X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=47f43d598ac4eb7341ab4ced55e331f5a57049b8;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=db24821687a8bb83bb2310d6cc44662ee09dfd71;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index db24821..47f43d5 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -18,316 +18,395 @@ */ package jalview.gui; +import jalview.datamodel.*; + import java.awt.*; import java.awt.event.*; + import javax.swing.*; -import jalview.datamodel.*; -public class IdPanel - extends JPanel implements MouseListener, +/** + * 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; - - 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 mouseDragged(MouseEvent e) - { - mouseDragging = true; - - int y = e.getY(); - - if (av.getWrapAlignment()) + 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) { - y -= (2 * av.charHeight); + 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 seq = av.getIndex(y); - - if (seq < 0) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseMoved(MouseEvent e) { - return; - } + 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()); - if (seq < lastid) - { - selectSeqs(lastid - 1, seq); + //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()); + } } - else if (seq > lastid) + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseDragged(MouseEvent e) { - selectSeqs(lastid + 1, seq); + 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(); } - 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 (e.getClickCount() < 2) + return; - if (av.getWrapAlignment()) - { - y -= (2 * av.charHeight); - } + 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 - int seq = av.getIndex(y); 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( - "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + - id + "]+-vn+2"); + jalview.util.BrowserLauncher.openURL(url); } 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(); + 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(); } } - } - public void mouseEntered(MouseEvent e) - { - if (scrollThread != null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) { - scrollThread.running = false; + if (scrollThread != null) + { + scrollThread.running = false; + } } - } - public void mouseExited(MouseEvent e) - { - if (av.getWrapAlignment()) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) { - return; - } + if (av.getWrapAlignment()) + { + return; + } - if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) - { - scrollThread = new ScrollThread(true); - } + 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); + if (mouseDragging && (e.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) + { + scrollThread = new ScrollThread(false); + } } - } - public void mousePressed(MouseEvent e) - { - if (e.getClickCount() == 2) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) { - return; - } + if (e.getClickCount() == 2) + { + return; + } - int y = e.getY(); + int seq = alignPanel.seqPanel.findSeq(e); - if (av.getWrapAlignment()) - { - y -= (2 * av.charHeight); - } - int seq = av.getIndex(y); + 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()); - if (seq == -1) - { - return; - } + return; + } - 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; - } - 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); + 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 = 0; i < sg.getSize(); i++) - { - selection.addSequence(sg.getSequenceAt(i), true); - } - av.setSelectionGroup(selection); + if (e.isShiftDown() && (lastid != -1)) + { + selectSeqs(lastid, seq); + } + else + { + selectSeq(seq); + } - return; + alignPanel.repaint(); } - if ( (av.getSelectionGroup() == null) || - (!e.isControlDown() && (av.getSelectionGroup() != null))) + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + */ + void selectSeq(int seq) { - av.setSelectionGroup(new SequenceGroup()); - } + lastid = seq; - av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1); - - if (e.isShiftDown() && (lastid != -1)) - { - selectSeqs(lastid, seq); + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); + av.getSelectionGroup().addOrRemove(pickedSeq, true); } - else - { - selectSeq(seq); - } - - alignPanel.repaint(); - } - - 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; - void selectSeqs(int start, int end) - { - lastid = start; + lastid = start; - if (end < start) - { - int tmp = start; - start = end; - end = tmp; - lastid = end; - } + 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); + for (int i = start; i <= end; i++) + { + av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), + true); + } } - } - public void mouseReleased(MouseEvent e) - { - if (scrollThread != null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseReleased(MouseEvent e) { - scrollThread.running = false; - } - - mouseDragging = false; - PaintRefresher.Refresh(av.alignment); - } - - public void highlightSearchResults(java.util.Vector found) - { - idCanvas.setHighlighted(found); + if (scrollThread != null) + { + scrollThread.running = false; + } - if (found == null) - { - return; + mouseDragging = false; + PaintRefresher.Refresh(av.alignment); } - int index = av.alignment.findIndex( (SequenceI) found.get(0)); - - // do we need to scroll the panel? - if ( (av.getStartSeq() > index) || (av.getEndSeq() < index)) + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ + public void highlightSearchResults(java.util.Vector found) { - alignPanel.setScrollValues(av.getStartRes(), index); - } - } + idCanvas.setHighlighted(found); - // this class allows scrolling off the bottom of the visible alignment - class ScrollThread - extends Thread - { - boolean running = false; - boolean up = true; + if (found == null) + { + return; + } - public ScrollThread(boolean up) - { - this.up = up; - start(); - } + int index = av.alignment.findIndex((SequenceI) found.get(0)); - public void stopScrolling() - { - running = false; + // do we need to scroll the panel? + if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) + { + alignPanel.setScrollValues(av.getStartRes(), index); + } } - public void run() + // this class allows scrolling off the bottom of the visible alignment + class ScrollThread extends Thread { - running = true; + boolean running = false; + boolean up = true; - while (running) - { - if (alignPanel.scrollUp(up)) + public ScrollThread(boolean 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; + this.up = up; + start(); } - alignPanel.repaint(); - - try + public void stopScrolling() { - Thread.sleep(100); + running = false; } - catch (Exception ex) + + 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) + { + } + } } - } } - } }