X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=f5e0f2f261a596d7d4bf76032f871775d4d8ccaa;hb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;hp=3444881b52a6d96f01fa2d96171c48813dd05adb;hpb=31a5f9724e7ba5c8f67a6db9a0c0f2356cd81b9d;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 3444881..f5e0f2f 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,229 +1,479 @@ +/* + * 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 + */ 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 y = e.getY(); - 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); - } + if (av.getWrapAlignment()) + { + y = getWrappedY(y); + } - public void mouseMoved(MouseEvent e) {} + final int seq = av.getIndex(y); + if(seq!=-1) + { + SequenceI sequence = av.alignment.getSequenceAt(seq); + StringBuffer tip = new StringBuffer(""); + 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(""); + } - public void mouseDragged(MouseEvent e) { - mouseDragging = true; + tip.append(""); + setToolTipText(tip.toString()); + } + } - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - int seq = av.getIndex(y); - if(seq<0) - return; + int getWrappedY(int y) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - if (seq < lastid) - selectSeqs(lastid - 1, seq); - else if (seq > lastid) - selectSeqs(lastid + 1, seq); + return y - hgap; + } - lastid = seq; - alignPanel.repaint(); - } - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() == 2) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseDragged(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){ex.printStackTrace();} - } + mouseDragging = true; + + int y = e.getY(); + + if (av.getWrapAlignment()) + { + y = getWrappedY(y); + } - } - public void mouseEntered(MouseEvent e) - { - if(scrollThread!=null) - scrollThread.running = false; - } + int seq = av.getIndex(y); - public void mouseExited (MouseEvent e) - { - if(av.getWrapAlignment()) - return; + if (seq < 0) + { + return; + } - if(mouseDragging && e.getY()<0 && av.getStartSeq()>0) - { - scrollThread = new ScrollThread(true); + if (seq < lastid) + { + selectSeqs(lastid - 1, seq); + } + else if (seq > lastid) + { + selectSeqs(lastid + 1, seq); + } + + lastid = seq; + alignPanel.repaint(); } - if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq()) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseClicked(MouseEvent e) { - scrollThread = new ScrollThread(false); - } - } + if (e.getClickCount() < 2) + return; + + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + return; + + int y = e.getY(); + + if (av.getWrapAlignment()) + { + y = getWrappedY(y); + } + + //DEFAULT LINK IS FIRST IN THE LINK LIST + int seq = av.getIndex(y); + if(seq==-1) + return; + 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; - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; + String url = links.elementAt(0).toString(); + url = url.substring(url.indexOf("|")+1); - int seq = av.getIndex(y); - if (seq == -1) - return; + int index = url.indexOf("$SEQUENCE_ID$"); + url = url.substring(0, index)+ id + url.substring(index+13); - if (javax.swing.SwingUtilities.isRightMouseButton(e)) + 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) { - 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 y = e.getY(); + + if (av.getWrapAlignment()) + { + y = getWrappedY(y); + } - av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1); + int seq = av.getIndex(y); - if(e.isShiftDown() && lastid!=-1) - selectSeqs(lastid, seq); - else - selectSeq(seq); + if (seq == -1) + { + 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(), y); - alignPanel.repaint(); - } + return; + } + + /* if (!e.isControlDown() && !e.isShiftDown() && + (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)) + { + System.out.println("no modifiers"); + SequenceGroup selection = new SequenceGroup(); + SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt( + seq)); + selection.setStartRes(0); + selection.setEndRes(av.alignment.getWidth() - 1); - void selectSeq(int seq) - { - lastid = seq; - SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq); - } + for (int i = 0; i < sg.getSize(); i++) + { + selection.addSequence(sg.getSequenceAt(i), true); + } - void selectSeqs(int start, int end) { + av.setSelectionGroup(selection); - lastid = start; - if (end < start) - { - int tmp = start; - start = end; - end = tmp; - lastid = end; - } + return; + }*/ - for (int i = start; i <= end; i++) - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i)); + 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); + } - } - public void mouseReleased(MouseEvent e) - { - if(scrollThread!=null) - scrollThread.running = false; + if (e.isShiftDown() && (lastid != -1)) + { + selectSeqs(lastid, seq); + } + else + { + selectSeq(seq); + } - mouseDragging = false; - PaintRefresher.Refresh(this); - } + alignPanel.repaint(); + } - // 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) + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + */ + void selectSeq(int seq) { - this.up = up; - start(); + lastid = seq; + + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); + av.getSelectionGroup().addOrRemove(pickedSeq, true); } - public void stopScrolling() + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + */ + void selectSeqs(int start, int end) { - running = false; + if(av.getSelectionGroup()==null) + return; + + 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); + } } - public void run() + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseReleased(MouseEvent e) { - running = true; - while (running) - { - if(alignPanel.scrollUp(up)) + if (scrollThread != null) { - // scroll was ok, so add new sequence to selection - int seq = av.getStartSeq(); - if(!up) - seq = av.getEndSeq(); + scrollThread.running = false; + } - if (seq < lastid) - selectSeqs(lastid - 1, seq); - else if (seq > lastid) - selectSeqs(lastid + 1, seq); + mouseDragging = false; + PaintRefresher.Refresh(av.alignment); + } + + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ + public void highlightSearchResults(java.util.Vector found) + { + idCanvas.setHighlighted(found); - lastid = seq; + if (found == null) + { + return; } - else - running = false; - alignPanel.repaint(); - try + int index = av.alignment.findIndex((SequenceI) found.get(0)); + + // do we need to scroll the panel? + if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) { - Thread.sleep(100); + alignPanel.setScrollValues(av.getStartRes(), index); } - catch (Exception ex) - {} - } } -} + // 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.repaint(); + + try + { + Thread.sleep(100); + } + catch (Exception ex) + { + } + } + } + } }