X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b9366ae7c72012f0b6350b78301d5653ccc52ee5;hb=fb1cdebe4a9d93839c81a2d3eb39e8da9cb83d64;hp=4236cf8666111e47e94d52752f77a892a294451f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 4236cf8..b9366ae 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,219 +1,386 @@ /* -* 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 -*/ - + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 java.awt.*; import java.awt.event.*; - -import jalview.datamodel.*; - import javax.swing.*; -public class IdPanel extends JPanel implements MouseListener, MouseMotionListener { +import jalview.datamodel.*; - protected IdCanvas idCanvas; - protected AlignViewport av; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class IdPanel + extends JPanel implements MouseListener, + MouseMotionListener, MouseWheelListener +{ + protected IdCanvas idCanvas; + protected AlignViewport av; protected AlignmentPanel alignPanel; ScrollThread scrollThread = null; - - int offy; - int width; + 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; + this.av = av; alignPanel = parent; idCanvas = new IdCanvas(av); setLayout(new BorderLayout()); add(idCanvas, BorderLayout.CENTER); addMouseListener(this); addMouseMotionListener(this); + addMouseWheelListener(this); + ToolTipManager.sharedInstance().registerComponent(this); } - public void mouseMoved(MouseEvent e) {} + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseMoved(MouseEvent e) + { + int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); + String tmp; + if (seq > -1 && seq < av.alignment.getHeight()) + { + SequenceI sequence = av.alignment.getSequenceAt(seq); + StringBuffer tip = new StringBuffer(); + tip.append(""); + int maxWidth = 0; + if (sequence.getDescription() != null) + { + tmp = sequence.getDescription(); + tip.append("
"+tmp); + maxWidth = Math.max(maxWidth, tmp.length()); + } - public void mouseDragged(MouseEvent e) { - mouseDragging = true; + DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); + if (dbrefs != null) + { + for (int i = 0; i < dbrefs.length; i++) + { + tip.append("
"); + tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId(); + tip.append(tmp); + maxWidth = Math.max(maxWidth, tmp.length()); + } + } - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - int seq = av.getIndex(y); - if(seq<0) - return; + //ADD NON POSITIONAL SEQUENCE INFO + SequenceFeature[] features = sequence.getDatasetSequence(). + getSequenceFeatures(); + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (features[i].begin == 0 && features[i].end == 0) + { + tmp = features[i].featureGroup + + " " + features[i].getType() + " " + + features[i].description; + tip.append("
" + tmp); + maxWidth = Math.max(maxWidth, tmp.length()); + } + } + } + + if(maxWidth > 60) + { + tip.insert(0, "
"); + tip.append("
"); + } + + tip.append(""); + + setToolTipText(""+sequence.getDisplayId(true)+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(); + alignPanel.paintAlignment(true); } + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + if (e.getWheelRotation() > 0) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.scrollUp(true); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void mouseClicked(MouseEvent e) { - if (e.getClickCount() == 2) + if (e.getClickCount() < 2) { - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - - int seq = av.getIndex(y); - String id = av.getAlignment().getSequenceAt(seq).getName(); - - try{ - jalview.util.BrowserLauncher.openURL( - "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id + - "]+-vn+2"); - }catch(Exception ex){ - // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration. - System.err.println( - ex.getMessage()+"\nUnixers: Try adding this jalview.browser property line \n" - +"in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" - +"jalview.browser=/usr/local/bin/firefox\n"); - //ex.printStackTrace(); - } + 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) + if (scrollThread != null) + { scrollThread.running = false; + } } - public void mouseExited (MouseEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) { - if(av.getWrapAlignment()) + if (av.getWrapAlignment()) + { return; + } - if(mouseDragging && e.getY()<0 && av.getStartSeq()>0) + if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) { scrollThread = new ScrollThread(true); } - if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq()) + if (mouseDragging && (e.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } } - - public void mousePressed(MouseEvent e) { + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) + { if (e.getClickCount() == 2) + { return; + } - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - - int seq = av.getIndex(y); - if (seq == -1) - 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)); - pop.show(this, e.getX(), y); - return; - } + (Sequence) av.getAlignment().getSequenceAt(seq), + Preferences.sequenceURLLinks); + pop.show(this, e.getX(), e.getY()); - if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null) - { - - SequenceGroup selection = new SequenceGroup(); - SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq)); - selection.setStartRes(0); - selection.setEndRes(av.alignment.getWidth()-1); - for (int i =0; i< sg.getSize(); i++) - selection.addSequence(sg.getSequenceAt(i)); - - av.setSelectionGroup(selection); return; } - if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null)) + 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); + } - av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1); - - if(e.isShiftDown() && lastid!=-1) + if (e.isShiftDown() && (lastid != -1)) + { selectSeqs(lastid, seq); + } else + { selectSeq(seq); + } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + */ void selectSeq(int seq) { lastid = seq; + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq); + av.getSelectionGroup().addOrRemove(pickedSeq, true); } - void selectSeqs(int start, int end) { + /** + * 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; - } + if (end >= av.getAlignment().getHeight()) + { + end = av.getAlignment().getHeight() - 1; + } - for (int i = start; i <= end; i++) - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i)); + 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) + if (scrollThread != null) + { scrollThread.running = false; + } mouseDragging = false; - PaintRefresher.Refresh(this); + PaintRefresher.Refresh(this, av.getSequenceSetId()); } - public void highlightSearchResults( java.util.Vector found ) + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ + public void highlightSearchResults(java.util.Vector found) { - idCanvas.setHighlighted( found ); + idCanvas.setHighlighted(found); - if(found == null) + if (found == null) + { return; + } - int index = av.alignment.findIndex( (SequenceI)found.get(0)); + int index = av.alignment.findIndex( (SequenceI) found.get(0)); // do we need to scroll the panel? - if(av.getStartSeq()>index || av.getEndSeq() index) || (av.getEndSeq() < index)) + { + alignPanel.setScrollValues(av.getStartRes(), index); + } } // this class allows scrolling off the bottom of the visible alignment @@ -222,6 +389,7 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene { boolean running = false; boolean up = true; + public ScrollThread(boolean up) { this.up = up; @@ -236,34 +404,45 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene public void run() { running = true; + while (running) { - if(alignPanel.scrollUp(up)) + if (alignPanel.scrollUp(up)) { // scroll was ok, so add new sequence to selection int seq = av.getStartSeq(); - if(!up) + + 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); - alignPanel.repaint(); try { Thread.sleep(100); } catch (Exception ex) - {} + { + } } } -} - + } }