X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=f0aefb1438fc998ff375e38abc873b7797f864dc;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=7f2e6695e2ffb57662c76ee46489f3adc4cbcdab;hpb=3ab93880136a581ebf1e50e38e780c2b2141bca9;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 7f2e669..f0aefb1 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * 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. * @@ -25,7 +25,9 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; -import jalview.util.UrlLink; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.event.MouseEvent; @@ -34,9 +36,7 @@ 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.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -48,12 +48,12 @@ import javax.swing.ToolTipManager; * @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; @@ -80,11 +80,11 @@ public class IdPanel extends JPanel implements MouseListener, { 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); @@ -101,18 +101,17 @@ public class IdPanel extends JPanel implements MouseListener, @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(64); - seqAnnotReport - .createSequenceAnnotationReport(tip, sequence, - av.isShowDbRefs(), av.isShowNpFeats(), - sp.seqCanvas.fr.minmax); - setToolTipText("" + sequence.getDisplayId(true) + " " - + tip.toString() + ""); + StringBuilder tip = new StringBuilder(64); + seqAnnotReport.createTooltipAnnotationReport(tip, sequence, + av.isShowDBRefs(), av.isShowNPFeats(), + sp.seqCanvas.fr.getMinMax()); + setToolTipText(JvSwingUtils.wrapTooltip(true, + sequence.getDisplayId(true) + " " + tip.toString())); } } @@ -127,7 +126,7 @@ public class IdPanel extends JPanel implements MouseListener, { mouseDragging = true; - int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); + int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e)); if (seq < lastid) { @@ -139,7 +138,7 @@ public class IdPanel extends JPanel implements MouseListener, } lastid = seq; - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false); } /** @@ -153,22 +152,22 @@ public class IdPanel extends JPanel implements MouseListener, { if (e.isShiftDown()) { - alignPanel.scrollRight(true); + av.getRanges().scrollRight(true); } - else + else if (!av.getWrapAlignment()) { - alignPanel.scrollUp(false); + av.getRanges().scrollUp(false); } } else { if (e.isShiftDown()) { - alignPanel.scrollRight(false); + av.getRanges().scrollRight(false); } - else + else if (!av.getWrapAlignment()) { - alignPanel.scrollUp(true); + av.getRanges().scrollUp(true); } } } @@ -192,63 +191,24 @@ public class IdPanel extends JPanel implements MouseListener, */ 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; } - Vector links = Preferences.sequenceURLLinks; - if (links == null || links.size() < 1) - { - return; - } - - int seq = alignPanel.seqPanel.findSeq(e); - String url = null; - int i = 0; + int seq = alignPanel.getSeqPanel().findSeq(e); 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.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } @@ -282,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener, return; } - if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging && (e.getY() < 0) + && (av.getRanges().getStartSeq() > 0)) { scrollThread = new ScrollThread(true); } if (mouseDragging && (e.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getRanges().getEndSeq())) { scrollThread = new ScrollThread(false); } @@ -315,46 +276,32 @@ public class IdPanel extends JPanel implements MouseListener, return; } - int seq = alignPanel.seqPanel.findSeq(e); - - if (SwingUtilities.isRightMouseButton(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); + 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 (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac()) + { 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); av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); } + int seq = alignPanel.getSeqPanel().findSeq(e); if (e.isShiftDown() && (lastid != -1)) { selectSeqs(lastid, seq); @@ -363,7 +310,42 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeq(seq); } - alignPanel.paintAlignment(true); + + av.isSelectionGroupChanged(true); + + alignPanel.paintAlignment(false); + } + + /** + * Build and show the popup-menu at the right-click mouse position + * + * @param e + */ + void showPopupMenu(MouseEvent e) + { + int seq2 = alignPanel.getSeqPanel().findSeq(e); + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2); + + /* + * build a new links menu based on the current links + * and any non-positional features + */ + List nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + List features = sq.getFeatures().getNonPositionalFeatures(); + for (SequenceFeature sf : features) + { + if (sf.links != null) + { + for (String link : sf.links) + { + nlinks.add(link); + } + } + } + + PopupMenu pop = new PopupMenu(alignPanel, sq, features, + Preferences.getGroupURLLinks()); + pop.show(this, e.getX(), e.getY()); } /** @@ -410,8 +392,8 @@ 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), + i == end); } } @@ -433,6 +415,11 @@ public class IdPanel extends JPanel implements MouseListener, 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); + } } /** @@ -443,7 +430,7 @@ public class IdPanel extends JPanel implements MouseListener, */ public void highlightSearchResults(List list) { - idCanvas.setHighlighted(list); + getIdCanvas().setHighlighted(list); if (list == null) { @@ -453,12 +440,23 @@ 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); } } + 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 { @@ -484,14 +482,14 @@ public class IdPanel extends JPanel implements MouseListener, while (running) { - if (alignPanel.scrollUp(up)) + if (av.getRanges().scrollUp(up)) { // scroll was ok, so add new sequence to selection - int seq = av.getStartSeq(); + int seq = av.getRanges().getStartSeq(); if (!up) { - seq = av.getEndSeq(); + seq = av.getRanges().getEndSeq(); } if (seq < lastid)