X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=3ce9d4d8ac97de97188d1335ad97fb4325662e4f;hb=5a631296dd1dcc1df7b50487a647c27333696c74;hp=f0aefb1438fc998ff375e38abc873b7797f864dc;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index f0aefb1..3ce9d4d 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,15 +20,6 @@ */ package jalview.gui; -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.Platform; -import jalview.viewmodel.AlignmentViewport; - import java.awt.BorderLayout; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; @@ -38,9 +29,21 @@ import java.awt.event.MouseWheelListener; import java.util.List; import javax.swing.JPanel; +import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; 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. @@ -59,8 +62,6 @@ public class IdPanel extends JPanel ScrollThread scrollThread = null; - String linkImageURL; - int offy; // int width; @@ -81,8 +82,7 @@ public class IdPanel extends JPanel this.av = av; alignPanel = parent; setIdCanvas(new IdCanvas(av)); - linkImageURL = getClass().getResource("/images/link.gif").toString(); - seqAnnotReport = new SequenceAnnotationReport(linkImageURL); + seqAnnotReport = new SequenceAnnotationReport(true); setLayout(new BorderLayout()); add(getIdCanvas(), BorderLayout.CENTER); addMouseListener(this); @@ -92,26 +92,46 @@ public class IdPanel extends JPanel } /** - * 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); - 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())); + 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()); + } } } @@ -126,7 +146,14 @@ public class IdPanel extends JPanel { 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) { @@ -138,7 +165,7 @@ public class IdPanel extends JPanel } lastid = seq; - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); } /** @@ -148,24 +175,25 @@ public class IdPanel extends JPanel public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { if (e.isShiftDown()) { av.getRanges().scrollRight(true); } - else if (!av.getWrapAlignment()) + else { av.getRanges().scrollUp(false); } } - else + else if (wheelRotation < 0) { if (e.isShiftDown()) { av.getRanges().scrollRight(false); } - else if (!av.getWrapAlignment()) + else { av.getRanges().scrollUp(true); } @@ -196,7 +224,13 @@ public class IdPanel extends JPanel return; } - int seq = alignPanel.getSeqPanel().findSeq(e); + 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); @@ -224,7 +258,7 @@ public class IdPanel extends JPanel { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.stopScrolling(); } } @@ -276,9 +310,11 @@ public class IdPanel extends JPanel return; } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + if (e.isPopupTrigger()) // Mac reports this in mousePressed { - showPopupMenu(e); + showPopupMenu(e, pos); return; } @@ -301,19 +337,18 @@ public class IdPanel extends JPanel 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(false); + alignPanel.paintAlignment(false, false); } /** @@ -321,30 +356,52 @@ public class IdPanel extends JPanel * * @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); + if (pos.isOverAnnotation()) + { + showAnnotationMenu(e, pos); + return; + } - /* - * 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) + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex); + if (sq != null) { - if (sf.links != null) - { - for (String link : sf.links) - { - nlinks.add(link); - } - } + PopupMenu pop = new PopupMenu(alignPanel, sq, + Preferences.getGroupURLLinks()); + pop.show(this, e.getX(), e.getY()); } + } - PopupMenu pop = new PopupMenu(alignPanel, sq, features, - Preferences.getGroupURLLinks()); + /** + * 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()); } @@ -358,7 +415,7 @@ public class IdPanel extends JPanel lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** @@ -393,7 +450,7 @@ public class IdPanel extends JPanel for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), - i == end); + false); } } @@ -408,8 +465,9 @@ public class IdPanel extends JPanel { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.stopScrolling(); } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -418,7 +476,7 @@ public class IdPanel extends JPanel if (e.isPopupTrigger()) // Windows reports this in mouseReleased { - showPopupMenu(e); + showPopupMenu(e, pos); } } @@ -432,7 +490,7 @@ public class IdPanel extends JPanel { getIdCanvas().setHighlighted(list); - if (list == null) + if (list == null || list.isEmpty()) { return; } @@ -457,24 +515,42 @@ public class IdPanel extends JPanel this.idCanvas = idCanvas; } - // this class allows scrolling off the bottom of the visible alignment + /** + * 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; + setName("IdPanel$ScrollThread$" + String.valueOf(up)); start(); } + /** + * 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. + */ @Override public void run() { @@ -482,33 +558,24 @@ public class IdPanel extends JPanel while (running) { - if (av.getRanges().scrollUp(up)) + ViewportRanges ranges = IdPanel.this.av.getRanges(); + if (ranges.scrollUp(up)) { - // scroll was ok, so add new sequence to selection - int seq = av.getRanges().getStartSeq(); - - if (!up) - { - seq = av.getRanges().getEndSeq(); - } - - if (seq < lastid) - { - selectSeqs(lastid - 1, seq); - } - else if (seq > lastid) - { - selectSeqs(lastid + 1, seq); - } - - lastid = seq; + int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq(); + int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1; + IdPanel.this.selectSeqs(fromSeq, toSeq); + + lastid = toSeq; } else { + /* + * scroll did nothing - reached limit of visible alignment + */ running = false; } - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); try {