/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 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 java.awt.*; import java.awt.event.*; import javax.swing.*; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class IdPanel extends JPanel implements MouseListener, MouseMotionListener { protected IdCanvas idCanvas; protected AlignViewport av; protected AlignmentPanel alignPanel; ScrollThread scrollThread = null; int offy; int width; int lastid = -1; boolean mouseDragging = false; /** * Creates a new IdPanel object. * * @param av DOCUMENT ME! * @param parent DOCUMENT ME! */ public IdPanel(AlignViewport av, AlignmentPanel parent) { this.av = av; alignPanel = parent; idCanvas = new IdCanvas(av); setLayout(new BorderLayout()); add(idCanvas, BorderLayout.CENTER); addMouseListener(this); addMouseMotionListener(this); ToolTipManager.sharedInstance().registerComponent(this); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseMoved(MouseEvent e) { int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); if(seq>-1 && seq"); tip.append(sequence.getDisplayId(true)); if (av.alignment.getSequenceAt(seq).getDescription() != null) { tip.append("

"); tip.append(av.alignment.getSequenceAt(seq).getDescription()); //ADD NON POSITIONAL SEQUENCE INFO SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); if(features!=null) { for(int i=0; i"+features[i].featureGroup +" "+ features[i].getType()+" "+features[i].description); } } } tip.append("

"); } DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); if (dbrefs != null) { tip.append(""); for (int i = 0; i < dbrefs.length; i++) { tip.append("
"); tip.append(dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId()); } tip.append(""); } tip.append(""); setToolTipText(tip.toString()); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseDragged(MouseEvent e) { mouseDragging = true; int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); if (seq < lastid) { selectSeqs(lastid - 1, seq); } else if (seq > lastid) { selectSeqs(lastid + 1, seq); } lastid = seq; alignPanel.repaint(); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) return; java.util.Vector links = Preferences.sequenceURLLinks; if (links == null || links.size() < 1) return; int seq = alignPanel.seqPanel.findSeq(e); //DEFAULT LINK IS FIRST IN THE LINK LIST String id = av.getAlignment().getSequenceAt(seq).getName(); if (id.indexOf("|") > -1) id = id.substring(id.lastIndexOf("|") + 1); String url = links.elementAt(0).toString(); url = url.substring(url.indexOf("|")+1); int index = url.indexOf("$SEQUENCE_ID$"); url = url.substring(0, index)+ id + url.substring(index+13); try { jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Unixers: Couldn't find default web browser." +"\nAdd the full path to your browser in Preferences.", "Web browser not found", JOptionPane.WARNING_MESSAGE ); ex.printStackTrace(); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseEntered(MouseEvent e) { if (scrollThread != null) { scrollThread.running = false; } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) { return; } if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) { scrollThread = new ScrollThread(true); } if (mouseDragging && (e.getY() >= getHeight()) && (av.alignment.getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mousePressed(MouseEvent e) { if (e.getClickCount() == 2) { return; } int seq = alignPanel.seqPanel.findSeq(e); if (javax.swing.SwingUtilities.isRightMouseButton(e)) { jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), Preferences.sequenceURLLinks); pop.show(this, e.getX(), e.getY()); return; } if ((av.getSelectionGroup() == null) || ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null)) { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1); } if (e.isShiftDown() && (lastid != -1)) { selectSeqs(lastid, seq); } else { selectSeq(seq); } alignPanel.repaint(); } /** * DOCUMENT ME! * * @param seq DOCUMENT ME! */ void selectSeq(int seq) { lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); av.getSelectionGroup().addOrRemove(pickedSeq, true); } /** * DOCUMENT ME! * * @param start DOCUMENT ME! * @param end DOCUMENT ME! */ void selectSeqs(int start, int end) { if(av.getSelectionGroup()==null) return; lastid = start; if (end < start) { int tmp = start; start = end; end = tmp; lastid = end; } for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), true); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void mouseReleased(MouseEvent e) { if (scrollThread != null) { scrollThread.running = false; } mouseDragging = false; PaintRefresher.Refresh(av.alignment); } /** * DOCUMENT ME! * * @param found DOCUMENT ME! */ public void highlightSearchResults(java.util.Vector found) { idCanvas.setHighlighted(found); if (found == null) { return; } int index = av.alignment.findIndex((SequenceI) found.get(0)); // do we need to scroll the panel? if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) { alignPanel.setScrollValues(av.getStartRes(), index); } } // this class allows scrolling off the bottom of the visible alignment class ScrollThread extends Thread { boolean running = false; boolean up = true; public ScrollThread(boolean up) { this.up = up; start(); } public void stopScrolling() { running = false; } public void run() { running = true; while (running) { if (alignPanel.scrollUp(up)) { // scroll was ok, so add new sequence to selection int seq = av.getStartSeq(); if (!up) { seq = av.getEndSeq(); } if (seq < lastid) { selectSeqs(lastid - 1, seq); } else if (seq > lastid) { selectSeqs(lastid + 1, seq); } lastid = seq; } else { running = false; } alignPanel.repaint(); try { Thread.sleep(100); } catch (Exception ex) { } } } } }