/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program 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 2 * of the License, or (at your option) any later version. * * This program 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 this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import jalview.datamodel.*; import jalview.commands.EditCommand; import jalview.schemes.*; import java.awt.*; import java.awt.event.*; import javax.swing.*; import java.util.Vector; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener { /** 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; StringBuffer tooltipText = new StringBuffer(""); String tmpString; EditCommand editCommand; /** * Creates a new SeqPanel object. * * @param avp DOCUMENT ME! * @param p DOCUMENT ME! */ public SeqPanel(AlignViewport avp, AlignmentPanel p) { linkImageURL = getClass().getResource("/images/link.gif"); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); this.av = avp; setBackground(Color.white); seqCanvas = new SeqCanvas(avp); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); ap = p; if (!av.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); } } int startWrapBlock = -1; int wrappedBlock = -1; int findRes(MouseEvent evt) { int res = 0; int x = evt.getX(); if (av.wrapAlignment) { int hgap = av.charHeight; if (av.scaleAboveWrapped) hgap += av.charHeight; int cHeight = av.getAlignment().getHeight() * av.charHeight + 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 { res = (x / av.getCharWidth()) + av.getStartRes(); } if (av.hasHiddenColumns) res = av.getColumnSelection().adjustForHiddenColumns(res); return res; } int findSeq(MouseEvent evt) { int seq = 0; int y = evt.getY(); if (av.wrapAlignment) { int hgap = av.charHeight; if (av.scaleAboveWrapped) hgap += av.charHeight; int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; seq = Math.min( (y % cHeight) / av.getCharHeight(), av.alignment.getHeight() - 1); } else { seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), av.alignment.getHeight() - 1); } return seq; } SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) { Vector tmp = new Vector(); SequenceFeature[] features = sequence.getSequenceFeatures(); if (features != null) { for (int i = 0; i < features.length; i++) { if (av.featuresDisplayed == null || !av.featuresDisplayed.containsKey(features[i].getType())) continue; if ( (features[i].getBegin() <= res) && (features[i].getEnd() >= res)) { tmp.addElement(features[i]); } } } features = new SequenceFeature[tmp.size()]; for(int i=0; i= res) { if (av.featuresDisplayed.containsKey(sf.getType())) { allFeatures.addElement(sf); } } index++; } } return allFeatures; } void endEditing() { if (editCommand!=null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); av.firePropertyChange("alignment", null, av.getAlignment().getSequences()); } startseq = -1; lastres = -1; editingSeqs = false; groupEditing = false; keyboardNo1 = null; keyboardNo2 = null; editCommand = null; } void setCursorRow() { seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; scrollToVisible(); } void setCursorColumn() { seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; scrollToVisible(); } void setCursorRowAndColumn() { if(keyboardNo2==null) { keyboardNo2 = new StringBuffer(); } else { seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; scrollToVisible(); } } void setCursorPosition() { SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex( getKeyboardNo(keyboardNo1)-1 ); scrollToVisible(); } void moveCursor(int dx, int dy) { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.alignment.getWidth(); while(!av.colSel.isVisible(seqCanvas.cursorX) && seqCanvas.cursorX0) { seqCanvas.cursorX += dx; } if(seqCanvas.cursorX>=maxWidth || !av.colSel.isVisible(seqCanvas.cursorX) ) { seqCanvas.cursorX = original; } } scrollToVisible(); } void scrollToVisible() { if (seqCanvas.cursorX < 0) seqCanvas.cursorX = 0; else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) seqCanvas.cursorX = av.alignment.getWidth() - 1; if (seqCanvas.cursorY < 0) seqCanvas.cursorY = 0; else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) seqCanvas.cursorY = av.alignment.getHeight() - 1; endEditing(); if(av.wrapAlignment) { ap.scrollToWrappedVisible(seqCanvas.cursorX); } else { while (seqCanvas.cursorY < av.startSeq) { ap.scrollUp(true); } while (seqCanvas.cursorY + 1 > av.endSeq) { ap.scrollUp(false); } if (!av.wrapAlignment) { while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) { if (!ap.scrollRight(false)) break; } while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) break; } } } setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); seqCanvas.repaint(); } void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); if(av.getSelectionGroup()!=null) { SequenceGroup sg = av.selectionGroup; //Find the top and bottom of this group int min = av.alignment.getHeight(), max = 0; for(int i=0; i max) max = index; if(index < min) min = index; } max ++; if(topLeft) { sg.setStartRes(seqCanvas.cursorX); if(sg.getEndRes()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(false).clear(); for (int i = min; i < max; i++) { sg.addSequence(av.alignment.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.repaint(); } void insertGapAtCursor(boolean group) { groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); endEditing(); } void deleteGapAtCursor(boolean group) { groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); editSequence(false, seqCanvas.cursorX); endEditing(); } void numberPressed(char value) { if(keyboardNo1==null) keyboardNo1 = new StringBuffer(); if(keyboardNo2!=null) keyboardNo2.append(value); else keyboardNo1.append(value); } int getKeyboardNo(StringBuffer kb) { if(kb==null) return 1; else return Integer.parseInt(kb.toString()); } /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { mouseDragging = false; mouseWheelPressed = false; if (!editingSeqs) { doMouseReleasedDefineMode(evt); return; } endEditing(); ap.repaint(); } /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); if (javax.swing.