X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=11ef52a6a8d169998b757c807f384e8ac1dda83f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=47f43d598ac4eb7341ab4ced55e331f5a57049b8;hpb=3cd893e800be2ae4548bf309b31a955947319a34;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 47f43d5..11ef52a 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,412 +1,514 @@ -/* - * 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 javax.swing.*; - - -/** - * 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); - } - - /** - * 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 (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(""); - } - - tip.append(""); - setToolTipText(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.repaint(); - } - - - /** - * 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); - - //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); - - 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) - { - 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.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; - - 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(av.alignment); - } - - /** - * 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.repaint(); - - try - { - Thread.sleep(100); - } - catch (Exception ex) - { - } - } - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + */ +package jalview.gui; + +import java.awt.*; +import java.awt.event.*; +import java.util.Vector; + +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; + + String linkImageURL; + + 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); + linkImageURL = getClass().getResource("/images/link.gif").toString(); + 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) + { + SeqPanel sp = alignPanel.seqPanel; + int seq = Math.max(0, sp.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 (av.isShowDbRefs() && 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(); + SequenceFeature[] tfeat = new SequenceFeature[1]; + if (av.isShowNpFeats() && features != null) + { + for (int i = 0; i < features.length; i++) + { + if (features[i].begin == 0 && features[i].end == 0) + { + int sz = -tip.length(); + tfeat[0] = features[i]; + sp.appendFeatures(tip, linkImageURL, 0, tfeat, + sp.seqCanvas.fr.minmax); + sz += tip.length(); + maxWidth = Math.max(maxWidth, sz); + } + } + } + + 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)) + { + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq); + // build a new links menu based on the current links + any non-positional + // features + Vector nlinks = new Vector(Preferences.sequenceURLLinks); + SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().getSequenceFeatures(); + for (int sl = 0; sf != null && sl < sf.length; sl++) + { + if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) + { + if (sf[sl].links != null && sf[sl].links.size() > 0) + { + for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++) + { + nlinks.addElement(sf[sl].links.elementAt(l)); + } + } + } + } + + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq, + nlinks, new Vector(Preferences.getGroupURLLinks())); + 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()); + // always send selection message when mouse is released + av.sendSelection(); + } + + /** + * 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) + { + } + } + } + } +}