X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d80c4b86144bc03388f143e62c974c1afaea856c;hb=50a8dcccc09f983c21f0c9a8a3653c379c348a4b;hp=4efef459777a53d992f6b4a8572c02fde8ec6b9b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 4efef45..d80c4b8 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -24,9 +24,15 @@ import javax.swing.*; import jalview.datamodel.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class IdPanel extends JPanel implements MouseListener, - MouseMotionListener + MouseMotionListener, MouseWheelListener { protected IdCanvas idCanvas; protected AlignViewport av; @@ -37,6 +43,12 @@ public class IdPanel 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; @@ -46,29 +58,74 @@ public class IdPanel 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)); + if (seq > -1 && seq < av.alignment.getHeight()) + { + SequenceI sequence = av.alignment.getSequenceAt(seq); + StringBuffer tip = new StringBuffer(""); + tip.append(sequence.getDisplayId(true)); + if (sequence.getDescription() != null) + { + tip.append("
"); + tip.append(sequence.getDescription()); - public void mouseDragged(MouseEvent e) - { - mouseDragging = true; + //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) + { + tip.append("
" + features[i].featureGroup + + " " + features[i].getType() + " " + + features[i].description); + } + } + } + tip.append("
"); + } - int y = e.getY(); + 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(""); + } - if (av.getWrapAlignment()) - { - y -= (2 * av.charHeight); + tip.append(""); + setToolTipText(tip.toString()); } + } - int seq = av.getIndex(y); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseDragged(MouseEvent e) + { + mouseDragging = true; - if (seq < 0) - { - return; - } + int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); if (seq < lastid) { @@ -80,42 +137,77 @@ public class IdPanel } 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(); + return; + } - if (av.getWrapAlignment()) - { - y -= (2 * av.charHeight); - } + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + { + return; + } - int seq = av.getIndex(y); - String id = av.getAlignment().getSequenceAt(seq).getName(); + int seq = alignPanel.seqPanel.findSeq(e); - 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"); + //DEFAULT LINK IS FIRST IN THE LINK LIST - //ex.printStackTrace(); - } + 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) @@ -124,6 +216,11 @@ public class IdPanel } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -143,6 +240,11 @@ public class IdPanel } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void mousePressed(MouseEvent e) { if (e.getClickCount() == 2) @@ -150,57 +252,26 @@ public class IdPanel 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; - } - - 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); + (Sequence) av.getAlignment().getSequenceAt(seq), + Preferences.sequenceURLLinks); + pop.show(this, e.getX(), e.getY()); return; } if ( (av.getSelectionGroup() == null) || - (!e.isControlDown() && (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)) { selectSeqs(lastid, seq); @@ -210,19 +281,40 @@ public class IdPanel 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); } + /** + * 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) @@ -235,10 +327,16 @@ public class IdPanel for (int i = start; i <= end; i++) { - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i)); + av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), + true); } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -247,9 +345,14 @@ public class IdPanel } mouseDragging = false; - PaintRefresher.Refresh(this); + PaintRefresher.Refresh(this, av.getSequenceSetId()); } + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ public void highlightSearchResults(java.util.Vector found) { idCanvas.setHighlighted(found); @@ -318,7 +421,7 @@ public class IdPanel running = false; } - alignPanel.repaint(); + alignPanel.paintAlignment(true); try {