X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=10641eb81b605a38310e19c322c8c521733018da;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=97e33668633e43c95bcf89f7f1df6208bddb4213;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 97e3366..10641eb 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,46 +1,65 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * 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. + * 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.AlignmentAnnotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.SeqPanel.MousePos; +import jalview.io.SequenceAnnotationReport; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; + +import java.awt.BorderLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +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.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; +import javax.swing.Timer; +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 +public class IdPanel extends JPanel + implements MouseListener, MouseMotionListener, MouseWheelListener { - protected IdCanvas idCanvas; + private IdCanvas idCanvas; - protected AlignViewport av; + protected AlignmentViewport av; protected AlignmentPanel alignPanel; @@ -61,19 +80,17 @@ public class IdPanel extends JPanel implements MouseListener, * 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); @@ -81,41 +98,68 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Responds to mouse movement by setting tooltip text for the sequence id + * under the mouse (or possibly annotation label, when in wrapped mode) * * @param e - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent e) { - SeqPanel sp = alignPanel.seqPanel; - 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); - setToolTipText("" + sequence.getDisplayId(true) + " " - + tip.toString() + ""); + SeqPanel sp = alignPanel.getSeqPanel(); + MousePos pos = sp.findMousePosition(e); + if (pos.isOverAnnotation()) + { + /* + * mouse is over an annotation label in wrapped mode + */ + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation annotation = anns[pos.annotationIndex]; + setToolTipText(AnnotationLabels.getTooltip(annotation)); + alignPanel.alignFrame.setStatus( + AnnotationLabels.getStatusMessage(annotation, anns)); + } + else + { + int seq = Math.max(0, pos.seqIndex); + if (seq < av.getAlignment().getHeight()) + { + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + StringBuilder tip = new StringBuilder(64); + tip.append(sequence.getDisplayId(true)).append(" "); + seqAnnotReport.createTooltipAnnotationReport(tip, sequence, + av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); + setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString())); + + StringBuilder text = new StringBuilder(); + text.append("Sequence ").append(String.valueOf(seq + 1)) + .append(" ID: ") + .append(sequence.getName()); + alignPanel.alignFrame.setStatus(text.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)); + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + if (pos.isOverAnnotation()) + { + // mouse is over annotation label in wrapped mode + return; + } + + int seq = Math.max(0, pos.seqIndex); if (seq < lastid) { @@ -127,123 +171,108 @@ public class IdPanel extends JPanel implements MouseListener, } lastid = seq; - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } + /** + * Response to the mouse wheel by scrolling the alignment panel. + */ @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { if (e.isShiftDown()) { - alignPanel.scrollRight(true); - + av.getRanges().scrollRight(true); } else { - alignPanel.scrollUp(false); + av.getRanges().scrollUp(false); } } - else + else if (wheelRotation < 0) { if (e.isShiftDown()) { - alignPanel.scrollRight(false); + av.getRanges().scrollRight(false); } else { - alignPanel.scrollUp(true); + av.getRanges().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)) { + // reinstate isRightMouseButton check to ignore mouse-related popup events + // note - this does nothing on default MacBookPro force-trackpad config! return; } - java.util.Vector links = Preferences.sequenceURLLinks; - if (links == null || links.size() < 1) + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + int seq = pos.seqIndex; + if (pos.isOverAnnotation() || seq < 0) { 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 url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); - 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); + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } - } /** - * DOCUMENT ME! + * On (re-)entering the panel, stop any scrolling * * @param e - * DOCUMENT ME! */ @Override public void mouseEntered(MouseEvent e) { + stopScrolling(); + } + + /** + * Interrupts the scroll thread if one is running + */ + void stopScrolling() + { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.stopScrolling(); + scrollThread = null; } } @@ -261,66 +290,117 @@ public class IdPanel extends JPanel implements MouseListener, return; } - if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging) { - scrollThread = new ScrollThread(true); + /* + * on mouse drag above or below the panel, start + * scrolling if there are more sequences to show + */ + ViewportRanges ranges = av.getRanges(); + if (e.getY() < 0 && ranges.getStartSeq() > 0) + { + startScrolling(true); + } + else if (e.getY() >= getHeight() + && ranges.getEndSeq() <= av.getAlignment().getHeight()) + { + startScrolling(false); + } } + } - if (mouseDragging && (e.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + /** + * Starts scrolling either up or down + * + * @param up + */ + void startScrolling(boolean up) + { + scrollThread = new ScrollThread(up); + if (Platform.isJS()) { - scrollThread = new ScrollThread(false); + /* + * for JalviewJS using Swing Timer + */ + Timer t = new Timer(20, new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (scrollThread != null) + { + // if (!scrollOnce() {t.stop();}) gives compiler error :-( + scrollThread.scrollOnce(); + } + } + }); + t.