X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=8a49092db31eaf9e943868b9f0f80a01333df189;hb=00816d26e65bf0c98538773087a8c7519aea672e;hp=1176df5583060aca696178a2dbdf6e45b0ac6f39;hpb=dc2734d988e10f3e76dda02d9913b611f6713552;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 1176df5..8a49092 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,6 +20,29 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Point; +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.ArrayList; +import java.util.Collections; +import java.util.List; + +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JToolTip; +import javax.swing.SwingUtilities; +import javax.swing.Timer; +import javax.swing.ToolTipManager; + import jalview.api.AlignViewportI; import jalview.bin.Cache; import jalview.commands.EditCommand; @@ -29,6 +52,7 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -50,23 +74,7 @@ import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; - -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Point; -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.Collections; -import java.util.List; - -import javax.swing.JPanel; -import javax.swing.SwingUtilities; -import javax.swing.ToolTipManager; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; /** * DOCUMENT ME! @@ -204,13 +212,21 @@ public class SeqPanel extends JPanel StringBuffer keyboardNo2; - java.net.URL linkImageURL; - private final SequenceAnnotationReport seqARep; - StringBuilder tooltipText = new StringBuilder(); + /* + * the last tooltip on mousing over the alignment (or annotation in wrapped mode) + * - the tooltip is not set again if unchanged + * - this is the tooltip text _before_ formatting as html + */ + private String lastTooltip; - String tmpString; + /* + * the last tooltip on mousing over the alignment (or annotation in wrapped mode) + * - used to decide where to place the tooltip in getTooltipLocation() + * - this is the tooltip text _after_ formatting as html + */ + private String lastFormattedTooltip; EditCommand editCommand; @@ -226,11 +242,12 @@ public class SeqPanel extends JPanel */ public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { - linkImageURL = getClass().getResource("/images/link.gif"); - seqARep = new SequenceAnnotationReport(linkImageURL.toString()); + seqARep = new SequenceAnnotationReport(true); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); + + this.av = viewport; setBackground(Color.white); @@ -832,11 +849,11 @@ public class SeqPanel extends JPanel * the start of the highlighted region. */ @Override - public void highlightSequence(SearchResultsI results) + public String highlightSequence(SearchResultsI results) { if (results == null || results.equals(lastSearchResults)) { - return; + return null; } lastSearchResults = results; @@ -857,11 +874,82 @@ public class SeqPanel extends JPanel ap.setToScrollComplementPanel(true); } - boolean noFastPaint = wasScrolled && av.getWrapAlignment(); - if (seqCanvas.highlightSearchResults(results, noFastPaint)) + boolean fastPaint = !(wasScrolled && av.getWrapAlignment()); + if (seqCanvas.highlightSearchResults(results, fastPaint)) { setStatusMessage(results); } + return results.isEmpty() ? null : getHighlightInfo(results); + } + + /** + * temporary hack: answers a message suitable to show on structure hover + * label. This is normally null. It is a peptide variation description if + * + * in which case the answer is of the format (e.g.) "p.Glu388Asp" + * + * @param results + * @return + */ + private String getHighlightInfo(SearchResultsI results) + { + /* + * ideally, just find mapped CDS (as we don't care about render style here); + * for now, go via split frame complement's FeatureRenderer + */ + AlignViewportI complement = ap.getAlignViewport().getCodingComplement(); + if (complement == null) + { + return null; + } + AlignFrame af = Desktop.getAlignFrameFor(complement); + FeatureRendererModel fr2 = af.getFeatureRenderer(); + + int j = results.getSize(); + List infos = new ArrayList<>(); + for (int i = 0; i < j; i++) + { + SearchResultMatchI match = results.getResults().get(i); + int pos = match.getStart(); + if (pos == match.getEnd()) + { + SequenceI seq = match.getSequence(); + SequenceI ds = seq.getDatasetSequence() == null ? seq + : seq.getDatasetSequence(); + MappedFeatures mf = fr2 + .findComplementFeaturesAtResidue(ds, pos); + if (mf != null) + { + for (SequenceFeature sf : mf.features) + { + String pv = mf.findProteinVariants(sf); + if (pv.length() > 0 && !infos.contains(pv)) + { + infos.add(pv); + } + } + } + } + } + + if (infos.isEmpty()) + { + return null; + } + StringBuilder sb = new StringBuilder(); + for (String info : infos) + { + if (sb.length() > 0) + { + sb.append("|"); + } + sb.append(info); + } + return sb.toString(); } @Override @@ -901,8 +989,10 @@ public class SeqPanel extends JPanel /* * just a pixel move without change of 'cell' */ + moveTooltip = false; return; } + moveTooltip = true; lastMousePosition = mousePos; if (mousePos.isOverAnnotation()) @@ -918,6 +1008,7 @@ public class SeqPanel extends JPanel lastMousePosition = null; setToolTipText(null); lastTooltip = null; + lastFormattedTooltip = null; ap.alignFrame.setStatus(""); return; } @@ -939,7 +1030,7 @@ public class SeqPanel extends JPanel mouseOverSequence(sequence, column, pos); } - tooltipText.setLength(6); // Cuts the buffer back to + StringBuilder tooltipText = new StringBuilder(64); SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) @@ -968,32 +1059,63 @@ public class SeqPanel extends JPanel * add features that straddle the gap (pos may be the residue before or * after the gap) */ + int unshownFeatures = 0; if (av.isShowSequenceFeatures()) { List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - seqARep.appendFeatures(tooltipText, pos, features, - this.ap.getSeqPanel().seqCanvas.fr); + unshownFeatures = seqARep.appendFeatures(tooltipText, pos, + features, this.ap.getSeqPanel().seqCanvas.fr, + MAX_TOOLTIP_LENGTH); + + /* + * add features in CDS/protein complement at the corresponding + * position if configured to do so + */ + if (av.isShowComplementFeatures()) + { + if (!Comparison.isGap(sequence.getCharAt(column))) + { + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + AlignFrame af = Desktop.getAlignFrameFor(complement); + FeatureRendererModel fr2 = af.getFeatureRenderer(); + MappedFeatures mf = fr2.findComplementFeaturesAtResidue(sequence, + pos); + if (mf != null) + { + unshownFeatures += seqARep.appendFeatures(tooltipText, + pos, mf, fr2, MAX_TOOLTIP_LENGTH); + } + } + } } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 0) // nothing added { setToolTipText(null); lastTooltip = null; } else { - if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant + if (tooltipText.length() > MAX_TOOLTIP_LENGTH) { tooltipText.setLength(MAX_TOOLTIP_LENGTH); tooltipText.append("..."); } + if (unshownFeatures > 0) + { + tooltipText.append("
").append("... ").append("") + .append(MessageManager.formatMessage( + "label.features_not_shown", unshownFeatures)) + .append(""); + } String textString = tooltipText.toString(); - if (lastTooltip == null || !lastTooltip.equals(textString)) + if (!textString.equals(lastTooltip)) { - String formattedTooltipText = JvSwingUtils.wrapTooltip(true, - textString); - setToolTipText(formattedTooltipText); lastTooltip = textString; + lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, + textString); + setToolTipText(lastFormattedTooltip); } } } @@ -1019,15 +1141,35 @@ public class SeqPanel extends JPanel String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column, anns); - setToolTipText(tooltip); - lastTooltip = tooltip; + if (!tooltip.equals(lastTooltip)) + { + lastTooltip = tooltip; + lastFormattedTooltip = tooltip == null ? null + : JvSwingUtils.wrapTooltip(true, tooltip); + setToolTipText(lastFormattedTooltip); + } String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, anns[rowIndex]); ap.alignFrame.setStatus(msg); } - private Point lastp = null; + /* + * if Shift key is held down while moving the mouse, + * the tooltip location is not changed once shown + */ + private Point lastTooltipLocation = null; + + /* + * this flag is false for pixel moves within a residue, + * to reduce tooltip flicker + */ + private boolean moveTooltip = true; + + /* + * a dummy tooltip used to estimate where to position tooltips + */ + private JToolTip tempTip = new JLabel().createToolTip(); /* * (non-Javadoc) @@ -1037,29 +1179,31 @@ public class SeqPanel extends JPanel @Override public Point getToolTipLocation(MouseEvent event) { - if (tooltipText == null || tooltipText.length() <= 6) + // BH 2018 + + if (lastTooltip == null || !moveTooltip) { - lastp = null; return null; } - int x = event.getX(); - int w = getWidth(); - // switch sides when tooltip is too close to edge - int wdth = (w - x < 200) ? -(w / 2) : 5; - Point p = lastp; - if (!event.isShiftDown() || p == null) + if (lastTooltipLocation != null && event.isShiftDown()) { - p = new Point(event.getX() + wdth, event.getY() - 20); - lastp = p; + return lastTooltipLocation; } - /* - * TODO: try to set position so region is not obscured by tooltip - */ - return p; - } - String lastTooltip; + int x = event.getX(); + int y = event.getY(); + int w = getWidth(); + + tempTip.setTipText(lastFormattedTooltip); + int tipWidth = (int) tempTip.getPreferredSize().getWidth(); + + // was x += (w - x < 200) ? -(w / 2) : 5; + x = (x + tipWidth < w ? x + 10 : w - tipWidth); + Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20? + + return lastTooltipLocation = p; + } /** * set when the current UI interaction has resulted in a change that requires @@ -1097,7 +1241,7 @@ public class SeqPanel extends JPanel { char sequenceChar = sequence.getCharAt(column); int pos = sequence.findPosition(column); - setStatusMessage(sequence, seqIndex, sequenceChar, pos); + setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos); return pos; } @@ -1113,7 +1257,7 @@ public class SeqPanel extends JPanel * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2) * * - * @param sequence + * @param seqName * @param seqIndex * sequence position in the alignment (1..) * @param sequenceChar @@ -1121,7 +1265,7 @@ public class SeqPanel extends JPanel * @param residuePos * the sequence residue position (if not over a gap) */ - protected void setStatusMessage(SequenceI sequence, int seqIndex, + protected void setStatusMessage(String seqName, int seqIndex, char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); @@ -1131,7 +1275,7 @@ public class SeqPanel extends JPanel */ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") - .append(sequence.getName()); + .append(seqName); String residue = null; @@ -1176,7 +1320,8 @@ public class SeqPanel extends JPanel { return; } - SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + SequenceI alignedSeq = al.getSequenceAt(sequenceIndex); + SequenceI ds = alignedSeq.getDatasetSequence(); for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); @@ -1188,8 +1333,8 @@ public class SeqPanel extends JPanel if (seq == ds) { int start = m.getStart(); - setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), - start); + setStatusMessage(alignedSeq.getName(), sequenceIndex, + seq.getCharAt(start - 1), start); return; } } @@ -1935,7 +2080,7 @@ public class SeqPanel extends JPanel if (mouseDragging && scrollThread == null) { - scrollThread = new ScrollThread(); + startScrolling(e.getPoint()); } } @@ -1954,7 +2099,7 @@ public class SeqPanel extends JPanel return; } - if (evt.getClickCount() > 1) + if (evt.getClickCount() > 1 && av.isShowSequenceFeatures()) { sg = av.getSelectionGroup(); if (sg != null && sg.getSize() == 1 @@ -1981,17 +2126,13 @@ public class SeqPanel extends JPanel SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); - seqCanvas.highlightSearchResults(highlight, false); + seqCanvas.highlightSearchResults(highlight, true); /* - * open the Amend Features dialog; clear highlighting afterwards, - * whether changes were made or not + * open the Amend Features dialog */ - List seqs = Collections.singletonList(sequence); - seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, - ap); - av.setSearchResults(null); // clear highlighting - seqCanvas.repaint(); // draw new/amended features + new FeatureEditor(ap, Collections.singletonList(sequence), features, + false).showDialog(); } } } @@ -2073,22 +2214,22 @@ public class SeqPanel extends JPanel } } - if (evt.isPopupTrigger()) // Mac: mousePressed - { - showPopupMenu(evt, 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 (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac()) + if (Platform.isWinRightButton(evt)) { return; } + if (evt.isPopupTrigger()) // Mac: mousePressed + { + showPopupMenu(evt, pos); + return; + } + if (av.cursorMode) { seqCanvas.cursorX = res; @@ -2159,11 +2300,11 @@ public class SeqPanel extends JPanel final int column = pos.column; final int seq = pos.seqIndex; SequenceI sequence = av.getAlignment().getSequenceAt(seq); - List features = ap.getFeatureRenderer() - .findFeaturesAtColumn(sequence, column + 1); - - PopupMenu pop = new PopupMenu(ap, null, features); - pop.show(this, evt.getX(), evt.getY()); + if (sequence != null) + { + PopupMenu pop = new PopupMenu(ap, sequence, column); + pop.show(this, evt.getX(), evt.getY()); + } } /** @@ -2381,29 +2522,73 @@ public class SeqPanel extends JPanel /** * Starts a thread to scroll the alignment, towards a given mouse position - * outside the panel bounds + * outside the panel bounds, unless the alignment is in wrapped mode * * @param mousePos */ void startScrolling(Point mousePos) { - if (scrollThread == null) + /* + * set this.mouseDragging in case this was called from + * a drag in ScalePanel or AnnotationPanel + */ + mouseDragging = true; + if (!av.getWrapAlignment() && scrollThread == null) { scrollThread = new ScrollThread(); + scrollThread.setMousePosition(mousePos); + if (Platform.isJS()) + { + /* + * Javascript - run every 20ms until scrolling stopped + * or reaches the limit of scrollable alignment + */ + 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) + { + // SeqPanel.stopScrolling called + t.stop(); + } + } + }); + t.start(); + } + else + { + /* + * Java - run in a new thread + */ + scrollThread.start(); + } } - - mouseDragging = true; - scrollThread.setMousePosition(mousePos); } /** - * Performs scrolling of the visible alignment left, right, up or down + * Performs scrolling of the visible alignment left, right, up or down, until + * scrolling is stopped by calling stopScrolling, mouse drag is ended, or the + * limit of the alignment is reached */ class ScrollThread extends Thread { private Point mousePos; - private volatile boolean threadRunning = true; + private volatile boolean keepRunning = true; /** * Constructor @@ -2411,12 +2596,14 @@ public class SeqPanel extends JPanel public ScrollThread() { setName("SeqPanel$ScrollThread"); - start(); } /** * Sets the position of the mouse that determines the direction of the - * scroll to perform + * scroll to perform. If this is called as the mouse moves, scrolling should + * respond accordingly. For example, if the mouse is dragged right, scroll + * right should start; if the drag continues down, scroll down should also + * happen. * * @param p */ @@ -2430,7 +2617,7 @@ public class SeqPanel extends JPanel */ public void stopScrolling() { - threadRunning = false; + keepRunning = false; } /** @@ -2441,48 +2628,12 @@ public class SeqPanel extends JPanel @Override public void run() { - while (threadRunning && mouseDragging) + while (keepRunning) { if (mousePos != null) { - boolean scrolled = false; - ViewportRanges ranges = SeqPanel.this.av.getRanges(); - - /* - * scroll up or down - */ - if (mousePos.y < 0) - { - // mouse is above this panel - try scroll up - scrolled = ranges.scrollUp(true); - } - else if (mousePos.y >= getHeight()) - { - // mouse is below this panel - try scroll down - scrolled = ranges.scrollUp(false); - } - - /* - * scroll left or right - */ - if (mousePos.x < 0) - { - scrolled |= ranges.scrollRight(false); - } - else if (mousePos.x >= getWidth()) - { - scrolled |= ranges.scrollRight(true); - } - if (!scrolled) - { - /* - * we have reached the limit of the visible alignment - quit - */ - threadRunning = false; - SeqPanel.this.ap.repaint(); - } + keepRunning = scrollOnce(); } - try { Thread.sleep(20); @@ -2490,6 +2641,60 @@ public class SeqPanel extends JPanel { } } + SeqPanel.this.scrollThread = null; + } + + /** + * Scrolls + *
    + *
  • one row up, if the mouse is above the panel
    • + *
  • one row down, if the mouse is below the panel
    • + *
  • one column left, if the mouse is left of the panel
    • + *
  • one column right, if the mouse is right of the panel
    • + *
+ * Answers true if a scroll was performed, false if not - meaning either + * that the mouse position is within the panel, or the edge of the alignment + * has been reached. + */ + boolean scrollOnce() + { + /* + * quit after mouseUp ensures interrupt in JalviewJS + */ + if (!mouseDragging) + { + return false; + } + + boolean scrolled = false; + ViewportRanges ranges = SeqPanel.this.av.getRanges(); + + /* + * scroll up or down + */ + if (mousePos.y < 0) + { + // mouse is above this panel - try scroll up + scrolled = ranges.scrollUp(true); + } + else if (mousePos.y >= getHeight()) + { + // mouse is below this panel - try scroll down + scrolled = ranges.scrollUp(false); + } + + /* + * scroll left or right + */ + if (mousePos.x < 0) + { + scrolled |= ranges.scrollRight(false); + } + else if (mousePos.x >= getWidth()) + { + scrolled |= ranges.scrollRight(true); + } + return scrolled; } } @@ -2657,7 +2862,7 @@ public class SeqPanel extends JPanel * Map sequence selection */ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av); - av.setSelectionGroup(sg); + av.setSelectionGroup(sg != null && sg.getSize() > 0 ? sg : null); av.isSelectionGroupChanged(true); /*