X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=827c3150ae2be532410136c86c7a64d12067b6d9;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=04ceea6c10a567dcf3466486a7674f2e727f9ec8;hpb=09976d9f77b1a3a6486735b0fd9caeb158f1834f;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 04ceea6..827c315 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,8 +20,31 @@ */ 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.bin.Console; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; @@ -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; @@ -50,28 +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.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.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.viewmodel.seqfeatures.FeatureRendererModel; /** * DOCUMENT ME! @@ -209,13 +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; @@ -231,8 +242,7 @@ 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); @@ -265,6 +275,9 @@ public class SeqPanel extends JPanel /** * Computes the column and sequence row (and possibly annotation row when in * wrapped mode) for the given mouse position + *

+ * Mouse position is not set if in wrapped mode with the cursor either between + * sequences, or over the left or right vertical scale. * * @param evt * @return @@ -321,8 +334,10 @@ public class SeqPanel extends JPanel } else { - seqIndex = Math.min((y / charHeight) + av.getRanges().getStartSeq(), + ViewportRanges ranges = av.getRanges(); + seqIndex = Math.min((y / charHeight) + ranges.getStartSeq(), alignmentHeight - 1); + seqIndex = Math.min(seqIndex, ranges.getEndSeq()); } return new MousePos(col, seqIndex, annIndex); @@ -330,6 +345,9 @@ public class SeqPanel extends JPanel /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one + *

+ * Returns -1 if in wrapped mode with the mouse over either left or right + * vertical scale. * * @param evt * @return @@ -465,47 +483,80 @@ public class SeqPanel extends JPanel void moveCursor(int dx, int dy) { - seqCanvas.cursorX += dx; - seqCanvas.cursorY += dy; - + moveCursor(dx, dy,false); + } + void moveCursor(int dx, int dy, boolean nextWord) + { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX)) + if (nextWord) { - int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - - if (!hidden.isVisible(seqCanvas.cursorX)) - { - int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx); - int[] region = hidden.getRegionWithEdgeAtRes(visx); - - if (region != null) // just in case + int maxHeight=av.getAlignment().getHeight(); + SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY); + // look for next gap or residue + boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX)); + int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR; + do + { + lastP = p; + lastR = r; + if (dy != 0) { - if (dx == 1) + r += dy; + if (r < 0) { - // moving right - seqCanvas.cursorX = region[1] + 1; + r = 0; } - else if (dx == -1) + if (r >= maxHeight) { - // moving left - seqCanvas.cursorX = region[0] - 1; + r = maxHeight - 1; } + seqAtRow = av.getAlignment().getSequenceAt(r); } - seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX; - } + p = nextVisible(hidden, maxWidth, p, dx); + } while ((dx != 0 ? p != lastP : r != lastR) + && isGap == Comparison.isGap(seqAtRow.getCharAt(p))); + seqCanvas.cursorX=p; + seqCanvas.cursorY=r; + } else { + int maxWidth = av.getAlignment().getWidth(); + seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx); + seqCanvas.cursorY += dy; + } + scrollToVisible(false); + } - if (seqCanvas.cursorX >= maxWidth - || !hidden.isVisible(seqCanvas.cursorX)) + private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx) + { + int newCursorX=original+dx; + if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX)) + { + int visx = hidden.absoluteToVisibleColumn(newCursorX - dx); + int[] region = hidden.getRegionWithEdgeAtRes(visx); + + if (region != null) // just in case { - seqCanvas.cursorX = original; + if (dx == 1) + { + // moving right + newCursorX = region[1] + 1; + } + else if (dx == -1) + { + // moving left + newCursorX = region[0] - 1; + } } } - - scrollToVisible(false); + newCursorX = (newCursorX < 0) ? 