X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=fdca7237f78d2ad8de05ff8112566005417776a4;hb=31714b90648bba773f68736b8c1700ae53805eee;hp=54aeef2284852fbc345669dd21bac7b6ac01d0ed;hpb=620da661f54acba8fdb13f388dbed8b77d9113ed;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 54aeef2..fdca723 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,18 +20,9 @@ */ 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.viewmodel.AlignmentViewport; - 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; @@ -40,9 +31,25 @@ 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; +import jalview.viewmodel.seqfeatures.IdColumn; +import jalview.viewmodel.seqfeatures.IdColumns; +import jalview.viewmodel.seqfeatures.IdColumns.ColumnCell; + /** * 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. @@ -61,8 +68,6 @@ public class IdPanel extends JPanel ScrollThread scrollThread = null; - String linkImageURL; - int offy; // int width; @@ -83,8 +88,7 @@ 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); @@ -94,11 +98,10 @@ 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) @@ -110,9 +113,12 @@ public class IdPanel extends JPanel /* * mouse is over an annotation label in wrapped mode */ - AlignmentAnnotation annotation = av.getAlignment() - .getAlignmentAnnotation()[pos.annotationIndex]; + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation annotation = anns[pos.annotationIndex]; setToolTipText(AnnotationLabels.getTooltip(annotation)); + alignPanel.alignFrame.setStatus( + AnnotationLabels.getStatusMessage(annotation, anns)); } else { @@ -121,14 +127,62 @@ public class IdPanel extends JPanel { SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuilder tip = new StringBuilder(64); - seqAnnotReport.createTooltipAnnotationReport(tip, sequence, - av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); - setToolTipText(JvSwingUtils.wrapTooltip(true, - sequence.getDisplayId(true) + " " + tip.toString())); + tip.append(sequence.getDisplayId(true)).append(" "); + IdColumn col = locateColumnFor(e); + if (col != null) + { + // tooltip for column + tip.append(getTooltipFor(col, sequence)); + } + else + { + 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()); } } } + private Object getTooltipFor(IdColumn col, SequenceI seq) + { + ColumnCell cell = av.getIdColumns().getCellFor(seq, col); + if (cell != null) + { + return "" + col.getLabel() + ": " + cell.label; + } + return ""; + } + + private IdColumn locateColumnFor(MouseEvent e) + { + // TODO COMBINE SAME CODE IN IDCANVAS!!! + + IdColumns id_cols = av.getIdColumns(); + List visible = id_cols.getVisible(); + /** + * width of an idColumn + */ + int colWid = 20; + int panelWidth = Math.max(idCanvas.getWidth() / 2, + idCanvas.getWidth() - (colWid * visible.size())); + int p = 0; + while (panelWidth < idCanvas.getWidth() && p < visible.size()) + { + + if (e.getX() >= panelWidth && e.getX() < panelWidth + colWid) + return visible.get(p); + p++; + panelWidth += colWid; + } + return null; + } + /** * Responds to a mouse drag by selecting the sequences under the dragged * region. @@ -219,13 +273,12 @@ public class IdPanel extends JPanel } MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.isOverAnnotation()) + int seq = pos.seqIndex; + if (pos.isOverAnnotation() || seq < 0) { - // mouse is over annotation label in wrapped mode return; } - int seq = pos.seqIndex; String id = av.getAlignment().getSequenceAt(seq).getName(); String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); @@ -243,17 +296,25 @@ public class IdPanel extends JPanel } /** - * 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; } } @@ -271,16 +332,72 @@ public class IdPanel extends JPanel return; } - if (mouseDragging && (e.getY() < 0) - && (av.getRanges().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.getRanges().getEndSeq())) + /** + * 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 = new ScrollThread(false); + scrollThread.start(); } } @@ -306,12 +423,7 @@ public class IdPanel extends JPanel } MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.isOverAnnotation()) - { - // mouse is over an annotation label in wrapped mode - return; - } - + if (e.isPopupTrigger()) // Mac reports this in mousePressed { showPopupMenu(e, pos); @@ -323,7 +435,7 @@ public class IdPanel extends JPanel * (where isPopupTrigger() will answer true) * NB isRightMouseButton is also true for Cmd-click on Mac */ - if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac()) + if (Platform.isWinRightButton(e)) { return; } @@ -358,24 +470,50 @@ public class IdPanel extends JPanel */ 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()); + } + } - /* - * 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) + /** + * 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) { - if (sf.links != null) - { - nlinks.addAll(sf.links); - } + 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; } - PopupMenu pop = new PopupMenu(alignPanel, sq, features, - Preferences.getGroupURLLinks()); + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop); pop.show(this, e.getX(), e.getY()); } @@ -389,7 +527,7 @@ public class IdPanel extends JPanel lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** @@ -424,7 +562,7 @@ public class IdPanel extends JPanel for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), - i == end); + false); } } @@ -439,14 +577,9 @@ public class IdPanel extends JPanel { if (scrollThread != null) { - scrollThread.running = false; + stopScrolling(); } MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.isOverAnnotation()) - { - // mouse is over an annotation label in wrapped mode - return; - } mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -469,7 +602,7 @@ public class IdPanel extends JPanel { getIdCanvas().setHighlighted(list); - if (list == null) + if (list == null || list.isEmpty()) { return; } @@ -494,24 +627,41 @@ 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; - 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() { @@ -519,34 +669,7 @@ public class IdPanel extends JPanel while (running) { - if (av.getRanges().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; - } - else - { - running = false; - } - - alignPanel.paintAlignment(false, false); - + running = scrollOnce(); try { Thread.sleep(100); @@ -554,6 +677,27 @@ public class IdPanel extends JPanel { } } + 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; } } }