/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import jalview.api.AlignViewportI; import jalview.bin.Cache; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResults.Match; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; import jalview.schemes.ResidueProperties; import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; import jalview.structure.SequenceListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.util.Comparison; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Point; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.List; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.130 $ */ public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener, SequenceListener, SelectionListener { /** DOCUMENT ME!! */ public SeqCanvas seqCanvas; /** DOCUMENT ME!! */ public AlignmentPanel ap; protected int lastres; protected int startseq; protected AlignViewport av; ScrollThread scrollThread = null; boolean mouseDragging = false; boolean editingSeqs = false; boolean groupEditing = false; // //////////////////////////////////////// // ///Everything below this is for defining the boundary of the rubberband // //////////////////////////////////////// int oldSeq = -1; boolean changeEndSeq = false; boolean changeStartSeq = false; boolean changeEndRes = false; boolean changeStartRes = false; SequenceGroup stretchGroup = null; boolean remove = false; Point lastMousePress; boolean mouseWheelPressed = false; StringBuffer keyboardNo1; StringBuffer keyboardNo2; java.net.URL linkImageURL; private final SequenceAnnotationReport seqARep; StringBuffer tooltipText = new StringBuffer(); String tmpString; EditCommand editCommand; StructureSelectionManager ssm; SearchResults lastSearchResults; /** * Creates a new SeqPanel object. * * @param avp * DOCUMENT ME! * @param p * DOCUMENT ME! */ public SeqPanel(AlignViewport av, AlignmentPanel ap) { linkImageURL = getClass().getResource("/images/link.gif"); seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); this.av = av; setBackground(Color.white); seqCanvas = new SeqCanvas(ap); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); this.ap = ap; if (!av.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); ssm = av.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } } int startWrapBlock = -1; int wrappedBlock = -1; /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one * * @param evt * @return */ int findRes(MouseEvent evt) { int res = 0; int x = evt.getX(); if (av.getWrapAlignment()) { int hgap = av.getCharHeight(); if (av.getScaleAboveWrapped()) { hgap += av.getCharHeight(); } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; x -= seqCanvas.LABEL_WEST; int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) { return 0; } wrappedBlock = y / cHeight; wrappedBlock += av.getStartRes() / cwidth; res = wrappedBlock * cwidth + x / av.getCharWidth(); } else { if (x > seqCanvas.getX() + seqCanvas.getWidth()) { // make sure we calculate relative to visible alignment, rather than // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } res = (x / av.getCharWidth()) + av.getStartRes(); if (res > av.getEndRes()) { // moused off right res = av.getEndRes(); } } if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } return res; } int findSeq(MouseEvent evt) { int seq = 0; int y = evt.getY(); if (av.getWrapAlignment()) { int hgap = av.getCharHeight(); if (av.getScaleAboveWrapped()) { hgap += av.getCharHeight(); } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() .getHeight() - 1); } else { seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av .getAlignment().getHeight() - 1); } return seq; } /** * When all of a sequence of edits are complete, put the resulting edit list * on the history stack (undo list), and reset flags for editing in progress. */ void endEditing() { try { if (editCommand != null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); av.firePropertyChange("alignment", null, av.getAlignment() .getSequences()); } } finally { /* * Tidy up come what may... */ startseq = -1; lastres = -1; editingSeqs = false; groupEditing = false; keyboardNo1 = null; keyboardNo2 = null; editCommand = null; } } void setCursorRow() { seqCanvas.cursorY = getKeyboardNo1() - 1; scrollToVisible(); } void setCursorColumn() { seqCanvas.cursorX = getKeyboardNo1() - 1; scrollToVisible(); } void setCursorRowAndColumn() { if (keyboardNo2 == null) { keyboardNo2 = new StringBuffer(); } else { seqCanvas.cursorX = getKeyboardNo1() - 1; seqCanvas.cursorY = getKeyboardNo2() - 1; scrollToVisible(); } } void setCursorPosition() { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); } void moveCursor(int dx, int dy) { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } } scrollToVisible(); } void