X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=88d0c6985c933954968846aa6bcb375caf1712b7;hb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;hp=7a2ecf769c989a0f7f4167efea398fffc39e586b;hpb=48b925b3dd950c86b1add0f2a90a2d0f8b6e316e;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 7a2ecf7..88d0c69 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,45 +1,61 @@ /* - * 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 - * + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * * 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 + * 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 . + * + * You should have received a copy of the GNU General Public License + * 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.io.SequenceAnnotationReport; -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 $Revision$ */ public class IdPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener { - protected IdCanvas idCanvas; + private IdCanvas idCanvas; - protected AlignViewport av; + protected AlignmentViewport av; protected AlignmentPanel alignPanel; @@ -53,65 +69,67 @@ public class IdPanel extends JPanel implements MouseListener, int lastid = -1; 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); ToolTipManager.sharedInstance().registerComponent(this); } + /** - * DOCUMENT ME! - * + * Respond to mouse movement by constructing tooltip text for the sequence id + * under the mouse. + * * @param e * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent e) { - SeqPanel sp = alignPanel.seqPanel; + SeqPanel sp = alignPanel.getSeqPanel(); int seq = Math.max(0, sp.findSeq(e)); if (seq > -1 && seq < av.getAlignment().getHeight()) { SequenceI sequence = av.getAlignment().getSequenceAt(seq); - StringBuffer tip = new StringBuffer(); - seqAnnotReport.createSequenceAnnotationReport(tip, sequence, - av.isShowDbRefs(), av.isShowNpFeats(), - sp.seqCanvas.fr.minmax); + StringBuffer tip = new StringBuffer(64); + seqAnnotReport + .createSequenceAnnotationReport(tip, sequence, + av.isShowDBRefs(), av.isShowNPFeats(), + sp.seqCanvas.fr.getMinMax()); setToolTipText("" + sequence.getDisplayId(true) + " " - + tip.toString()+""); + + 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) { @@ -126,6 +144,9 @@ public class IdPanel extends JPanel implements MouseListener, alignPanel.paintAlignment(true); } + /** + * Response to the mouse wheel by scrolling the alignment panel. + */ @Override public void mouseWheelMoved(MouseWheelEvent e) { @@ -135,8 +156,9 @@ public class IdPanel extends JPanel implements MouseListener, if (e.isShiftDown()) { alignPanel.scrollRight(true); - - } else { + } + else + { alignPanel.scrollUp(false); } } @@ -145,33 +167,43 @@ public class IdPanel extends JPanel implements MouseListener, if (e.isShiftDown()) { alignPanel.scrollRight(false); - } else { + } + 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(); @@ -216,17 +248,15 @@ public class IdPanel extends JPanel implements MouseListener, 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); + 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! */ @@ -241,7 +271,7 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ @@ -266,28 +296,35 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * 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 Vector nlinks = new Vector(Preferences.sequenceURLLinks); - SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().getSequenceFeatures(); + SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) { if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) @@ -326,14 +363,16 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeq(seq); } + // TODO is this addition ok here? + av.isSelectionGroupChanged(true); + alignPanel.paintAlignment(true); } /** - * DOCUMENT ME! - * + * Toggle whether the sequence is part of the current selection group. + * * @param seq - * DOCUMENT ME! */ void selectSeq(int seq) { @@ -344,12 +383,11 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! - * + * Add contiguous rows of the alignment to the current selection group. Does + * nothing if there is no selection group. + * * @param start - * DOCUMENT ME! * @param end - * DOCUMENT ME! */ void selectSeqs(int start, int end) { @@ -376,15 +414,15 @@ public class IdPanel extends JPanel implements MouseListener, for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence( - av.getAlignment().getSequenceAt(i), i==end); + av.getAlignment().getSequenceAt(i), i == end); } } /** - * DOCUMENT ME! - * + * Respond to mouse released. Refreshes the display and triggers broadcast of + * the new selection group to any listeners. + * * @param e - * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent e) @@ -401,14 +439,14 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! - * + * Highlight sequence ids that match the given list, and if necessary scroll + * to the start sequence of the list. + * * @param list - * DOCUMENT ME! */ public void highlightSearchResults(List list) { - idCanvas.setHighlighted(list); + getIdCanvas().setHighlighted(list); if (list == null) { @@ -424,6 +462,16 @@ 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 {