X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=7b491e47e59ec10f8abdb2e39764bc66dff6bcb0;hb=7f3e371b7fbae94e9b731956cbdebc866742c692;hp=5db5e2e97ddafb9850dab16236862b62f13c6169;hpb=635fa3269e8ebfbbe3fca3fa535e5d7f22649174;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 5db5e2e..7b491e4 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,245 +1,657 @@ -package jalview.gui; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; - -import javax.swing.*; - -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; - - 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); - } - - public void mouseMoved(MouseEvent e) {} - - - public void mouseDragged(MouseEvent e) { - mouseDragging = true; - - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - int seq = av.getIndex(y); - - if(seq<0) - return; - - if (seq < lastid) - selectSeqs(lastid - 1, seq); - else if (seq > lastid) - selectSeqs(lastid + 1, seq); - - lastid = seq; - alignPanel.repaint(); - } - - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() == 2) - { - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - - int seq = av.getIndex(y); - String id = av.getAlignment().getSequenceAt(seq).getName(); - - try{ - jalview.util.BrowserLauncher.openURL( - "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id + - "]+-vn+2"); - }catch(Exception ex){System.err.println( - "Try adding the jalview.browser property to your jalview.properties file:\n" - +"jalview.browser=firefox"); ex.printStackTrace();} - } - - } - public void mouseEntered(MouseEvent e) - { - if(scrollThread!=null) - scrollThread.running = false; - } - - 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); - } - } - - - public void mousePressed(MouseEvent e) { - if (e.getClickCount() == 2) - return; - - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - - int seq = av.getIndex(y); - if (seq == -1) - return; - - if (javax.swing.SwingUtilities.isRightMouseButton(e)) - { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, - (Sequence)av.getAlignment().getSequenceAt(seq)); - pop.show(this, e.getX(), y); - return; - } - - if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null) - { - - SequenceGroup selection = new SequenceGroup(); - SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq)); - selection.setStartRes(0); - selection.setEndRes(av.alignment.getWidth()-1); - for (int i =0; i< sg.getSize(); i++) - selection.addSequence(sg.getSequenceAt(i)); - - av.setSelectionGroup(selection); - return; - } - - if(av.getSelectionGroup()==null || ( !e.isControlDown() && 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(); - } - - void selectSeq(int seq) - { - lastid = seq; - SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq); - } - - void selectSeqs(int start, int end) { - - 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)); - - } - - - public void mouseReleased(MouseEvent e) - { - if(scrollThread!=null) - scrollThread.running = false; - - mouseDragging = false; - PaintRefresher.Refresh(this); - } - - 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() 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 ($$Version-Rel$$) + * 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 + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +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 javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; +import javax.swing.Timer; +import javax.swing.ToolTipManager; + +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; + +/** + * 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 +{ + private IdCanvas idCanvas; + + protected AlignmentViewport av; + + protected AlignmentPanel alignPanel; + + ScrollThread scrollThread = null; + + int offy; + + // int width; + int lastid = -1; + + boolean mouseDragging = false; + + private final SequenceAnnotationReport seqAnnotReport; + + /** + * Creates a new IdPanel object. + * + * @param av + * @param parent + */ + public IdPanel(AlignViewport av, AlignmentPanel parent) + { + this.av = av; + alignPanel = parent; + setIdCanvas(new IdCanvas(av)); + seqAnnotReport = new SequenceAnnotationReport(true); + setLayout(new BorderLayout()); + add(getIdCanvas(), BorderLayout.CENTER); + addMouseListener(this); + addMouseMotionListener(this); + addMouseWheelListener(this); + ToolTipManager.sharedInstance().registerComponent(this); + } + + /** + * 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 + */ + @Override + public void mouseMoved(MouseEvent e) + { + 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()); + } + } + } + + /** + * Responds to a mouse drag by selecting the sequences under the dragged + * region. + * + * @param e + */ + @Override + public void mouseDragged(MouseEvent e) + { + mouseDragging = true; + + 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) + { + selectSeqs(lastid - 1, seq); + } + else if (seq > lastid) + { + selectSeqs(lastid + 1, seq); + } + + lastid = seq; + alignPanel.paintAlignment(false, false); + } + + /** + * Response to the mouse wheel by scrolling the alignment panel. + */ + @Override + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) + { + if (e.isShiftDown()) + { + av.getRanges().scrollRight(true); + } + else + { + av.getRanges().scrollUp(false); + } + } + else if (wheelRotation < 0) + { + if (e.isShiftDown()) + { + av.getRanges().scrollRight(false); + } + else + { + av.getRanges().scrollUp(true); + } + } + } + + /** + * 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 + */ + @Override + public void mouseClicked(MouseEvent e) + { + /* + * 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; + } + + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + int seq = pos.seqIndex; + if (pos.isOverAnnotation() || seq < 0) + { + return; + } + + String id = av.getAlignment().getSequenceAt(seq).getName(); + String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); + + try + { + jalview.util.BrowserLauncher.openURL(url); + } catch (Exception ex) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JvOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + } + + /** + * On (re-)entering the panel, stop any scrolling + * + * @param e + */ + @Override + public void mouseEntered(MouseEvent e) + { + stopScrolling(); + } + + /** + * Interrupts the scroll thread if one is running + */ + void stopScrolling() + { + if (scrollThread != null) + { + scrollThread.stopScrolling(); + scrollThread = null; + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void mouseExited(MouseEvent e) + { + if (av.getWrapAlignment()) + { + return; + } + + if (mouseDragging) + { + /* + * 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); + } + } + } + + /** + * Starts scrolling either up or down + * + * @param up + */ + void startScrolling(boolean up) + { + scrollThread = new ScrollThread(up); + if (Platform.isJS()) + { + /* + * 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(); + } + } + + /** + * 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 + */ + @Override + public void mousePressed(MouseEvent e) + { + if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e)) + { + return; + } + + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + + if (e.isPopupTrigger()) // Mac reports this in mousePressed + { + 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) + || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() + && av.getSelectionGroup() != null)) + { + av.setSelectionGroup(new SequenceGroup()); + av.getSelectionGroup().setStartRes(0); + av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); + } + + if (e.isShiftDown() && (lastid != -1)) + { + selectSeqs(lastid, pos.seqIndex); + } + else + { + selectSeq(pos.seqIndex); + } + + av.isSelectionGroupChanged(true); + + alignPanel.paintAlignment(false, false); + } + + /** + * 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 + */ + void selectSeq(int seq) + { + lastid = seq; + + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); + av.getSelectionGroup().addOrRemove(pickedSeq, false); + } + + /** + * Add contiguous rows of the alignment to the current selection group. Does + * nothing if there is no selection group. + * + * @param start + * @param end + */ + 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), + false); + } + } + + /** + * Respond to mouse released. Refreshes the display and triggers broadcast of + * the new selection group to any listeners. + * + * @param e + */ + @Override + public void mouseReleased(MouseEvent e) + { + if (scrollThread != null) + { + 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); + } + } + + /** + * Highlight sequence ids that match the given list, and if necessary scroll + * to the start sequence of the list. + * + * @param list + */ + public void highlightSearchResults(List list) + { + getIdCanvas().setHighlighted(list); + + if (list == null || list.isEmpty()) + { + return; + } + + int index = av.getAlignment().findIndex(list.get(0)); + + // do we need to scroll the panel? + if ((av.getRanges().getStartSeq() > index) + || (av.getRanges().getEndSeq() < index)) + { + av.getRanges().setStartSeq(index); + } + } + + 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 + { + private boolean running = false; + + private boolean up; + + /** + * Constructor for a thread that scrolls either up or down + * + * @param up + */ + public ScrollThread(boolean up) + { + this.up = up; + 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() + { + running = true; + + while (running) + { + running = scrollOnce(); + try + { + Thread.sleep(100); + } catch (Exception ex) + { + } + } + 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; + } + } +}