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; } /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ 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); if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) return; SequenceI sequence = av.getAlignment().getSequenceAt(seq); if (res > sequence.getLength()) { return; } if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) { seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); } setStatusMessage(sequence, res, seq); // use aa to see if the mouse pointer is on a if (av.showSequenceFeatures) { tooltipText.setLength(6); // Cuts the buffer back to SequenceFeature[] features = findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(res)); if(features!=null) { for (int i = 0; i < features.length; i++) { if (features[i].getType().equals("disulfide bond")) { if (features[i].getBegin() == sequence.findPosition(res) || features[i].getEnd() == sequence.findPosition(res)) { if (tooltipText.length() > 6) tooltipText.append("
"); tooltipText.append("disulfide bond " + features[i].getBegin() + ":" + features[i].getEnd()); if (features[i].links != null) tooltipText.append("

"); } } else { if (tooltipText.length() > 6) tooltipText.append("
"); tooltipText.append(features[i].getType() + " " + features[i].begin); if (features[i].begin != features[i].end) tooltipText.append(" " + features[i].end); if (features[i].getDescription() != null && !features[i].description.equals(features[i].getType())) { tmpString = features[i].getDescription(); int startTag=tmpString.toUpperCase().indexOf(""); if(startTag>-1) { tmpString = tmpString.substring(startTag + 6); } int endTag=tmpString.toUpperCase().indexOf(""); if(endTag>-1) { tmpString = tmpString.substring(0, endTag); } endTag = tmpString.toUpperCase().indexOf(""); if(endTag>-1) { tmpString = tmpString.substring(0, endTag); } if(startTag>-1) { tooltipText.append("; " + tmpString); } else { if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1) { //The description does not specify html is to //be used, so we must remove < > symbols tmpString = tmpString.replaceAll("<", "<"); tmpString = tmpString.replaceAll(">", ">"); tooltipText.append("; "); tooltipText.append(tmpString); } else tooltipText.append("; "+tmpString); } } if (features[i].getValue("status") != null ) { String status = features[i].getValue("status").toString(); if(status.length()>0) tooltipText.append("; (" + features[i].getValue("status") + ")"); } if (features[i].links != null) tooltipText.append("

"); } // else if(features[i].begin==0 && features[i].end==0) { // seqSpecific.append(features[i].featureGroup+": " // + features[i].getType()+" " // +features[i].getDescription()+"
"); } } if(tooltipText.length()==6) // { setToolTipText(""); } else { tooltipText.append(""); setToolTipText(tooltipText.toString()); } } else setToolTipText(""); } } void setStatusMessage(SequenceI sequence, int res, int seq) { StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + sequence.getName()); Object obj = null; if (av.alignment.isNucleotide()) { obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + ""); if (obj != null) text.append(" Nucleotide: "); } else { obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); if (obj != null) text.append(" Residue: "); } if (obj != null) { if (obj != "") { text.append(obj + " (" + sequence.findPosition(res) + ")"); } } ap.alignFrame.statusBar.setText(text.toString()); } /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) { int oldWidth = av.charWidth; //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)); av.charWidth = oldWidth; ap.fontChanged(); } else { if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) { av.charWidth--; } else if (evt.getX() > lastMousePress.getX()) { av.charWidth++; } ap.repaint(); } FontMetrics fm = getFontMetrics(av.getFont()); av.validCharWidth = fm.charWidth('M') <= av.charWidth; 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, res); } else editSequence(true, res); mouseDragging = true; if(scrollThread!=null) scrollThread.setEvent(evt); } synchronized void editSequence(boolean insertGap, int startres) { int fixedLeft = -1; int fixedRight = -1; boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); if (!groupEditing && av.hasHiddenRows) { if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) { groupEditing = true; } } //No group, but the sequence may represent a group if (groupEditing && sg == null && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null) { groupEditing = false; } SequenceI seq = av.alignment.getSequenceAt(startseq); StringBuffer message = new StringBuffer(); if (groupEditing) { message.append("Edit group:"); if (editCommand == null) editCommand = new EditCommand("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("Edit "+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(true).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) { sg = new SequenceGroup(null, null, false, false, false, 0, av.alignment.getWidth()-1); sg.addSequence(av.alignment.getSequenceAt(startseq), false); } 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(fixedLefty2 || fixedRight==-1)) { if(startres>=y2) { fixedLeft = y2; } else { fixedRight = y2 - 1; } } } if (groupEditing) { Vector vseqs = sg.getSequences(true); int g, groupSize = vseqs.size(); SequenceI[] groupSeqs = new SequenceI[groupSize]; for (g = 0; g < groupSeqs.length; g++) groupSeqs[g] = (SequenceI) vseqs.elementAt(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.alignment.getWidth()-1 ) { sg.setEndRes(av.alignment.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 (!jalview.util.Comparison.isGap( groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; } } } if (blank) break; } if (!blank) { if(sg.getSize(false) == av.alignment.getHeight() ) { if((av.hasHiddenColumns && startresalWidth) 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 (!jalview.util.