
128 ssm.addSelectionListener(this);
132 int startWrapBlock = -1;
134 int wrappedBlock = -1;
136 int findRes(MouseEvent evt)
141 if (av.wrapAlignment)
144 int hgap = av.charHeight;
145 if (av.scaleAboveWrapped)
147 hgap += av.charHeight;
150 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
151 + seqCanvas.getAnnotationHeight();
155 x -= seqCanvas.LABEL_WEST;
157 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
163 wrappedBlock = y / cHeight;
164 wrappedBlock += av.getStartRes() / cwidth;
166 res = wrappedBlock * cwidth + x / av.getCharWidth();
171 if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
173 // make sure we calculate relative to visible alignment, rather than right-hand gutter
174 x = seqCanvas.getX()+seqCanvas.getWidth();
176 res = (x / av.getCharWidth()) + av.getStartRes();
179 if (av.hasHiddenColumns())
181 res = av.getColumnSelection().adjustForHiddenColumns(res);
188 int findSeq(MouseEvent evt)
193 if (av.wrapAlignment)
195 int hgap = av.charHeight;
196 if (av.scaleAboveWrapped)
198 hgap += av.charHeight;
201 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
202 + seqCanvas.getAnnotationHeight();
206 seq = Math.min((y % cHeight) / av.getCharHeight(),
207 av.getAlignment().getHeight() - 1);
211 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
212 av.getAlignment().getHeight() - 1);
218 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
220 Vector tmp = new Vector();
221 SequenceFeature[] features = sequence.getSequenceFeatures();
222 if (features != null)
224 for (int i = 0; i < features.length; i++)
226 if (av.featuresDisplayed == null
227 || !av.featuresDisplayed.containsKey(features[i].getType()))
232 if (features[i].featureGroup != null
233 && seqCanvas.fr.featureGroups != null
234 && seqCanvas.fr.featureGroups
235 .containsKey(features[i].featureGroup)
236 && !((Boolean) seqCanvas.fr.featureGroups
237 .get(features[i].featureGroup)).booleanValue())
240 if ((features[i].getBegin() <= res)
241 && (features[i].getEnd() >= res))
243 tmp.addElement(features[i]);
248 features = new SequenceFeature[tmp.size()];
249 tmp.copyInto(features);
256 if (editCommand != null && editCommand.getSize() > 0)
258 ap.alignFrame.addHistoryItem(editCommand);
259 av.firePropertyChange("alignment", null, av.getAlignment()
266 groupEditing = false;
274 seqCanvas.cursorY = getKeyboardNo1() - 1;
278 void setCursorColumn()
280 seqCanvas.cursorX = getKeyboardNo1() - 1;
284 void setCursorRowAndColumn()
286 if (keyboardNo2 == null)
288 keyboardNo2 = new StringBuffer();
292 seqCanvas.cursorX = getKeyboardNo1() - 1;
293 seqCanvas.cursorY = getKeyboardNo2() - 1;
298 void setCursorPosition()
300 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
303 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
307 void moveCursor(int dx, int dy)
309 seqCanvas.cursorX += dx;
310 seqCanvas.cursorY += dy;
311 if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
313 int original = seqCanvas.cursorX - dx;
314 int maxWidth = av.getAlignment().getWidth();
316 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
317 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
319 seqCanvas.cursorX += dx;
322 if (seqCanvas.cursorX >= maxWidth
323 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
325 seqCanvas.cursorX = original;
332 void scrollToVisible()
334 if (seqCanvas.cursorX < 0)
336 seqCanvas.cursorX = 0;
338 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
340 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
343 if (seqCanvas.cursorY < 0)
345 seqCanvas.cursorY = 0;
347 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
349 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
353 if (av.wrapAlignment)
355 ap.scrollToWrappedVisible(seqCanvas.cursorX);
359 while (seqCanvas.cursorY < av.startSeq)
363 while (seqCanvas.cursorY + 1 > av.endSeq)
367 if (!av.wrapAlignment)
369 while (seqCanvas.cursorX < av.getColumnSelection()
