X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=04c1efe535818a8401b53e58c7ced7a8c5708cd4;hb=237972562c84b83dbd287071cdd839d97aaf7d4b;hp=4236cf8666111e47e94d52752f77a892a294451f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 4236cf8..04c1efe 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,269 +1,417 @@ /* -* 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) 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 java.awt.*; import java.awt.event.*; -import jalview.datamodel.*; - import javax.swing.*; -public class IdPanel extends JPanel implements MouseListener, MouseMotionListener { - protected IdCanvas idCanvas; - protected AlignViewport av; - protected AlignmentPanel alignPanel; - ScrollThread scrollThread = null; +/** + * 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); + } - int offy; - int width; - int lastid = -1; - boolean mouseDragging = false; + /** + * 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 (sequence.getDescription() != null) + { + tip.append("
"); + tip.append(sequence.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("
"); + } - 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); - } + 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(""); + } - public void mouseMoved(MouseEvent e) {} + tip.append(""); + setToolTipText(tip.toString()); + } + } - public void mouseDragged(MouseEvent e) { - mouseDragging = true; + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseDragged(MouseEvent e) + { + mouseDragging = true; - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - int seq = av.getIndex(y); + int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); - if(seq<0) - return; + if (seq < lastid) + { + selectSeqs(lastid - 1, seq); + } + else if (seq > lastid) + { + selectSeqs(lastid + 1, seq); + } - if (seq < lastid) - selectSeqs(lastid - 1, seq); - else if (seq > lastid) - selectSeqs(lastid + 1, seq); + lastid = seq; + alignPanel.repaint(); + } - lastid = seq; - alignPanel.repaint(); - } - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() == 2) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseClicked(MouseEvent e) { - 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(); - } - } + if (e.getClickCount() < 2) + return; - } - public void mouseEntered(MouseEvent e) - { - if(scrollThread!=null) - scrollThread.running = false; - } + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + return; - public void mouseExited (MouseEvent e) - { - if(av.getWrapAlignment()) - return; + int seq = alignPanel.seqPanel.findSeq(e); - if(mouseDragging && e.getY()<0 && av.getStartSeq()>0) - { - scrollThread = new ScrollThread(true); - } + //DEFAULT LINK IS FIRST IN THE LINK LIST - if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq()) - { - scrollThread = new ScrollThread(false); - } - } + String id = av.getAlignment().getSequenceAt(seq).getName(); + if (id.indexOf("|") > -1) + id = id.substring(id.lastIndexOf("|") + 1); - public void mousePressed(MouseEvent e) { - if (e.getClickCount() == 2) - return; + String url = links.elementAt(0).toString(); + url = url.substring(url.indexOf("|")+1); - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; + int index = url.indexOf("$SEQUENCE_ID$"); + url = url.substring(0, index)+ id + url.substring(index+13); - int seq = av.getIndex(y); - if (seq == -1) - return; + 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(); + } + } - if (javax.swing.SwingUtilities.isRightMouseButton(e)) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, - (Sequence)av.getAlignment().getSequenceAt(seq)); - pop.show(this, e.getX(), y); - return; + if (scrollThread != null) + { + scrollThread.running = false; + } } - if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) { + if (av.getWrapAlignment()) + { + return; + } - 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)); + if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) + { + scrollThread = new ScrollThread(true); + } - av.setSelectionGroup(selection); - return; + if (mouseDragging && (e.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) + { + scrollThread = new ScrollThread(false); + } } - if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null)) - av.setSelectionGroup(new SequenceGroup()); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) + { + if (e.getClickCount() == 2) + { + return; + } + + int seq = alignPanel.seqPanel.findSeq(e); - av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1); - if(e.isShiftDown() && lastid!=-1) - selectSeqs(lastid, seq); - else - selectSeq(seq); + 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()); - alignPanel.repaint(); - } + return; + } - void selectSeq(int seq) - { - lastid = seq; - SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq); - } - void selectSeqs(int start, int end) { - lastid = start; - if (end < start) - { - int tmp = start; - start = end; - end = tmp; - lastid = end; - } + 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); + } - for (int i = start; i <= end; i++) - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i)); - } + if (e.isShiftDown() && (lastid != -1)) + { + selectSeqs(lastid, seq); + } + else + { + selectSeq(seq); + } + alignPanel.repaint(); + } - public void mouseReleased(MouseEvent e) - { - if(scrollThread!=null) - scrollThread.running = false; + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + */ + void selectSeq(int seq) + { + lastid = seq; - mouseDragging = false; - PaintRefresher.Refresh(this); - } + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); + av.getSelectionGroup().addOrRemove(pickedSeq, true); + } - public void highlightSearchResults( java.util.Vector found ) - { - idCanvas.setHighlighted( found ); + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + */ + void selectSeqs(int start, int end) + { + if(av.getSelectionGroup()==null) + return; - if(found == null) - return; + if (end >= av.getAlignment().getHeight()) + { + end = av.getAlignment().getHeight() - 1; + } - int index = av.alignment.findIndex( (SequenceI)found.get(0)); + lastid = start; - // do we need to scroll the panel? - if(av.getStartSeq()>index || av.getEndSeq() lastid) - selectSeqs(lastid + 1, seq); + int index = av.alignment.findIndex((SequenceI) found.get(0)); - lastid = seq; + // do we need to scroll the panel? + if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) + { + alignPanel.setScrollValues(av.getStartRes(), index); } - else - running = false; + } - alignPanel.repaint(); - try + // 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) { - Thread.sleep(100); + this.up = up; + start(); } - catch (Exception ex) - {} - } - } -} + 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) + { + } + } + } + } }