X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=a781830d18a3f2de3174eed626d52a5b1420a590;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=4509ab3391b31325ab1dbf74e70c8cf67be84c2a;hpb=c5898a03d9b066d4ccc2e22d3cb72a8ca3cc656e;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 4509ab3..a781830 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,133 +1,487 @@ -package jalview.gui; - -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; - - protected int offy; - public int width; - public int lastid; - - - 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); - } - - public void mouseMoved(MouseEvent e) {} - - public void selectSeqs(int start, int end) { - if (end < start) { - int tmp = start; - start = end; - end = tmp; - } - - for (int i = start; i <= end; i++) - { - SequenceI pickedSeq = av.getAlignment().getSequenceAt(i); - - if (av.getSelection().contains(pickedSeq)) - av.getSelection().removeElement(pickedSeq); - else - av.getSelection().addElement(pickedSeq); - - } - - repaint(); - - } - - public void mouseDragged(MouseEvent e) { - int y = e.getY(); - int seq = av.getIndex(y); - - - - - if (seq < lastid) - selectSeqs(lastid - 1, seq); - else if (seq > lastid) - selectSeqs(lastid + 1, seq); - - lastid = seq; - - return; - } - - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() == 2) - { - 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();} - } - - } - public void mouseEntered(MouseEvent e) { } - public void mouseExited (MouseEvent e) { } - - public void mousePressed(MouseEvent e) { - if (e.getClickCount() == 2) - return; - - int y = e.getY(); - int seq = av.getIndex(y); - - - 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) - { - av.getAlignment().getSequenceAt(seq).setName(s); - alignPanel.RefreshPanels(); - } - - } - else - { - if (seq != -1) - selectSeqs(seq,seq); - - lastid = seq; - } - return; - } - - public void mouseReleased(MouseEvent e) - { - lastid = -1; - PaintRefresher.Refresh(this); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 javax.swing.*; + +import jalview.datamodel.*; +import jalview.util.UrlLink; + +/** + * 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 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); + addMouseWheelListener(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)); + 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()); + } + + 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()); + } + } + + // 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.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) + { + return; + } + + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + { + return; + } + + int seq = alignPanel.seqPanel.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, + "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.paintAlignment(true); + } + + /** + * 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; + } + + 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); + } + } + + // 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.paintAlignment(false); + + try + { + Thread.sleep(100); + } catch (Exception ex) + { + } + } + } + } +}