370 .adjustForHiddenColumns(av.startRes))
372 if (!ap.scrollRight(false))
377 while (seqCanvas.cursorX > av.getColumnSelection()
378 .adjustForHiddenColumns(av.endRes))
380 if (!ap.scrollRight(true))
387 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
388 seqCanvas.cursorX, seqCanvas.cursorY);
393 void setSelectionAreaAtCursor(boolean topLeft)
395 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
398 if (av.getSelectionGroup() != null)
400 SequenceGroup sg = av.getSelectionGroup();
401 // Find the top and bottom of this group
402 int min = av.getAlignment().getHeight(), max = 0;
403 for (int i = 0; i < sg.getSize(); i++)
405 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
420 sg.setStartRes(seqCanvas.cursorX);
421 if (sg.getEndRes() < seqCanvas.cursorX)
423 sg.setEndRes(seqCanvas.cursorX);
426 min = seqCanvas.cursorY;
430 sg.setEndRes(seqCanvas.cursorX);
431 if (sg.getStartRes() > seqCanvas.cursorX)
433 sg.setStartRes(seqCanvas.cursorX);
436 max = seqCanvas.cursorY + 1;
441 // Only the user can do this
442 av.setSelectionGroup(null);
446 // Now add any sequences between min and max
447 sg.getSequences(null).clear();
448 for (int i = min; i < max; i++)
450 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
455 if (av.getSelectionGroup() == null)
457 SequenceGroup sg = new SequenceGroup();
458 sg.setStartRes(seqCanvas.cursorX);
459 sg.setEndRes(seqCanvas.cursorX);
460 sg.addSequence(sequence, false);
461 av.setSelectionGroup(sg);
464 ap.paintAlignment(false);
468 void insertGapAtCursor(boolean group)
470 groupEditing = group;
471 startseq = seqCanvas.cursorY;
472 lastres = seqCanvas.cursorX;
473 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
477 void deleteGapAtCursor(boolean group)
479 groupEditing = group;
480 startseq = seqCanvas.cursorY;
481 lastres = seqCanvas.cursorX + getKeyboardNo1();
482 editSequence(false, false, seqCanvas.cursorX);
486 void insertNucAtCursor(boolean group,String nuc){
487 groupEditing = group;
488 startseq = seqCanvas.cursorY;
489 lastres = seqCanvas.cursorX;
490 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
494 void numberPressed(char value)
496 if (keyboardNo1 == null)
498 keyboardNo1 = new StringBuffer();
501 if (keyboardNo2 != null)
503 keyboardNo2.append(value);
507 keyboardNo1.append(value);
513 if (keyboardNo1 == null)
517 int value = Integer.parseInt(keyboardNo1.toString());
525 if (keyboardNo2 == null)
529 int value = Integer.parseInt(keyboardNo2.toString());
541 public void mouseReleased(MouseEvent evt)
543 mouseDragging = false;
544 mouseWheelPressed = false;
548 doMouseReleasedDefineMode(evt);
561 public void mousePressed(MouseEvent evt)
563 lastMousePress = evt.getPoint();
565 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
567 mouseWheelPressed = true;
571 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
573 if (evt.isAltDown() || evt.isControlDown())
581 doMousePressedDefineMode(evt);
585 int seq = findSeq(evt);
586 int res = findRes(evt);
588 if (seq < 0 || res < 0)
593 if ((seq < av.getAlignment().getHeight())
594 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
610 public void mouseOverSequence(SequenceI sequence, int index, int pos)
612 String tmp = sequence.hashCode() + " " + index + " " + pos;
614 if (lastMessage == null || !lastMessage.equals(tmp))
616 // System.err.println("mouseOver Sequence: "+tmp);
617 ssm.mouseOverSequence(sequence, index, pos, av);
622 public void highlightSequence(SearchResults results)
624 if (av.followHighlight)
626 if (ap.scrollToPosition(results, false))
628 seqCanvas.revalidate();
631 seqCanvas.highlightSearchResults(results);
634 public void updateColours(SequenceI seq, int index)
636 System.out.println("update the seqPanel colours");
646 public void mouseMoved(MouseEvent evt)
650 // This is because MacOSX creates a mouseMoved
651 // If control is down, other platforms will not.
