X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=e3a81dc7678fe775202154eb2f1a75b61e88edec;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=04c1efe535818a8401b53e58c7ced7a8c5708cd4;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 04c1efe..e3a81dc 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) 2006 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 @@ -18,13 +18,11 @@ */ package jalview.gui; -import jalview.datamodel.*; - import java.awt.*; import java.awt.event.*; - import javax.swing.*; +import jalview.datamodel.*; /** * DOCUMENT ME! @@ -32,386 +30,393 @@ import javax.swing.*; * @author $author$ * @version $Revision$ */ -public class IdPanel extends JPanel implements MouseListener, +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) + 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); + } + + /** + * 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()) { - this.av = av; - alignPanel = parent; - idCanvas = new IdCanvas(av); - setLayout(new BorderLayout()); - add(idCanvas, BorderLayout.CENTER); - addMouseListener(this); - addMouseMotionListener(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"); + tip.append(sequence.getDisplayId(true)); + if (sequence.getDescription() != null) { - 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()); + tip.append("
"); + tip.append(sequence.getDescription()); - //ADD NON POSITIONAL SEQUENCE INFO - SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); - if(features!=null) + //ADD NON POSITIONAL SEQUENCE INFO + SequenceFeature[] features = sequence.getDatasetSequence(). + getSequenceFeatures(); + if (features != null) + { + for (int i = 0; i < features.length; i++) { - for(int i=0; i"+features[i].featureGroup - +" "+ features[i].getType()+" "+features[i].description); - } + tip.append("
" + features[i].featureGroup + + " " + features[i].getType() + " " + + features[i].description); } } - tip.append("
"); } + tip.append("
"); + } - DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); - if (dbrefs != null) + DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); + if (dbrefs != null) + { + tip.append(""); + for (int i = 0; i < dbrefs.length; i++) { - tip.append(""); - for (int i = 0; i < dbrefs.length; i++) - { - tip.append("
"); - tip.append(dbrefs[i].getSource() + " " - + dbrefs[i].getAccessionId()); - } - tip.append(""); + tip.append("
"); + tip.append(dbrefs[i].getSource() + " " + + dbrefs[i].getAccessionId()); } - - tip.append(""); - setToolTipText(tip.toString()); + tip.append(""); } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseDragged(MouseEvent e) - { - mouseDragging = true; + tip.append(""); + setToolTipText(tip.toString()); + } + } - int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseDragged(MouseEvent e) + { + mouseDragging = true; - if (seq < lastid) - { - selectSeqs(lastid - 1, seq); - } - else if (seq > lastid) - { - selectSeqs(lastid + 1, seq); - } + int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); - lastid = seq; - alignPanel.repaint(); + if (seq < lastid) + { + selectSeqs(lastid - 1, seq); } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseClicked(MouseEvent e) + else if (seq > lastid) { - if (e.getClickCount() < 2) - return; + selectSeqs(lastid + 1, seq); + } - java.util.Vector links = Preferences.sequenceURLLinks; - if (links == null || links.size() < 1) - return; + lastid = seq; + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() < 2) + { + return; + } - int seq = alignPanel.seqPanel.findSeq(e); + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + { + return; + } - //DEFAULT LINK IS FIRST IN THE LINK LIST + int seq = alignPanel.seqPanel.findSeq(e); - String id = av.getAlignment().getSequenceAt(seq).getName(); - if (id.indexOf("|") > -1) - id = id.substring(id.lastIndexOf("|") + 1); + //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); + } - String url = links.elementAt(0).toString(); - url = url.substring(url.indexOf("|")+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); + 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(); - } + try + { + jalview.util.BrowserLauncher.openURL(url); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseEntered(MouseEvent e) + catch (Exception ex) { - if (scrollThread != null) - { - scrollThread.running = false; - } + 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 mouseExited(MouseEvent e) + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + if (scrollThread != null) { - 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); - } + scrollThread.running = false; + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) + { + if (av.getWrapAlignment()) + { + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mousePressed(MouseEvent e) + if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) { - if (e.getClickCount() == 2) - { - return; - } + scrollThread = new ScrollThread(true); + } - int seq = alignPanel.seqPanel.findSeq(e); + 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()); + 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; - } + 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); + } - 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); - } + alignPanel.repaint(); + } + + /** + * 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; + } - if (e.isShiftDown() && (lastid != -1)) - { - selectSeqs(lastid, seq); - } - else - { - selectSeq(seq); - } + lastid = start; - alignPanel.repaint(); + if (end < start) + { + int tmp = start; + start = end; + end = tmp; + lastid = end; } - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - void selectSeq(int seq) + for (int i = start; i <= end; i++) { - lastid = seq; - - SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), + true); } - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - */ - void selectSeqs(int start, int end) + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseReleased(MouseEvent e) + { + if (scrollThread != null) { - if(av.getSelectionGroup()==null) - return; + scrollThread.running = false; + } - if (end >= av.getAlignment().getHeight()) - { - end = av.getAlignment().getHeight() - 1; - } + mouseDragging = false; + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } - lastid = start; + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ + public void highlightSearchResults(java.util.Vector found) + { + idCanvas.setHighlighted(found); - if (end < start) - { - int tmp = start; - start = end; - end = tmp; - lastid = end; - } + if (found == null) + { + return; + } - for (int i = start; i <= end; i++) - { - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), - true); - } + 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); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseReleased(MouseEvent e) + // 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) { - if (scrollThread != null) - { - scrollThread.running = false; - } + this.up = up; + start(); + } - mouseDragging = false; - PaintRefresher.Refresh(this, av.getSequenceSetId()); + public void stopScrolling() + { + running = false; } - /** - * DOCUMENT ME! - * - * @param found DOCUMENT ME! - */ - public void highlightSearchResults(java.util.Vector found) + public void run() { - idCanvas.setHighlighted(found); + running = true; - if (found == null) + while (running) + { + if (alignPanel.scrollUp(up)) { - return; - } - - int index = av.alignment.findIndex((SequenceI) found.get(0)); + // scroll was ok, so add new sequence to selection + int seq = av.getStartSeq(); - // do we need to scroll the panel? - if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) - { - alignPanel.setScrollValues(av.getStartRes(), index); - } - } + if (!up) + { + seq = av.getEndSeq(); + } - // this class allows scrolling off the bottom of the visible alignment - class ScrollThread extends Thread - { - boolean running = false; - boolean up = true; + if (seq < lastid) + { + selectSeqs(lastid - 1, seq); + } + else if (seq > lastid) + { + selectSeqs(lastid + 1, seq); + } - public ScrollThread(boolean up) + lastid = seq; + } + else { - this.up = up; - start(); + running = false; } - public void stopScrolling() + alignPanel.repaint(); + + try { - running = false; + Thread.sleep(100); } - - public void run() + catch (Exception ex) { - 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) - { - } - } } + } } + } }