0 : newCursorX; + if (newCursorX >= maxWidth + || !hidden.isVisible(newCursorX)) + { + newCursorX = original; + } + return newCursorX; } - /** * Scroll to make the cursor visible in the viewport. * @@ -817,8 +868,6 @@ public class SeqPanel extends JPanel String lastMessage; - private String formattedTooltipText; - @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { @@ -839,11 +888,11 @@ 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; @@ -869,6 +918,78 @@ public class SeqPanel extends JPanel { 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(); + + List matches = results.getResults(); + int j = matches.size(); + List infos = new ArrayList<>(); + for (int i = 0; i < j; i++) + { + SearchResultMatchI match = matches.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 @@ -908,8 +1029,10 @@ public class SeqPanel extends JPanel /* * just a pixel move without change of 'cell' */ + moveTooltip = false; return; } + moveTooltip = true; lastMousePosition = mousePos; if (mousePos.isOverAnnotation()) @@ -925,6 +1048,7 @@ public class SeqPanel extends JPanel lastMousePosition = null; setToolTipText(null); lastTooltip = null; + lastFormattedTooltip = null; ap.alignFrame.setStatus(""); return; } @@ -946,7 +1070,7 @@ public class SeqPanel extends JPanel mouseOverSequence(sequence, column, pos); } - tooltipText.setLength(6); // "" + StringBuilder tooltipText = new StringBuilder(64); SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) @@ -975,32 +1099,63 @@ 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)) { - formattedTooltipText = JvSwingUtils.wrapTooltip(true, - textString); - setToolTipText(formattedTooltipText); lastTooltip = textString; + lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, + textString); + setToolTipText(lastFormattedTooltip); } } } @@ -1026,16 +1181,34 @@ 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(); /* @@ -1048,33 +1221,30 @@ public class SeqPanel extends JPanel { // BH 2018 - if (tooltipText == null || tooltipText.length() <= 6) + if (lastTooltip == null || !moveTooltip) { return null; } - if (lastp != null && event.isShiftDown()) + if (lastTooltipLocation != null && event.isShiftDown()) { - return lastp; + return lastTooltipLocation; } - Point p = lastp; int x = event.getX(); int y = event.getY(); int w = getWidth(); - tempTip.setTipText(formattedTooltipText); + 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); - p = new Point(x, y + 20); // BH 2018 was - 20? + Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20? - return lastp = p; + return lastTooltipLocation = p; } - String lastTooltip; - /** * set when the current UI interaction has resulted in a change that requires * shading in overviews and structures to be recalculated. this could be @@ -1111,7 +1281,7 @@ 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; } @@ -1127,7 +1297,7 @@ 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 @@ -1135,7 +1305,7 @@ 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); @@ -1145,7 +1315,7 @@ 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; @@ -1190,7 +1360,8 @@ 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(); @@ -1202,8 +1373,8 @@ 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; } } @@ -1940,6 +2111,7 @@ public class SeqPanel extends JPanel @Override public void mouseExited(MouseEvent e) { + lastMousePosition = null; ap.alignFrame.setStatus(" "); if (av.getWrapAlignment()) { @@ -1967,7 +2139,7 @@ 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 @@ -2168,11 +2340,11 @@ 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()); + } } /** @@ -2405,14 +2577,7 @@ public class SeqPanel extends JPanel { scrollThread = new ScrollThread(); scrollThread.setMousePosition(mousePos); - if (!Platform.isJS()) - { - /* - * Java - run in a new thread - */ - scrollThread.start(); - } - else + if (Platform.isJS()) { /* * Javascript - run every 20ms until scrolling stopped @@ -2444,6 +2609,13 @@ public class SeqPanel extends JPanel }); t.start(); } + else + { + /* + * Java - run in a new thread + */ + scrollThread.start(); + } } } @@ -2630,7 +2802,7 @@ public class SeqPanel extends JPanel { if (av.getAlignment() == null) { - Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + " ViewId=" + av.getViewId() + " 's alignment is NULL! returning immediately."); return; @@ -2730,7 +2902,7 @@ 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); /*