655 int res = findRes(evt);
656 int seq = findSeq(evt);
658 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
663 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
665 if (res >= sequence.getLength())
670 pos = setStatusMessage(sequence, res, seq);
671 if (ssm != null && pos > -1)
672 mouseOverSequence(sequence, res, pos);
674 tooltipText.setLength(6); // Cuts the buffer back to <html>
676 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
679 for (int g = 0; g < groups.length; g++)
681 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
683 if (tooltipText.length() > 6)
685 tooltipText.append("<br>");
688 if (!groups[g].getName().startsWith("JTreeGroup")
689 && !groups[g].getName().startsWith("JGroup"))
691 tooltipText.append(groups[g].getName());
694 if (groups[g].getDescription() != null)
696 tooltipText.append(": " + groups[g].getDescription());
702 // use aa to see if the mouse pointer is on a
703 if (av.showSequenceFeatures)
706 SequenceFeature[] features = findFeaturesAtRes(
707 sequence.getDatasetSequence(),
708 rpos = sequence.findPosition(res));
709 appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
710 this.ap.seqPanel.seqCanvas.fr.minmax);
712 if (tooltipText.length() == 6) // <html></html>
714 setToolTipText(null);
719 tooltipText.append("</html>");
720 if (lastTooltip == null
721 || !lastTooltip.equals(tooltipText.toString()))
723 setToolTipText(tooltipText.toString());
724 lastTooltip = tooltipText.toString();
731 private Point lastp = null;
736 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
738 public Point getToolTipLocation(MouseEvent event)
740 int x = event.getX(), w = getWidth();
741 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
744 if (!event.isShiftDown() || p == null)
746 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
747 event.getX() + wdth, event.getY() - 20) : null;
750 * TODO: try to modify position region is not obcured by tooltip
756 * appends the features at rpos to the given stringbuffer ready for display in
759 * @param tooltipText2
760 * @param linkImageURL
763 * TODO refactor to Jalview 'utilities' somehow.
765 public void appendFeatures(StringBuffer tooltipText2,
766 String linkImageURL, int rpos, SequenceFeature[] features)
768 appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
771 public void appendFeatures(StringBuffer tooltipText2, String string,
772 int rpos, SequenceFeature[] features, Hashtable minmax)
775 if (features != null)
777 for (int i = 0; i < features.length; i++)
779 if (features[i].getType().equals("disulfide bond"))
781 if (features[i].getBegin() == rpos
782 || features[i].getEnd() == rpos)
784 if (tooltipText2.length() > 6)
786 tooltipText2.append("<br>");
788 tooltipText2.append("disulfide bond " + features[i].getBegin()
789 + ":" + features[i].getEnd());
790 if (features[i].links != null)
792 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
798 if (tooltipText2.length() > 6)
800 tooltipText2.append("<br>");
802 // TODO: remove this hack to display link only features
803 boolean linkOnly = features[i].getValue("linkonly") != null;
806 tooltipText2.append(features[i].getType() + " ");
809 // we are marking a positional feature
810 tooltipText2.append(features[i].begin);
812 if (features[i].begin != features[i].end)
814 tooltipText2.append(" " + features[i].end);
817 if (features[i].getDescription() != null
818 && !features[i].description.equals(features[i]
821 tmpString = features[i].getDescription();
822 String tmp2up=tmpString.toUpperCase();
823 int startTag = tmp2up.indexOf("<HTML>");
826 tmpString = tmpString.substring(startTag + 6);
827 tmp2up = tmp2up.substring(startTag+6);
829 int endTag = tmp2up.indexOf("</BODY>");
832 tmpString = tmpString.substring(0, endTag);
833 tmp2up = tmp2up.substring(0, endTag);
835 endTag = tmp2up.indexOf("</HTML>");
838 tmpString = tmpString.substring(0, endTag);
843 tooltipText2.append("; " + tmpString);
847 if (tmpString.indexOf("<") > -1
848 || tmpString.indexOf(">") > -1)
850 // The description does not specify html is to
851 // be used, so we must remove < > symbols
852 tmpString = tmpString.replaceAll("<", "<");
853 tmpString = tmpString.replaceAll(">", ">");
855 tooltipText2.append("; ");
856 tooltipText2.append(tmpString);
861 tooltipText2.append("; " + tmpString);
865 // check score should be shown
866 if (features[i].getScore() != Float.NaN)
868 float[][] rng = (minmax == null) ? null : ((float[][]) minmax
869 .get(features[i].getType()));
870 if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
872 tooltipText2.append(" Score=" + features[i].getScore());
875 if (features[i].getValue("status") != null)
877 String status = features[i].getValue("status").toString();
878 if (status.length() > 0)
880 tooltipText2.append("; (" + features[i].getValue("status")
885 if (features[i].links != null)
887 tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
898 * Set status message in alignment panel
901 * aligned sequence object
905 * index of sequence in alignment
906 * @return position of res in sequence
908 int setStatusMessage(SequenceI sequence, int res, int seq)
911 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
912 + sequence.getName());
915 if (av.getAlignment().isNucleotide())
917 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
921 text.append(" Nucleotide: ");
926 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
929 text.append(" Residue: ");
935 pos = sequence.findPosition(res);
938 text.append(obj + " (" + pos + ")");
941 ap.alignFrame.statusBar.setText(text.toString());
951 public void mouseDragged(MouseEvent evt)
953 if (mouseWheelPressed)
955 int oldWidth = av.charWidth;
957 // Which is bigger, left-right or up-down?
