X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=1fd9e492dd7fa30acd753ed3420a41be44b21d52;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=a65be7b1175dc42fc2920699ab96b43e73c0d773;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index a65be7b..1fd9e49 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,14 +20,15 @@ */ package jalview.gui; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; 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.util.UrlLink; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; @@ -37,10 +38,9 @@ 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.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -51,8 +51,8 @@ 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 { private IdCanvas idCanvas; @@ -95,26 +95,46 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * Respond to mouse movement by constructing tooltip text for the sequence id - * under the mouse. + * 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.getSeqPanel(); - int seq = Math.max(0, sp.findSeq(e)); - if (seq > -1 && seq < av.getAlignment().getHeight()) + 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 { - SequenceI sequence = av.getAlignment().getSequenceAt(seq); - StringBuffer tip = new StringBuffer(64); - seqAnnotReport.createSequenceAnnotationReport(tip, sequence, - av.isShowDBRefs(), av.isShowNPFeats(), - sp.seqCanvas.fr.getMinMax()); - setToolTipText(JvSwingUtils.wrapTooltip(true, - sequence.getDisplayId(true) + " " + tip.toString())); + 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()); + } } } @@ -129,7 +149,14 @@ public class IdPanel extends JPanel implements MouseListener, { mouseDragging = true; - int seq = Math.max(0, alignPanel.getSeqPanel().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) { @@ -141,7 +168,7 @@ public class IdPanel extends JPanel implements MouseListener, } lastid = seq; - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -151,26 +178,27 @@ public class IdPanel extends JPanel implements MouseListener, 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); } } } @@ -199,58 +227,25 @@ public class IdPanel extends JPanel implements MouseListener, return; } - 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.getSeqPanel().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, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } @@ -284,13 +279,14 @@ 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); } @@ -317,9 +313,11 @@ public class IdPanel extends JPanel implements MouseListener, return; } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + if (e.isPopupTrigger()) // Mac reports this in mousePressed { - showPopupMenu(e); + showPopupMenu(e, pos); return; } @@ -334,27 +332,26 @@ public class IdPanel extends JPanel implements MouseListener, } if ((av.getSelectionGroup() == null) - || (!jalview.util.Platform.isControlDown(e) && !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); + selectSeqs(lastid, pos.seqIndex); } else { - selectSeq(seq); + selectSeq(pos.seqIndex); } av.isSelectionGroupChanged(true); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -362,37 +359,72 @@ public class IdPanel extends JPanel implements MouseListener, * * @param e */ - void showPopupMenu(MouseEvent e) + void showPopupMenu(MouseEvent e, MousePos pos) { - int seq2 = alignPanel.getSeqPanel().findSeq(e); - Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2); - // build a new links menu based on the current links + any non-positional - // features - Vector nlinks = new Vector(Preferences.sequenceURLLinks); - SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures(); - if (sfs != null) - { - for (SequenceFeature sf : sfs) + if (pos.isOverAnnotation()) + { + showAnnotationMenu(e, pos); + return; + } + + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex); + + /* + * build a new links menu based on the current links + * and any non-positional features + */ + List features = null; + if (sq != null) + { + List nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + features = sq.getFeatures().getNonPositionalFeatures(); + for (SequenceFeature sf : features) + { + if (sf.links != null) { - if (sf.begin == sf.end && sf.begin == 0) - { - if (sf.links != null && sf.links.size() > 0) - { - for (int l = 0, lSize = sf.links.size(); l < lSize; l++) - { - nlinks.addElement(sf.links.elementAt(l)); - } - } - } + nlinks.addAll(sf.links); } } + } - PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks, + PopupMenu pop = new PopupMenu(alignPanel, sq, features, 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 @@ -402,7 +434,7 @@ public class IdPanel extends JPanel implements MouseListener, lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** @@ -436,8 +468,8 @@ 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), + false); } } @@ -454,6 +486,7 @@ public class IdPanel extends JPanel implements MouseListener, { scrollThread.running = false; } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -462,7 +495,7 @@ public class IdPanel extends JPanel implements MouseListener, if (e.isPopupTrigger()) // Windows reports this in mouseReleased { - showPopupMenu(e); + showPopupMenu(e, pos); } } @@ -484,9 +517,10 @@ 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); } } @@ -525,14 +559,14 @@ 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) @@ -551,7 +585,7 @@ public class IdPanel extends JPanel implements MouseListener, running = false; } - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); try {