/* * 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.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; import jalview.util.MessageManager; import jalview.util.UrlLink; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; 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.List; import java.util.Vector; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** * This panel hosts alignment sequence ids and responds to mouse clicks on them, * as well as highlighting ids matched by a search from the Find menu. * * @author $author$ * @version $Revision$ */ public class IdPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener { private IdCanvas idCanvas; protected AlignmentViewport av; protected AlignmentPanel alignPanel; ScrollThread scrollThread = null; String linkImageURL; int offy; // int width; int lastid = -1; boolean mouseDragging = false; private final SequenceAnnotationReport seqAnnotReport; /** * Creates a new IdPanel object. * * @param av * @param parent */ public IdPanel(AlignViewport av, AlignmentPanel parent) { this.av = av; alignPanel = parent; setIdCanvas(new IdCanvas(av)); linkImageURL = getClass().getResource("/images/link.gif").toString(); seqAnnotReport = new SequenceAnnotationReport(linkImageURL); setLayout(new BorderLayout()); add(getIdCanvas(), BorderLayout.CENTER); addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(this); ToolTipManager.sharedInstance().registerComponent(this); } /** * Respond to mouse movement by constructing tooltip text for the sequence id * under the mouse. * * @param e * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent e) { SeqPanel sp = alignPanel.getSeqPanel(); int seq = Math.max(0, sp.findSeq(e)); if (seq > -1 && seq < av.getAlignment().getHeight()) { SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuffer tip = new StringBuffer(64); seqAnnotReport .createSequenceAnnotationReport(tip, sequence, av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr.getMinMax()); setToolTipText("" + sequence.getDisplayId(true) + " " + tip.toString() + ""); } } /** * Responds to a mouse drag by selecting the sequences under the dragged * region. * * @param e */ @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e)); if (seq < lastid) { selectSeqs(lastid - 1, seq); } else if (seq > lastid) { selectSeqs(lastid + 1, seq); } lastid = seq; alignPanel.paintAlignment(true); } /** * Response to the mouse wheel by scrolling the alignment panel. */ @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); if (e.getWheelRotation() > 0) { if (e.isShiftDown()) { alignPanel.scrollRight(true); } else { alignPanel.scrollUp(false); } } else { if (e.isShiftDown()) { alignPanel.scrollRight(false); } else { alignPanel.scrollUp(true); } } } /** * Handle a mouse click event. Currently only responds to a double-click. The * action is to try to open a browser window at a URL that searches for the * selected sequence id. The search URL is configured in Preferences | * Connections | URL link from Sequence ID. For example: * * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$ * * @param e */ @Override public void mouseClicked(MouseEvent e) { /* * Ignore single click. Ignore 'left' click followed by 'right' click (user * selects a row then its pop-up menu). */ if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e)) { return; } Vector links = Preferences.sequenceURLLinks; if (links == null || links.size() < 1) { return; } int seq = alignPanel.getSeqPanel().findSeq(e); String url = null; int i = 0; String id = av.getAlignment().getSequenceAt(seq).getName(); while (url == null && i < links.size()) { // DEFAULT LINK IS FIRST IN THE LINK LIST // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED url = links.elementAt(i++).toString(); jalview.util.UrlLink urlLink = null; try { urlLink = new UrlLink(url); } catch (Exception foo) { jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'", foo); url = null; continue; } ; if (!urlLink.isValid()) { jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); url = null; continue; } String urls[] = urlLink.makeUrls(id, true); if (urls == null || urls[0] == null || urls[0].length() < 4) { url = null; continue; } // just take first URL made from regex url = urls[1]; } try { jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { JOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) { scrollThread.running = false; } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override 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.getAlignment().getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } } /** * Respond to a mouse press. Does nothing for (left) double-click as this is * handled by mouseClicked(). * * Right mouse down - construct and show context menu. * * Ctrl-down or Shift-down - add to or expand current selection group if there * is one. * * Mouse down - select this sequence. * * @param e */ @Override public void mousePressed(MouseEvent e) { if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e)) { return; } int seq = alignPanel.getSeqPanel().findSeq(e); if (SwingUtilities.isRightMouseButton(e)) { Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq); // build a new links menu based on the current links + any non-positional // features Vector nlinks = new Vector(Preferences.sequenceURLLinks); SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) { if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) { if (sf[sl].links != null && sf[sl].links.size() > 0) { for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++) { nlinks.addElement(sf[sl].links.elementAt(l)); } } } } jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq, nlinks, new Vector(Preferences.getGroupURLLinks())); 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.getAlignment().getWidth() - 1); } if (e.isShiftDown() && (lastid != -1)) { selectSeqs(lastid, seq); } else { selectSeq(seq); } // TODO is this addition ok here? av.isSelectionGroupChanged(true); alignPanel.paintAlignment(true); } /** * Toggle whether the sequence is part of the current selection group. * * @param seq */ void selectSeq(int seq) { lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); av.getSelectionGroup().addOrRemove(pickedSeq, true); } /** * Add contiguous rows of the alignment to the current selection group. Does * nothing if there is no selection group. * * @param start * @param end */ void selectSeqs(int start, int end) { if (av.getSelectionGroup() == null) { return; } if (end >= av.getAlignment().getHeight()) { end = av.getAlignment().getHeight() - 1; } 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), i == end); } } /** * Respond to mouse released. Refreshes the display and triggers broadcast of * the new selection group to any listeners. * * @param e */ @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) { scrollThread.running = false; } mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); // always send selection message when mouse is released av.sendSelection(); } /** * Highlight sequence ids that match the given list, and if necessary scroll * to the start sequence of the list. * * @param list */ public void highlightSearchResults(List list) { getIdCanvas().setHighlighted(list); if (list == null) { return; } int index = av.getAlignment().findIndex(list.get(0)); // do we need to scroll the panel? if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) { alignPanel.setScrollValues(av.getStartRes(), index); } } public IdCanvas getIdCanvas() { return idCanvas; } public void setIdCanvas(IdCanvas idCanvas) { this.idCanvas = idCanvas; } // 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; } @Override 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.paintAlignment(false); try { Thread.sleep(100); } catch (Exception ex) { } } } } }