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (scrollThread == null) + { + // IdPanel.stopScrolling called + t.stop(); + } + } + }); + t.start(); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + scrollThread.start(); } } /** - * 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); - - if (javax.swing.SwingUtilities.isRightMouseButton(e)) + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + + if (e.isPopupTrigger()) // Mac reports this in mousePressed { - 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()); + showPopupMenu(e, pos); + return; + } + /* + * defer right-mouse click handling to mouseReleased on Windows + * (where isPopupTrigger() will answer true) + * NB isRightMouseButton is also true for Cmd-click on Mac + */ + if (Platform.isWinRightButton(e)) + { return; } if ((av.getSelectionGroup() == null) - || ((!e.isControlDown() && !e.isShiftDown()) && av - .getSelectionGroup() != null)) + || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() + && av.getSelectionGroup() != null)) { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); @@ -329,36 +409,91 @@ public class IdPanel extends JPanel implements MouseListener, if (e.isShiftDown() && (lastid != -1)) { - selectSeqs(lastid, seq); + selectSeqs(lastid, pos.seqIndex); } else { - selectSeq(seq); + selectSeq(pos.seqIndex); } - alignPanel.paintAlignment(true); + + av.isSelectionGroupChanged(true); + + alignPanel.paintAlignment(false, false); } /** - * DOCUMENT ME! + * Build and show the popup-menu at the right-click mouse position + * + * @param e + */ + void showPopupMenu(MouseEvent e, MousePos pos) + { + if (pos.isOverAnnotation()) + { + showAnnotationMenu(e, pos); + return; + } + + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex); + if (sq != null) + { + PopupMenu pop = new PopupMenu(alignPanel, sq, + Preferences.getGroupURLLinks()); + pop.show(this, e.getX(), e.getY()); + } + } + + /** + * On right mouse click on a Consensus annotation label, shows a limited popup + * menu, with options to configure the consensus calculation and rendering. + * + * @param e + * @param pos + * @see AnnotationLabels#showPopupMenu(MouseEvent) + */ + void showAnnotationMenu(MouseEvent e, MousePos pos) + { + if (pos.annotationIndex == -1) + { + return; + } + AlignmentAnnotation[] anns = this.av.getAlignment() + .getAlignmentAnnotation(); + if (anns == null || pos.annotationIndex >= anns.length) + { + return; + } + AlignmentAnnotation ann = anns[pos.annotationIndex]; + if (!ann.label.contains("Consensus")) + { + return; + } + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop); + pop.show(this, e.getX(), e.getY()); + } + + /** + * Toggle whether the sequence is part of the current selection group. * * @param seq - * DOCUMENT ME! */ void selectSeq(int seq) { lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** - * 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) { @@ -384,42 +519,48 @@ public class IdPanel extends JPanel implements MouseListener, for (int i = start; i <= end; i++) { - av.getSelectionGroup().addSequence( - av.getAlignment().getSequenceAt(i), i == end); + av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), + false); } } /** - * 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) { if (scrollThread != null) { - scrollThread.running = false; + stopScrolling(); } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); // always send selection message when mouse is released av.sendSelection(); + + if (e.isPopupTrigger()) // Windows reports this in mouseReleased + { + showPopupMenu(e, pos); + } } /** - * 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) + if (list == null || list.isEmpty()) { return; } @@ -427,30 +568,58 @@ public class IdPanel extends JPanel implements MouseListener, int index = av.getAlignment().findIndex(list.get(0)); // do we need to scroll the panel? - if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) + if ((av.getRanges().getStartSeq() > index) + || (av.getRanges().getEndSeq() < index)) { - alignPanel.setScrollValues(av.getStartRes(), index); + av.getRanges().setStartSeq(index); } } - // this class allows scrolling off the bottom of the visible alignment + public IdCanvas getIdCanvas() + { + return idCanvas; + } + + public void setIdCanvas(IdCanvas idCanvas) + { + this.idCanvas = idCanvas; + } + + /** + * Performs scrolling of the visible alignment up or down, adding newly + * visible sequences to the current selection + */ class ScrollThread extends Thread { - boolean running = false; + private boolean running = false; - boolean up = true; + private boolean up; + /** + * Constructor for a thread that scrolls either up or down + * + * @param up + */ public ScrollThread(boolean up) { this.up = up; - start(); + setName("IdPanel$ScrollThread$" + String.valueOf(up)); } + /** + * Sets a flag to stop the scrolling + */ public void stopScrolling() { running = false; } + /** + * Scrolls the alignment either up or down, one row at a time, adding newly + * visible sequences to the current selection. Speed is limited to a maximum + * of ten rows per second. The thread exits when the end of the alignment is + * reached or a flag is set to stop it by a call to stopScrolling. + */ @Override public void run() { @@ -458,34 +627,7 @@ public class IdPanel extends JPanel implements MouseListener, 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); - + running = scrollOnce(); try { Thread.sleep(100); @@ -493,6 +635,27 @@ public class IdPanel extends JPanel implements MouseListener, { } } + IdPanel.this.scrollThread = null; + } + + /** + * Scrolls one row up or down. Answers true if a scroll could be done, false + * if not (top or bottom of alignment reached). + */ + boolean scrollOnce() + { + ViewportRanges ranges = IdPanel.this.av.getRanges(); + if (ranges.scrollUp(up)) + { + int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq(); + int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1; + IdPanel.this.selectSeqs(fromSeq, toSeq); + lastid = toSeq; + alignPanel.paintAlignment(false, false); + return true; + } + + return false; } } }