scrollToVisible() { if (seqCanvas.cursorX < 0) { seqCanvas.cursorX = 0; } else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1) { seqCanvas.cursorX = av.getAlignment().getWidth() - 1; } if (seqCanvas.cursorY < 0) { seqCanvas.cursorY = 0; } else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1) { seqCanvas.cursorY = av.getAlignment().getHeight() - 1; } endEditing(); if (av.getWrapAlignment()) { ap.scrollToWrappedVisible(seqCanvas.cursorX); } else { while (seqCanvas.cursorY < av.startSeq) { ap.scrollUp(true); } while (seqCanvas.cursorY + 1 > av.endSeq) { ap.scrollUp(false); } if (!av.getWrapAlignment()) { while (seqCanvas.cursorX < av.getColumnSelection() .adjustForHiddenColumns(av.startRes)) { if (!ap.scrollRight(false)) { break; } } while (seqCanvas.cursorX > av.getColumnSelection() .adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) { break; } } } } setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); seqCanvas.repaint(); } void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); if (av.getSelectionGroup() != null) { SequenceGroup sg = av.getSelectionGroup(); // Find the top and bottom of this group int min = av.getAlignment().getHeight(), max = 0; for (int i = 0; i < sg.getSize(); i++) { int index = av.getAlignment().findIndex(sg.getSequenceAt(i)); if (index > max) { max = index; } if (index < min) { min = index; } } max++; if (topLeft) { sg.setStartRes(seqCanvas.cursorX); if (sg.getEndRes() < seqCanvas.cursorX) { sg.setEndRes(seqCanvas.cursorX); } min = seqCanvas.cursorY; } else { sg.setEndRes(seqCanvas.cursorX); if (sg.getStartRes() > seqCanvas.cursorX) { sg.setStartRes(seqCanvas.cursorX); } max = seqCanvas.cursorY + 1; } if (min > max) { // Only the user can do this av.setSelectionGroup(null); } else { // Now add any sequences between min and max sg.getSequences(null).clear(); for (int i = min; i < max; i++) { sg.addSequence(av.getAlignment().getSequenceAt(i), false); } } } if (av.getSelectionGroup() == null) { SequenceGroup sg = new SequenceGroup(); sg.setStartRes(seqCanvas.cursorX); sg.setEndRes(seqCanvas.cursorX); sg.addSequence(sequence, false); av.setSelectionGroup(sg); } ap.paintAlignment(false); av.sendSelection(); } void insertGapAtCursor(boolean group) { groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } void deleteGapAtCursor(boolean group) { groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX + getKeyboardNo1(); editSequence(false, false, seqCanvas.cursorX); endEditing(); } void insertNucAtCursor(boolean group, String nuc) { // TODO not called - delete? groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } void numberPressed(char value) { if (keyboardNo1 == null) { keyboardNo1 = new StringBuffer(); } if (keyboardNo2 != null) { keyboardNo2.append(value); } else { keyboardNo1.append(value); } } int getKeyboardNo1() { try { if (keyboardNo1 != null) { int value = Integer.parseInt(keyboardNo1.toString()); keyboardNo1 = null; return value; } } catch (Exception x) { } keyboardNo1 = null; return 1; } int getKeyboardNo2() { try { if (keyboardNo2 != null) { int value = Integer.parseInt(keyboardNo2.toString()); keyboardNo2 = null; return value; } } catch (Exception x) { } keyboardNo2 = null; return 1; } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent evt) { mouseDragging = false; mouseWheelPressed = false; if (!editingSeqs) { doMouseReleasedDefineMode(evt); return; } endEditing(); } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); if (SwingUtilities.isMiddleMouseButton(evt)) { mouseWheelPressed = true; return; } if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) { if (evt.isAltDown() || evt.isControlDown()) { groupEditing = true; } editingSeqs = true; } else { doMousePressedDefineMode(evt); return; } int seq = findSeq(evt); int res = findRes(evt); if (seq < 0 || res < 0) { return; } if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) { startseq = seq; lastres = res; } else { startseq = -1; lastres = -1; } return; } String lastMessage; @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { String tmp = sequence.hashCode() + " " + index + " " + pos; if (lastMessage == null || !lastMessage.equals(tmp)) { // System.err.println("mouseOver Sequence: "+tmp); ssm.mouseOverSequence(sequence, index, pos, av); } lastMessage = tmp; } /** * Highlight the mapped region described by the search results object (unless * unchanged). This supports highlight of protein while mousing over linked * cDNA and vice versa. The status bar is also updated to show the location of * the start of the highlighted region. */ @Override public void highlightSequence(SearchResults results) { if (results == null || results.equals(lastSearchResults)) { return; } lastSearchResults = results; if (av.isFollowHighlight()) { /* * if scrollToPosition requires a scroll adjustment, this flag prevents * another scroll event being propagated back to the originator * * @see AlignmentPanel#adjustmentValueChanged */ ap.setDontScrollComplement(true); if (ap.scrollToPosition(results, false)) { seqCanvas.revalidate(); } } setStatusMessage(results); seqCanvas.highlightSearchResults(results); } @Override public VamsasSource getVamsasSource() { return this.ap == null ? null : this.ap.av; } @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); // repaint(); } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) { if (editingSeqs) { // This is because MacOSX creates a mouseMoved // If control is down, other platforms will not. mouseDragged(evt); } int res = findRes(evt); int seq = findSeq(evt); int pos; if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { return; } SequenceI sequence = av.getAlignment().getSequenceAt(seq); if (res >= sequence.getLength()) { return; } pos = setStatusMessage(sequence, res, seq); if (ssm != null && pos > -1) { mouseOverSequence(sequence, res, pos); } tooltipText.setLength(6); // Cuts the buffer back to SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) { for (int g = 0; g < groups.length; g++) { if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res) { if (!groups[g].getName().startsWith("JTreeGroup") && !groups[g].getName().startsWith("JGroup")) { tooltipText.append(groups[g].getName()); } if (groups[g].getDescription() != null) { tooltipText.append(": " + groups[g].getDescription()); } } } } // use aa to see if the mouse pointer is on a if (av.isShowSequenceFeatures()) { int rpos; List features = ap.getFeatureRenderer() .findFeaturesAtRes(sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); seqARep.appendFeatures(tooltipText, rpos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; } else { if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString())) { String formatedTooltipText = JvSwingUtils.wrapTooltip(true, tooltipText.toString()); // String formatedTooltipText = tooltipText.toString(); setToolTipText(formatedTooltipText); lastTooltip = tooltipText.toString(); } } } private Point lastp = null; /* * (non-Javadoc) * * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) */ @Override public Point getToolTipLocation(MouseEvent event) { int x = event.getX(), w = getWidth(); int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too // close to edge Point p = lastp; if (!event.isShiftDown() || p == null) { p = (tooltipText != null && tooltipText.length() > 6) ? new Point( event.getX() + wdth, event.getY() - 20) : null; } /* * TODO: try to modify position region is not obcured by tooltip */ return lastp = p; } String lastTooltip; /** * set when the current UI interaction has resulted in a change that requires * overview shading to be recalculated. this could be changed to something * more expressive that indicates what actually has changed, so selective * redraws can be applied */ private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller /** * set if av.getSelectionGroup() refers to a group that is defined on the * alignment view, rather than a transient selection */ private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller or viewModel /** * Set status message in alignment panel * * @param sequence * aligned sequence object * @param res * alignment column * @param seq * index of sequence in alignment * @return position of res in sequence */ int setStatusMessage(SequenceI sequence, int res, int seq) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ String seqno = seq == -1 ? "" : " " + (seq + 1); text.append("Sequence").append(seqno).append(" ID: ") .append(sequence.getName()); String residue = null; /* * Try to translate the display character to residue name (null for gap). */ final String displayChar = String.valueOf(sequence.getCharAt(res)); if (av.getAlignment().isNucleotide()) { residue = ResidueProperties.nucleotideName.get(displayChar); if (residue != null) { text.append(" Nucleotide: ").append(residue); } } else { residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet .get(displayChar)); if (residue != null) { text.append(" Residue: ").append(residue); } } int pos = -1; if (residue != null) { pos = sequence.findPosition(res); text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); return pos; } /** * Set the status bar message to highlight the first matched position in * search results. * * @param results */ private void setStatusMessage(SearchResults results) { AlignmentI al = this.av.getAlignment(); int sequenceIndex = al.findIndex(results); if (sequenceIndex == -1) { return; } SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); for (Match m : results.getResults()) { SequenceI seq = m.getSequence(); if (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } if (seq == ds) { /* * Convert position in sequence (base 1) to sequence character array * index (base 0) */ int start = m.getStart() - m.getSequence().getStart(); setStatusMessage(seq, start, sequenceIndex); return; } } } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) { int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt .getX() - lastMousePress.getX())) { int fontSize = av.font.getSize(); if (evt.getY() < lastMousePress.getY()) { fontSize--; } else if (evt.getY() > lastMousePress.getY()) { fontSize++; } if (fontSize < 1) { fontSize = 1; } av.setFont( new Font(av.font.getName(), av.font.getStyle(), fontSize), true); av.setCharWidth(oldWidth); ap.fontChanged(); } else { if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) { av.setCharWidth(av.getCharWidth() - 1); } else if (evt.getX() > lastMousePress.getX()) { av.setCharWidth(av.getCharWidth() + 1); } ap.paintAlignment(false); } FontMetrics fm = getFontMetrics(av.getFont()); av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); lastMousePress = evt.getPoint(); return; } if (!editingSeqs) { doMouseDraggedDefineMode(evt); return; } int res = findRes(evt); if (res < 0) { res = 0; } if ((lastres == -1) || (lastres == res)) { return; } if ((res < av.getAlignment().getWidth()) && (res < lastres)) { // dragLeft, delete gap editSequence(false, false, res); } else { editSequence(true, false, res); } mouseDragging = true; if (scrollThread != null) { scrollThread.setEvent(evt); } } // TODO: Make it more clever than many booleans synchronized void editSequence(boolean insertGap, boolean editSeq, int startres) { int fixedLeft = -1; int fixedRight = -1; boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); SequenceI seq = av.getAlignment().getSequenceAt(startseq); // No group, but the sequence may represent a group if (!groupEditing && av.hasHiddenRows()) { if (av.isHiddenRepSequence(seq)) { sg = av.getRepresentedSequences(seq); groupEditing = true; } } StringBuilder message = new StringBuilder(64); if (groupEditing) { message.append("Edit group:"); if (editCommand == null) { editCommand = new EditCommand( MessageManager.getString("action.edit_group")); } } else { message.append("Edit sequence: " + seq.getName()); String label = seq.getName(); if (label.length() > 10) { label = label.substring(0, 10); } if (editCommand == null) { editCommand = new EditCommand(MessageManager.formatMessage( "label.edit_params", new String[] { label })); } } if (insertGap) { message.append(" insert "); } else { message.append(" delete "); } message.append(Math.abs(startres - lastres) + " gaps."); ap.alignFrame.statusBar.setText(message.toString()); // Are we editing within a selection group? if (groupEditing || (sg != null && sg.getSequences(av.getHiddenRepSequences()) .contains(seq))) { fixedColumns = true; // sg might be null as the user may only see 1 sequence, // but the sequence represents a group if (sg == null) { if (!av.isHiddenRepSequence(seq)) { endEditing(); return; } sg = av.getRepresentedSequences(seq); } fixedLeft = sg.getStartRes(); fixedRight = sg.getEndRes(); if ((startres < fixedLeft && lastres >= fixedLeft) || (startres >= fixedLeft && lastres < fixedLeft) || (startres > fixedRight && lastres <= fixedRight) || (startres <= fixedRight && lastres > fixedRight)) { endEditing(); return; } if (fixedLeft > startres) { fixedRight = fixedLeft - 1; fixedLeft = 0; } else if (fixedRight < startres) { fixedLeft = fixedRight; fixedRight = -1; } } if (av.hasHiddenColumns()) { fixedColumns = true; int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); if ((insertGap && startres > y1 && lastres < y1) || (!insertGap && startres < y2 && lastres > y2)) { endEditing(); return; } // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); // Selection spans a hidden region if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) { if (startres >= y2) { fixedLeft = y2; } else { fixedRight = y2 - 1; } } } if (groupEditing) { List vseqs = sg.getSequences(av.getHiddenRepSequences()); int g, groupSize = vseqs.size(); SequenceI[] groupSeqs = new SequenceI[groupSize]; for (g = 0; g < groupSeqs.length; g++) { groupSeqs[g] = vseqs.get(g); } // drag to right if (insertGap) { // If the user has selected the whole sequence, and is dragging to // the right, we can still extend the alignment and selectionGroup if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight && sg.getEndRes() == av.getAlignment().getWidth() - 1) { sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); fixedRight = sg.getEndRes(); } // Is it valid with fixed columns?? // Find the next