958 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
959 .getX() - lastMousePress.getX()))
961 int fontSize = av.font.getSize();
963 if (evt.getY() < lastMousePress.getY())
967 else if (evt.getY() > lastMousePress.getY())
977 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
978 av.charWidth = oldWidth;
983 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
987 else if (evt.getX() > lastMousePress.getX())
992 ap.paintAlignment(false);
995 FontMetrics fm = getFontMetrics(av.getFont());
996 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
998 lastMousePress = evt.getPoint();
1005 doMouseDraggedDefineMode(evt);
1009 int res = findRes(evt);
1016 if ((lastres == -1) || (lastres == res))
1021 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1023 // dragLeft, delete gap
1024 editSequence(false, false,res);
1028 editSequence(true, false,res);
1031 mouseDragging = true;
1032 if (scrollThread != null)
1034 scrollThread.setEvent(evt);
1038 //TODO: Make it more clever than many booleans
1039 synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
1042 int fixedRight = -1;
1043 boolean fixedColumns = false;
1044 SequenceGroup sg = av.getSelectionGroup();
1046 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1048 // No group, but the sequence may represent a group
1049 if (!groupEditing && av.hasHiddenRows())
1051 if (av.isHiddenRepSequence(seq))
1053 sg = av.getRepresentedSequences(seq);
1054 groupEditing = true;
1058 StringBuffer message = new StringBuffer();
1061 message.append("Edit group:");
1062 if (editCommand == null)
1064 editCommand = new EditCommand("Edit Group");
1069 message.append("Edit sequence: " + seq.getName());
1070 String label = seq.getName();
1071 if (label.length() > 10)
1073 label = label.substring(0, 10);
1075 if (editCommand == null)
1077 editCommand = new EditCommand("Edit " + label);
1083 message.append(" insert ");
1087 message.append(" delete ");
1090 message.append(Math.abs(startres - lastres) + " gaps.");
1091 ap.alignFrame.statusBar.setText(message.toString());
1093 // Are we editing within a selection group?
1095 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1098 fixedColumns = true;
1100 // sg might be null as the user may only see 1 sequence,
1101 // but the sequence represents a group
1104 if (!av.isHiddenRepSequence(seq))
1109 sg = av.getRepresentedSequences(seq);
1112 fixedLeft = sg.getStartRes();
1113 fixedRight = sg.getEndRes();
1115 if ((startres < fixedLeft && lastres >= fixedLeft)
1116 || (startres >= fixedLeft && lastres < fixedLeft)
1117 || (startres > fixedRight && lastres <= fixedRight)
1118 || (startres <= fixedRight && lastres > fixedRight))
1124 if (fixedLeft > startres)
1126 fixedRight = fixedLeft - 1;
1129 else if (fixedRight < startres)
1131 fixedLeft = fixedRight;
1136 if (av.hasHiddenColumns())
1138 fixedColumns = true;
1139 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1140 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1142 if ((insertGap && startres > y1 && lastres < y1)
1143 || (!insertGap && startres < y2 && lastres > y2))
1149 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1150 // Selection spans a hidden region
1151 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1159 fixedRight = y2 - 1;
1166 Vector vseqs = sg.getSequences(av.getHiddenRepSequences());
1167 int g, groupSize = vseqs.size();
1168 SequenceI[] groupSeqs = new SequenceI[groupSize];
1169 for (g = 0; g < groupSeqs.length; g++)
1171 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
1177 // If the user has selected the whole sequence, and is dragging to
1178 // the right, we can still extend the alignment and selectionGroup
1179 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1180 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1182 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1183 fixedRight = sg.getEndRes();
1186 // Is it valid with fixed columns??
