X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d6dff1474dc8d3bbee3548b754f0c3e5c8aab0bb;hb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;hp=032992666ef7f19a9139403244ca53f0e9f81382;hpb=dba30c55e191417596da163caeef250c78de132d;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 0329926..d6dff14 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,141 +1,417 @@ +/* + * 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; +/** + * 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); + } - protected int offy; - public int width; - public int lastid; + /** + * 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)); - boolean mouseDown; - boolean mouseUp; + if (seq < lastid) + { + selectSeqs(lastid - 1, seq); + } + else if (seq > lastid) + { + selectSeqs(lastid + 1, seq); + } - 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); - } + lastid = seq; + alignPanel.repaint(); + } - public void mouseMoved(MouseEvent e) {} - public void selectSeqs(int start, int end) { - if (end < start) { - int tmp = start; - start = end; - end = tmp; - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() < 2) + return; - for (int i = start; i <= end; i++) { - SequenceI pickedSeq = av.getAlignment().getSequenceAt(i); + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + return; - if (av.getSelection().contains(pickedSeq)) { - av.getSelection().removeElement(pickedSeq); - } else { - av.getSelection().addElement(pickedSeq); - } - } + int seq = alignPanel.seqPanel.findSeq(e); - repaint(); + //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); - public void mouseDragged(MouseEvent e) { - int y = e.getY(); - int seq = av.getIndex(y); + String url = links.elementAt(0).toString(); + url = url.substring(url.indexOf("|")+1); - if (mouseDown == true) { - if (seq < lastid) { - selectSeqs(lastid-1,seq); - } else if (seq > lastid) { - selectSeqs(lastid+1,seq); + 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(); } - lastid = seq; } - return; - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + if (scrollThread != null) + { + scrollThread.running = false; + } + } - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() == 2) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) { - int seq = av.getIndex(e.getY()); - 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){ex.printStackTrace();} + 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); + } } - } - public void mouseEntered(MouseEvent e) { } - public void mouseExited (MouseEvent e) { } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) + { + if (e.getClickCount() == 2) + { + return; + } + + int seq = alignPanel.seqPanel.findSeq(e); + - public void mousePressed(MouseEvent e) { - if (e.getClickCount() == 2) - return; + 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()); - int y = e.getY(); - int seq = av.getIndex(y); + return; + } - mouseDown = true; - if( javax.swing.SwingUtilities.isRightMouseButton(e)) - { - String id = av.getAlignment().getSequenceAt(seq).getName(); - String s = (String)JOptionPane.showInternalInputDialog( - this, - "Edit sequence name", - "Edit sequence name", - JOptionPane.PLAIN_MESSAGE, - null, - null, - id); - if(s!=null) + if ((av.getSelectionGroup() == null) || + ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null)) { - av.getAlignment().getSequenceAt(seq).setName(s); - alignPanel.RefreshPanels(); + av.setSelectionGroup(new SequenceGroup()); + av.getSelectionGroup().setStartRes(0); + av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1); } - } - else - { - if (seq != -1) - selectSeqs(seq,seq); + 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; - } - return; - } - public void mouseReleased(MouseEvent e) { - lastid = -1; + 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; + + 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), + true); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseReleased(MouseEvent e) + { + if (scrollThread != null) + { + scrollThread.running = false; + } + + mouseDragging = false; + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } + + /** + * 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); + } + } - mouseDown = false; - mouseUp = true; + // 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(); + } - PaintRefresher.Refresh(this); + 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) + { + } + } + } + } }