gap before the end // of the visible region boundary boolean blank = false; for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--) { blank = true; for (g = 0; g < groupSize; g++) { for (int j = 0; j < startres - lastres; j++) { if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; } } } if (blank) { break; } } if (!blank) { if (sg.getSize() == av.getAlignment().getHeight()) { if ((av.hasHiddenColumns() && startres < av .getColumnSelection().getHiddenBoundaryRight(startres))) { endEditing(); return; } int alWidth = av.getAlignment().getWidth(); if (av.hasHiddenRows()) { int hwidth = av.getAlignment().getHiddenSequences() .getWidth(); if (hwidth > alWidth) { alWidth = hwidth; } } // We can still insert gaps if the selectionGroup // contains all the sequences sg.setEndRes(sg.getEndRes() + startres - lastres); fixedRight = alWidth + startres - lastres; } else { endEditing(); return; } } } // drag to left else if (!insertGap) { // / Are we able to delete? // ie are all columns blank? for (g = 0; g < groupSize; g++) { for (int j = startres; j < lastres; j++) { if (groupSeqs[g].getLength() <= j) { continue; } if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid endEditing(); return; } } } } if (insertGap) { // dragging to the right if (fixedColumns && fixedRight != -1) { for (int j = lastres; j < startres; j++) { insertChar(j, groupSeqs, fixedRight); } } else { appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres - lastres); } } else { // dragging to the left if (fixedColumns && fixedRight != -1) { for (int j = lastres; j > startres; j--) { deleteChar(startres, groupSeqs, fixedRight); } } else { appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres - startres); } } } else // ///Editing a single sequence/////////// { if (insertGap) { // dragging to the right if (fixedColumns && fixedRight != -1) { for (int j = lastres; j < startres; j++) { insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, startres - lastres); } } else { if (!editSeq) { // dragging to the left if (fixedColumns && fixedRight != -1) { for (int j = lastres; j > startres; j--) { if (!Comparison.isGap(seq.getCharAt(startres))) { endEditing(); break; } deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else { // could be a keyboard edit trying to delete none gaps int max = 0; for (int m = startres; m < lastres; m++) { if (!Comparison.isGap(seq.getCharAt(m))) { break; } max++; } if (max > 0) { appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, startres, max); } } } else {// insertGap==false AND editSeq==TRUE; if (fixedColumns && fixedRight != -1) { for (int j = lastres; j < startres; j++) { insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, startres - lastres); } } } } lastres = startres; seqCanvas.repaint(); } void insertChar(int j, SequenceI[] seq, int fixedColumn) { int blankColumn = fixedColumn; for (int s = 0; s < seq.length; s++) { // Find the next gap before the end of the visible region boundary // If lastCol > j, theres a boundary after the gap insertion for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { if (Comparison.isGap(seq[s].getCharAt(blankColumn))) { // Theres a space, so break and insert the gap break; } } if (blankColumn <= j) { blankColumn = fixedColumn; endEditing(); return; } } appendEdit(Action.DELETE_GAP, seq, blankColumn, 1); appendEdit(Action.INSERT_GAP, seq, j, 1); } /** * Helper method to add and perform one edit action. * * @param action * @param seq * @param pos * @param count */ protected void appendEdit(Action action, SequenceI[] seq, int pos, int count) { final Edit edit = new EditCommand().new Edit(action, seq, pos, count, av.getAlignment().getGapCharacter()); editCommand.appendEdit(edit, av.getAlignment(), true, null); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) { appendEdit(Action.DELETE_GAP, seq, j, 1); appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) { oldSeq = 0; } if (scrollThread != null) { scrollThread.running = false; scrollThread = null; } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) { return; } if (mouseDragging) { scrollThread = new ScrollThread(); } } @Override public void mouseClicked(MouseEvent evt) { SequenceGroup sg = null; SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { sg = av.getSelectionGroup(); if (sg != null && sg.getSize() == 1 && sg.getEndRes() - sg.getStartRes() < 2) { av.setSelectionGroup(null); } List features = seqCanvas.getFeatureRenderer() .findFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); if (features != null && features.size() > 0) { SearchResults highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } if (features != null && features.size() > 0) { seqCanvas.getFeatureRenderer().amendFeatures( new