1187 // Find the next gap before the end
1188 // of the visible region boundary
1189 boolean blank = false;
1190 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1194 for (g = 0; g < groupSize; g++)
1196 for (int j = 0; j < startres - lastres; j++)
1198 if (!jalview.util.Comparison.isGap(groupSeqs[g]
1199 .getCharAt(fixedRight - j)))
1214 if (sg.getSize() == av.getAlignment().getHeight())
1216 if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
1217 .getHiddenBoundaryRight(startres)))
1223 int alWidth = av.getAlignment().getWidth();
1224 if (av.hasHiddenRows())
1226 int hwidth = av.getAlignment().getHiddenSequences().getWidth();
1227 if (hwidth > alWidth)
1232 // We can still insert gaps if the selectionGroup
1233 // contains all the sequences
1234 sg.setEndRes(sg.getEndRes() + startres - lastres);
1235 fixedRight = alWidth + startres - lastres;
1246 else if (!insertGap)
1248 // / Are we able to delete?
1249 // ie are all columns blank?
1251 for (g = 0; g < groupSize; g++)
1253 for (int j = startres; j < lastres; j++)
1255 if (groupSeqs[g].getLength() <= j)
1260 if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
1262 // Not a gap, block edit not valid
1272 // dragging to the right
1273 if (fixedColumns && fixedRight != -1)
1275 for (int j = lastres; j < startres; j++)
1277 insertChar(j, groupSeqs, fixedRight);
1282 editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
1283 startres, startres - lastres, av.getAlignment(), true);
1288 // dragging to the left
1289 if (fixedColumns && fixedRight != -1)
1291 for (int j = lastres; j > startres; j--)
1293 deleteChar(startres, groupSeqs, fixedRight);
1298 editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
1299 startres, lastres - startres, av.getAlignment(), true);
1305 // ///Editing a single sequence///////////
1309 // dragging to the right
1310 if (fixedColumns && fixedRight != -1)
1312 for (int j = lastres; j < startres; j++)
1314 insertChar(j, new SequenceI[]
1315 { seq }, fixedRight);
1320 editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
1321 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1327 // dragging to the left
1328 if (fixedColumns && fixedRight != -1)
1330 for (int j = lastres; j > startres; j--)
1332 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1337 deleteChar(startres, new SequenceI[]
1338 { seq }, fixedRight);
1343 // could be a keyboard edit trying to delete none gaps
1345 for (int m = startres; m < lastres; m++)
1347 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1356 editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
1357 { seq }, startres, max, av.getAlignment(), true);
1360 }else{//insertGap==false AND editSeq==TRUE;
1361 if (fixedColumns && fixedRight != -1)
1363 for (int j = lastres; j < startres; j++)
1365 insertChar(j, new SequenceI[]
1366 { seq }, fixedRight);
1371 editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
1372 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1379 seqCanvas.repaint();
1382 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1384 int blankColumn = fixedColumn;
1385 for (int s = 0; s < seq.length; s++)
1387 // Find the next gap before the end of the visible region boundary
1388 // If lastCol > j, theres a boundary after the gap insertion
1390 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1392 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1394 // Theres a space, so break and insert the gap
1399 if (blankColumn <= j)
1401 blankColumn = fixedColumn;
1407 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
1408 av.getAlignment(), true);
1410 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
1415 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1418 editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
1421 editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
1422 av.getAlignment(), true);
1431 public void mouseEntered(MouseEvent e)
1438 if (scrollThread != null)
1440 scrollThread.running = false;
1441 scrollThread = null;
1451 public void mouseExited(MouseEvent e)
1453 if (av.getWrapAlignment())
1460 scrollThread = new ScrollThread();
1464 public void mouseClicked(MouseEvent evt)
1466 SequenceGroup sg = null;
1467 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1468 if (evt.getClickCount() > 1)
1470 sg = av.getSelectionGroup();
1471 if (sg != null && sg.getSize() == 1
1472 && sg.getEndRes() - sg.getStartRes() < 2)
1474 av.setSelectionGroup(null);
1477 SequenceFeature[] features = findFeaturesAtRes(
1478 sequence.getDatasetSequence(),
1479 sequence.findPosition(findRes(evt)));
1481 if (features != null && features.length > 0)
1483 SearchResults highlight = new SearchResults();
1484 highlight.addResult(sequence, features[0].getBegin(),
1485 features[0].getEnd());
1486 seqCanvas.highlightSearchResults(highlight);
1488 if (features != null && features.length > 0)
1490 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
1491 { sequence }, features, false, ap);
1493 seqCanvas.highlightSearchResults(null);
1498 public void mouseWheelMoved(MouseWheelEvent e)
1501 if (e.getWheelRotation() > 0)
1509 // TODO Update tooltip for new position.