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 { editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, startres, startres-lastres, av.getGapCharacter(), true); } } else { // dragging to the left if (fixedColumns && fixedRight != -1) { for (int j = lastres; j > startres; j--) { deleteChar(startres, groupSeqs, fixedRight); } } else editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, startres, lastres - startres, av.getGapCharacter(), true); } } 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 { editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] {seq}, lastres, startres-lastres, av.getGapCharacter(), true); } } else { // dragging to the left if (fixedColumns && fixedRight != -1) { for (int j = lastres; j > startres; j--) { if (!jalview.util.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; m0) { editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] {seq}, startres, max, av.getGapCharacter(), true); } } } } lastres = startres; seqCanvas.repaint(); } void insertChar(int j, SequenceI [] seq, int fixedColumn) { int blankColumn = fixedColumn; for(int s=0; s j, theres a boundary after the gap insertion for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) { //Theres a space, so break and insert the gap break; } } if (blankColumn <= j) { blankColumn = fixedColumn; endEditing(); return; } } editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, av.getGapCharacter(), true); editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getGapCharacter(), true); } void deleteChar(int j, SequenceI [] seq, int fixedColumn) { editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getGapCharacter(), true); editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, av.getGapCharacter(), true); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseEntered(MouseEvent e) { if(oldSeq < 0) oldSeq = 0; if (scrollThread != null) { scrollThread.running = false; scrollThread = null; } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) { return; } if (mouseDragging) { scrollThread = new ScrollThread(); } } public void mouseClicked(MouseEvent evt) { SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) ); if(evt.getClickCount()>1) { if (av.getSelectionGroup().getSize(false) == 1 && av.getSelectionGroup().getEndRes() - av.getSelectionGroup().getStartRes() < 2) av.setSelectionGroup(null); SequenceFeature[] features = findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition( findRes(evt) ) ); if(features!=null && features.length==1) { SearchResults highlight = new SearchResults(); highlight.addResult(sequence, features[0].getBegin(), features[0].getEnd()); seqCanvas.highlightSearchResults(highlight); } if(features!=null && features.length>0) { seqCanvas.getFeatureRenderer().amendFeatures( new SequenceI[] {sequence}, features, false); seqCanvas.highlightSearchResults(null); } } } public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); /* if (mouseWheelPressed) { Font font = av.getFont(); int fontSize = font.getSize(); if (e.getWheelRotation() > 0 && fontSize < 51) fontSize++; else if (fontSize > 1) fontSize--; av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); ap.fontChanged(); } else*/ { if (e.getWheelRotation() > 0) ap.scrollUp(false); else ap.scrollUp(true); } } /** * 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.wrapAlignment && seq>av.alignment.getHeight()) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Cannot edit annotations in wrapped view.", "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); return; } if(seq<0 || res<0) return; SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) { return; } stretchGroup = av.getSelectionGroup(); if (stretchGroup == null) { stretchGroup = av.alignment.findGroup(sequence); if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && (res < stretchGroup.getEndRes())) { av.setSelectionGroup(stretchGroup); } else { stretchGroup = null; } } else if (!stretchGroup.getSequences(false).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { stretchGroup = null; SequenceGroup[] allGroups = av.alignment.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]; break; } } } av.setSelectionGroup(stretchGroup); } if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); for (int i = 0; i < allFeatures.size(); i++) { SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); if (sf.links != null) { for (int j = 0; j < sf.links.size(); j++) { links.addElement(sf.links.elementAt(j)); } } } jalview.gui.PopupMenu pop = new jalview.gui.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); 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; } if(stretchGroup.cs!=null) { if (stretchGroup.cs instanceof ClustalxColourScheme) { ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( stretchGroup.getSequences(true), stretchGroup.getWidth()); } if (stretchGroup.cs instanceof Blosum62ColourScheme || stretchGroup.cs instanceof PIDColourScheme || stretchGroup.cs.conservationApplied() || stretchGroup.cs.getThreshold()>0) stretchGroup.recalcConservation(); if (stretchGroup.cs.conservationApplied()) { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); } else { SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); } } changeEndRes = false; changeStartRes = false; stretchGroup = null; PaintRefresher.Refresh(this, av.getSequenceSetId()); } /** * 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.alignment.getWidth()) { res = av.alignment.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); } } else if (changeStartRes) { if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); } } int dragDirection = 0; if (y > oldSeq) { dragDirection = 1; } else if (y < oldSeq) { dragDirection = -1; } while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.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(false).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); } else { if (seq != null) { stretchGroup.addSequence(seq, false); } stretchGroup.addSequence(nextSeq, false); } } 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; } 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.alignment.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) { } } } } }