SequenceI[] { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); seqCanvas.highlightSearchResults(null); } } } @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); if (e.getWheelRotation() > 0) { if (e.isShiftDown()) { ap.scrollRight(true); } else { ap.scrollUp(false); } } else { if (e.isShiftDown()) { ap.scrollRight(false); } else { ap.scrollUp(true); } } // TODO Update tooltip for new position. } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ public void doMousePressedDefineMode(MouseEvent evt) { int res = findRes(evt); int seq = findSeq(evt); oldSeq = seq; startWrapBlock = wrappedBlock; if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), JOptionPane.WARNING_MESSAGE); return; } if (seq < 0 || res < 0) { return; } SequenceI sequence = av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) { return; } stretchGroup = av.getSelectionGroup(); if (stretchGroup == null) { stretchGroup = av.getAlignment().findGroup(sequence); if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && (res < stretchGroup.getEndRes())) { av.setSelectionGroup(stretchGroup); editingDefinedGroup = true; } else { stretchGroup = null; editingDefinedGroup = false; } } else if (!stretchGroup.getSequences(null).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { stretchGroup = null; SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); if (allGroups != null) { for (int i = 0; i < allGroups.length; i++) { if ((allGroups[i].getStartRes() <= res) && (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; editingDefinedGroup = true; break; } } } av.setSelectionGroup(stretchGroup); } if (evt.isPopupTrigger()) { List allFeatures = ap.getFeatureRenderer() .findFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(res)); List links = new ArrayList(); for (SequenceFeature sf : allFeatures) { if (sf.links != null) { for (String link : sf.links) { links.add(link); } } } PopupMenu pop = new PopupMenu(ap, null, links); pop.show(this, evt.getX(), evt.getY()); return; } if (av.cursorMode) { seqCanvas.cursorX = findRes(evt); seqCanvas.cursorY = findSeq(evt); seqCanvas.repaint(); return; } if (stretchGroup == null) { // Only if left mouse button do we want to change group sizes // define a new group here SequenceGroup sg = new SequenceGroup(); sg.setStartRes(res); sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); editingDefinedGroup = false; stretchGroup = sg; if (av.getConservationSelected()) { SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background"); } if (av.getAbovePIDThreshold()) { SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background"); } if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) { // Edit end res position of selected group changeEndRes = true; } else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) { // Edit end res position of selected group changeStartRes = true; } stretchGroup.getWidth(); } seqCanvas.repaint(); } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ public void doMouseReleasedDefineMode(MouseEvent evt) { if (stretchGroup == null) { return; } // always do this - annotation has own state // but defer colourscheme update until hidden sequences are passed in boolean vischange = stretchGroup.recalcConservation(true); needOverviewUpdate |= vischange && editingDefinedGroup; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, av.getHiddenRepSequences()); if (stretchGroup.cs.conservationApplied()) { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); } else { SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); ap.paintAlignment(needOverviewUpdate); needOverviewUpdate =false; editingDefinedGroup = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; av.sendSelection(); } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ public void doMouseDraggedDefineMode(MouseEvent evt) { int res = findRes(evt); int y = findSeq(evt); if (wrappedBlock != startWrapBlock) { return; } if (stretchGroup == null) { return; } if (res >= av.getAlignment().getWidth()) { res = av.getAlignment().getWidth() - 1; } if (stretchGroup.getEndRes() == res) { // Edit end res position of selected group changeEndRes = true; } else if (stretchGroup.getStartRes() == res) { // Edit start res position of selected group changeStartRes = true; } if (res < av.getStartRes()) { res = av.getStartRes(); } if (changeEndRes) { if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); needOverviewUpdate |= editingDefinedGroup; } } else if (changeStartRes) { if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); needOverviewUpdate |= editingDefinedGroup; } } int dragDirection = 0; if (y > oldSeq) { dragDirection = 1; } else if (y < oldSeq) { dragDirection = -1; } while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); oldSeq += dragDirection; if (oldSeq < 0) { break; } Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); needOverviewUpdate |= editingDefinedGroup; } else { if (seq != null) { stretchGroup.addSequence(seq, false); } stretchGroup.addSequence(nextSeq, false); needOverviewUpdate |= editingDefinedGroup; } } if (oldSeq < 0) { oldSeq = -1; } mouseDragging = true; if (scrollThread != null) { scrollThread.setEvent(evt); } seqCanvas.repaint(); } void scrollCanvas(MouseEvent evt) { if (evt == null) { if (scrollThread != null) { scrollThread.running = false; scrollThread = null; } mouseDragging = false; } else { if (scrollThread == null) { scrollThread = new ScrollThread(); } mouseDragging = true; scrollThread.setEvent(evt); } } // this class allows scrolling off the bottom of the visible alignment class ScrollThread extends Thread { MouseEvent evt; boolean running = false; public ScrollThread() { start(); } public void setEvent(MouseEvent e) { evt = e; } public void stopScrolling() { running = false; } @Override public void run() { running = true; while (running) { if (evt != null) { if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0)) { running = ap.scrollUp(true); } if (mouseDragging && (evt.getY() >= getHeight()) && (av.getAlignment().getHeight() > av.getEndSeq())) { running = ap.scrollUp(false); } if (mouseDragging && (evt.getX() < 0)) { running = ap.scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { running = ap.scrollRight(true); } } try { Thread.sleep(20); } catch (Exception ex) { } } } } /** * modify current selection according to a received message. */ @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { // TODO: fix this hack - source of messages is align viewport, but SeqPanel // handles selection messages... // TODO: extend config options to allow user to control if selections may be // shared between viewports. boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))); if (iSentTheSelection || !av.followSelection) { return; } /* * Ignore the selection if there is one of our own pending. */ if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) { return; } /* * Check for selection in a view of which this one is a dna/protein * complement. */ if (selectionFromTranslation(seqsel, colsel, source)) { return; } // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) /* * only copy colsel if there is a real intersection between * sequence selection and this panel's alignment */ boolean repaint = false; boolean copycolsel = false; SequenceGroup sgroup = null; if (seqsel != null && seqsel.getSize() > 0) { if (av.getAlignment() == null) { Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + " ViewId=" + av.getViewId() + " 's alignment is NULL! returning immediately."); return; } sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); if ((sgroup != null && sgroup.getSize() > 0)) { copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) { av.setSelectionGroup(sgroup); } else { av.setSelectionGroup(null); } av.isSelectionGroupChanged(true); repaint = true; if (copycolsel) { // the current selection is unset or from a previous message // so import the new colsel. if (colsel == null || colsel.isEmpty()) { if (av.getColumnSelection() != null) { av.getColumnSelection().clear(); repaint = true; } } else { // TODO: shift colSel according to the intersecting sequences if (av.getColumnSelection() == null) { av.setColumnSelection(new ColumnSelection(colsel)); } else { av.getColumnSelection().setElementsFrom(colsel); } } av.isColSelChanged(true); repaint = true; } if (copycolsel && av.hasHiddenColumns() && (av.getColumnSelection() == null || av.getColumnSelection() .getHiddenColumns() == null)) { System.err.println("Bad things"); } if (repaint) // always true! { // probably finessing with multiple redraws here PaintRefresher.Refresh(this, av.getSequenceSetId()); // ap.paintAlignment(false); } } /** * If this panel is a cdna/protein translation view of the selection source, * tries to map the source selection to a local one, and returns true. Else * returns false. * * @param seqsel * @param colsel * @param source */ protected boolean selectionFromTranslation(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { if (!(source instanceof AlignViewportI)) { return false; } final AlignViewportI sourceAv = (AlignViewportI) source; if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv) { return false; } /* * Map sequence selection */ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av); av.setSelectionGroup(sg); av.isSelectionGroupChanged(true); /* * Map column selection */ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, av); av.setColumnSelection(cs); PaintRefresher.Refresh(this, av.getSequenceSetId()); return true; } }