1518 public void doMousePressedDefineMode(MouseEvent evt)
1520 int res = findRes(evt);
1521 int seq = findSeq(evt);
1524 startWrapBlock = wrappedBlock;
1526 if (av.wrapAlignment && seq > av.getAlignment().getHeight())
1528 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1529 "Cannot edit annotations in wrapped view.",
1530 "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
1534 if (seq < 0 || res < 0)
1539 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
1541 if ((sequence == null) || (res > sequence.getLength()))
1546 stretchGroup = av.getSelectionGroup();
1548 if (stretchGroup == null)
1550 stretchGroup = av.getAlignment().findGroup(sequence);
1552 if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
1553 && (res < stretchGroup.getEndRes()))
1555 av.setSelectionGroup(stretchGroup);
1559 stretchGroup = null;
1562 else if (!stretchGroup.getSequences(null).contains(sequence)
1563 || (stretchGroup.getStartRes() > res)
1564 || (stretchGroup.getEndRes() < res))
1566 stretchGroup = null;
1568 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1570 if (allGroups != null)
1572 for (int i = 0; i < allGroups.length; i++)
1574 if ((allGroups[i].getStartRes() <= res)
1575 && (allGroups[i].getEndRes() >= res))
1577 stretchGroup = allGroups[i];
1583 av.setSelectionGroup(stretchGroup);
1587 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
1589 SequenceFeature[] allFeatures = findFeaturesAtRes(
1590 sequence.getDatasetSequence(), sequence.findPosition(res));
1591 Vector links = new Vector();
1592 for (int i = 0; i < allFeatures.length; i++)
1594 if (allFeatures[i].links != null)
1596 for (int j = 0; j < allFeatures[i].links.size(); j++)
1598 links.addElement(allFeatures[i].links.elementAt(j));
1603 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
1604 pop.show(this, evt.getX(), evt.getY());
1610 seqCanvas.cursorX = findRes(evt);
1611 seqCanvas.cursorY = findSeq(evt);
1612 seqCanvas.repaint();
1616 if (stretchGroup == null)
1618 // Only if left mouse button do we want to change group sizes
1620 // define a new group here
1621 SequenceGroup sg = new SequenceGroup();
1622 sg.setStartRes(res);
1624 sg.addSequence(sequence, false);
1625 av.setSelectionGroup(sg);
1629 if (av.getConservationSelected())
1631 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1635 if (av.getAbovePIDThreshold())
1637 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1640 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1642 // Edit end res position of selected group
1643 changeEndRes = true;
1645 else if ((stretchGroup != null)
1646 && (stretchGroup.getStartRes() == res))
1648 // Edit end res position of selected group
1649 changeStartRes = true;
1651 stretchGroup.getWidth();
1654 seqCanvas.repaint();
1663 public void doMouseReleasedDefineMode(MouseEvent evt)
1665 if (stretchGroup == null)
1670 stretchGroup.recalcConservation(); // always do this - annotation has own
1672 if (stretchGroup.cs != null)
1674 if (stretchGroup.cs instanceof ClustalxColourScheme)
1676 ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
1677 stretchGroup.getSequences(av.getHiddenRepSequences()),
1678 stretchGroup.getWidth());
1681 if (stretchGroup.cs.conservationApplied())
1683 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1684 stretchGroup.getName());
1688 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1689 stretchGroup.getName());
1692 PaintRefresher.Refresh(this, av.getSequenceSetId());
1693 ap.paintAlignment(true);
1695 changeEndRes = false;
1696 changeStartRes = false;
1697 stretchGroup = null;
1707 public void doMouseDraggedDefineMode(MouseEvent evt)
1709 int res = findRes(evt);
1710 int y = findSeq(evt);
1712 if (wrappedBlock != startWrapBlock)
1717 if (stretchGroup == null)
1722 if (res >= av.getAlignment().getWidth())
1724 res = av.getAlignment().getWidth() - 1;
1727 if (stretchGroup.getEndRes() == res)
1729 // Edit end res position of selected group
1730 changeEndRes = true;
1732 else if (stretchGroup.getStartRes() == res)
1734 // Edit start res position of selected group
1735 changeStartRes = true;
1738 if (res < av.getStartRes())
1740 res = av.getStartRes();
1745 if (res > (stretchGroup.getStartRes() - 1))
1747 stretchGroup.setEndRes(res);
1750 else if (changeStartRes)
1752 if (res < (stretchGroup.getEndRes() + 1))
1754 stretchGroup.setStartRes(res);
1758 int dragDirection = 0;
1764 else if (y < oldSeq)
1769 while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
1771 // This routine ensures we don't skip any sequences, as the
1772 // selection is quite slow.
