X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b5569c3ba2c9a7ee430475a29847b2cac81fdc4c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6330926478a681b334f431fda3fab14de2f3013b;hpb=486e70a70e56b8ac23fd191c2ac9f8c7366f4fd7;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 6330926..b5569c3 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,34 +1,51 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.*; -import java.awt.event.*; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.SequenceAnnotationReport; +import jalview.util.MessageManager; +import jalview.util.UrlLink; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.util.List; import java.util.Vector; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.util.UrlLink; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** - * DOCUMENT ME! + * This panel hosts alignment sequence ids and responds to mouse clicks on them, + * as well as highlighting ids matched by a search from the Find menu. * * @author $author$ * @version $Revision$ @@ -36,15 +53,16 @@ import jalview.util.UrlLink; public class IdPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener { - protected IdCanvas idCanvas; + private IdCanvas idCanvas; - protected AlignViewport av; + protected AlignmentViewport av; protected AlignmentPanel alignPanel; ScrollThread scrollThread = null; + String linkImageURL; - + int offy; // int width; @@ -52,22 +70,23 @@ public class IdPanel extends JPanel implements MouseListener, boolean mouseDragging = false; + private final SequenceAnnotationReport seqAnnotReport; + /** * 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); + setIdCanvas(new IdCanvas(av)); linkImageURL = getClass().getResource("/images/link.gif").toString(); + seqAnnotReport = new SequenceAnnotationReport(linkImageURL); setLayout(new BorderLayout()); - add(idCanvas, BorderLayout.CENTER); + add(getIdCanvas(), BorderLayout.CENTER); addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(this); @@ -75,85 +94,41 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Respond to mouse movement by constructing tooltip text for the sequence id + * under the mouse. * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent e) { - SeqPanel sp = alignPanel.seqPanel; + SeqPanel sp = alignPanel.getSeqPanel(); int seq = Math.max(0, sp.findSeq(e)); - String tmp; - if (seq > -1 && seq < av.alignment.getHeight()) + if (seq > -1 && seq < av.getAlignment().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()); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + StringBuffer tip = new StringBuffer(64); + seqAnnotReport.createSequenceAnnotationReport(tip, sequence, + av.isShowDBRefs(), av.isShowNPFeats(), + sp.seqCanvas.fr.getMinMax()); + setToolTipText("" + sequence.getDisplayId(true) + " " + + tip.toString() + ""); } } /** - * DOCUMENT ME! + * Responds to a mouse drag by selecting the sequences under the dragged + * region. * * @param e - * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; - int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); + int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e)); if (seq < lastid) { @@ -163,44 +138,71 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeqs(lastid + 1, seq); } - + lastid = seq; alignPanel.paintAlignment(true); } + /** + * Response to the mouse wheel by scrolling the alignment panel. + */ + @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); if (e.getWheelRotation() > 0) { - alignPanel.scrollUp(false); + if (e.isShiftDown()) + { + alignPanel.scrollRight(true); + } + else + { + alignPanel.scrollUp(false); + } } else { - alignPanel.scrollUp(true); + if (e.isShiftDown()) + { + alignPanel.scrollRight(false); + } + else + { + alignPanel.scrollUp(true); + } } } /** - * DOCUMENT ME! + * Handle a mouse click event. Currently only responds to a double-click. The + * action is to try to open a browser window at a URL that searches for the + * selected sequence id. The search URL is configured in Preferences | + * Connections | URL link from Sequence ID. For example: + * + * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$ * * @param e - * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent e) { - if (e.getClickCount() < 2) + /* + * Ignore single click. Ignore 'left' click followed by 'right' click (user + * selects a row then its pop-up menu). + */ + if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e)) { return; } - java.util.Vector links = Preferences.sequenceURLLinks; + Vector links = Preferences.sequenceURLLinks; if (links == null || links.size() < 1) { return; } - int seq = alignPanel.seqPanel.findSeq(e); + int seq = alignPanel.getSeqPanel().findSeq(e); String url = null; int i = 0; String id = av.getAlignment().getSequenceAt(seq).getName(); @@ -242,23 +244,21 @@ public class IdPanel extends JPanel implements MouseListener, 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); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } - } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -271,8 +271,9 @@ public class IdPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -286,50 +287,57 @@ public class IdPanel extends JPanel implements MouseListener, } if (mouseDragging && (e.getY() >= getHeight()) - && (av.alignment.getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } } /** - * DOCUMENT ME! + * Respond to a mouse press. Does nothing for (left) double-click as this is + * handled by mouseClicked(). + * + * Right mouse down - construct and show context menu. + * + * Ctrl-down or Shift-down - add to or expand current selection group if there + * is one. + * + * Mouse down - select this sequence. * * @param e - * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent e) { - if (e.getClickCount() == 2) + if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e)) { return; } - int seq = alignPanel.seqPanel.findSeq(e); + int seq = alignPanel.getSeqPanel().findSeq(e); - if (javax.swing.SwingUtilities.isRightMouseButton(e)) + if (SwingUtilities.isRightMouseButton(e)) { - Sequence sq = (Sequence) av - .getAlignment().getSequenceAt(seq); - // build a new links menu based on the current links + any non-positional features + 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.getDatasetSequence().getSequenceFeatures(); - for (int sl=0;sf!=null && sl0) + if (sf[sl].links != null && sf[sl].links.size() > 0) { - for (int l=0, lSize=sf[sl].links.size(); l list) { - idCanvas.setHighlighted(found); + getIdCanvas().setHighlighted(list); - if (found == null) + if (list == null) { return; } - int index = av.alignment.findIndex((SequenceI) found.get(0)); + int index = av.getAlignment().findIndex(list.get(0)); // do we need to scroll the panel? if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) @@ -453,6 +460,16 @@ public class IdPanel extends JPanel implements MouseListener, } } + public IdCanvas getIdCanvas() + { + return idCanvas; + } + + public void setIdCanvas(IdCanvas idCanvas) + { + this.idCanvas = idCanvas; + } + // this class allows scrolling off the bottom of the visible alignment class ScrollThread extends Thread { @@ -471,6 +488,7 @@ public class IdPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true;