1773 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1775 oldSeq += dragDirection;
1782 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1784 if (stretchGroup.getSequences(null).contains(nextSeq))
1786 stretchGroup.deleteSequence(seq, false);
1792 stretchGroup.addSequence(seq, false);
1795 stretchGroup.addSequence(nextSeq, false);
1804 mouseDragging = true;
1806 if (scrollThread != null)
1808 scrollThread.setEvent(evt);
1811 seqCanvas.repaint();
1814 void scrollCanvas(MouseEvent evt)
1818 if (scrollThread != null)
1820 scrollThread.running = false;
1821 scrollThread = null;
1823 mouseDragging = false;
1827 if (scrollThread == null)
1829 scrollThread = new ScrollThread();
1832 mouseDragging = true;
1833 scrollThread.setEvent(evt);
1838 // this class allows scrolling off the bottom of the visible alignment
1839 class ScrollThread extends Thread
1843 boolean running = false;
1845 public ScrollThread()
1850 public void setEvent(MouseEvent e)
1855 public void stopScrolling()
1868 if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
1870 running = ap.scrollUp(true);
1873 if (mouseDragging && (evt.getY() >= getHeight())
1874 && (av.getAlignment().getHeight() > av.getEndSeq()))
1876 running = ap.scrollUp(false);
1879 if (mouseDragging && (evt.getX() < 0))
1881 running = ap.scrollRight(false);
1883 else if (mouseDragging && (evt.getX() >= getWidth()))
1885 running = ap.scrollRight(true);
1892 } catch (Exception ex)
1900 * modify current selection according to a received message.
1902 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1903 SelectionSource source)
1905 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1906 // handles selection messages...
1907 // TODO: extend config options to allow user to control if selections may be
1908 // shared between viewports.
1910 || !av.followSelection
1911 || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
1912 || (source instanceof AlignViewport && ((AlignViewport) source)
1913 .getSequenceSetId().equals(av.getSequenceSetId())))
1917 // do we want to thread this ? (contention with seqsel and colsel locks, I
1919 // rules are: colsel is copied if there is a real intersection between
1920 // sequence selection
1921 boolean repaint = false, copycolsel = true;
1922 // if (!av.isSelectionGroupChanged(false))
1924 SequenceGroup sgroup = null;
1925 if (seqsel != null && seqsel.getSize()>0)
1927 if (av.getAlignment() == null)
1929 jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
1930 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1931 + " 's alignment is NULL! returning immediatly.");
1934 sgroup = seqsel.intersect(av.getAlignment(),
1935 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1936 if ((sgroup == null || sgroup.getSize() == 0)
1937 || (colsel == null || colsel.size() == 0))
1939 // don't copy columns if the region didn't intersect.
1943 if (sgroup != null && sgroup.getSize() > 0)
1945 av.setSelectionGroup(sgroup);
1949 av.setSelectionGroup(null);
1951 av.isSelectionGroupChanged(true);
1956 // the current selection is unset or from a previous message
1957 // so import the new colsel.
1958 if (colsel == null || colsel.size() == 0)
1960 if (av.getColumnSelection() != null)
1962 av.getColumnSelection().clear();
1968 // TODO: shift colSel according to the intersecting sequences
1969 if (av.getColumnSelection() == null)
1971 av.setColumnSelection(new ColumnSelection(colsel));
1975 av.getColumnSelection().setElementsFrom(colsel);
1978 av.isColSelChanged(true);
1981 if (copycolsel && av.hasHiddenColumns()
1982 && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
1984 System.err.println("Bad things");
1988 // probably finessing with multiple redraws here
1989 PaintRefresher.Refresh(this, av.getSequenceSetId());
1990 // ap.paintAlignment(false);