X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=407acd604947876413118cbd9b4df130fb679fc8;hb=182633dda3eeb2c46366789855e8be509238ba17;hp=08c74e8ac761a79cc912e438bc20eec5eb05e957;hpb=c9b03515daddb7666215ef3d0f19026aa601534b;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 08c74e8..407acd6 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,6 +20,24 @@ */ 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.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.JPanel; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; + import jalview.api.AlignViewportI; import jalview.bin.Cache; import jalview.commands.EditCommand; @@ -29,6 +47,7 @@ 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 +69,7 @@ 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! @@ -204,8 +207,6 @@ public class SeqPanel extends JPanel StringBuffer keyboardNo2; - java.net.URL linkImageURL; - private final SequenceAnnotationReport seqARep; StringBuilder tooltipText = new StringBuilder(); @@ -226,8 +227,7 @@ 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); @@ -255,11 +255,6 @@ public class SeqPanel extends JPanel int wrappedBlock = -1; - MousePos findMousePosition(MouseEvent evt) - { - return findMousePosition(evt, false); - } - /** * Computes the column and sequence row (and possibly annotation row when in * wrapped mode) for the given mouse position @@ -267,22 +262,15 @@ public class SeqPanel extends JPanel * @param evt * @return */ - MousePos findMousePosition(MouseEvent evt, boolean debug) + MousePos findMousePosition(MouseEvent evt) { - int col = findColumn(evt, debug); + int col = findColumn(evt); int seqIndex = -1; int annIndex = -1; int y = evt.getY(); int charHeight = av.getCharHeight(); int alignmentHeight = av.getAlignment().getHeight(); - if (debug) - { - System.out.println(String.format( - "charHeight %d alHeight %d canvasWidth %d canvasHeight %d", - charHeight, alignmentHeight, seqCanvas.getWidth(), - seqCanvas.getHeight())); - } if (av.getWrapAlignment()) { seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(), @@ -343,11 +331,6 @@ public class SeqPanel extends JPanel */ int findColumn(MouseEvent evt) { - return findColumn(evt, true); - } - - int findColumn(MouseEvent evt, boolean debug) - { int res = 0; int x = evt.getX(); @@ -368,12 +351,6 @@ public class SeqPanel extends JPanel int y = evt.getY(); y = Math.max(0, y - hgap); x -= seqCanvas.getLabelWidthWest(); - if (debug) - { - System.out.println( - String.format("findColumn: x %d labelWest %d charWidth %d ", - x, seqCanvas.getLabelWidthWest(), charWidth)); - } if (x < 0) { // mouse is over left scale @@ -387,10 +364,6 @@ public class SeqPanel extends JPanel } if (x >= cwidth * charWidth) { - if (debug) - { - System.out.println("findColumn: cwidth = " + cwidth); - } // mouse is over right scale return -1; } @@ -487,47 +460,80 @@ 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); + } + + 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 (seqCanvas.cursorX >= maxWidth - || !hidden.isVisible(seqCanvas.cursorX)) + 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. * @@ -859,11 +865,11 @@ 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; @@ -889,6 +895,78 @@ public class SeqPanel extends JPanel { setStatusMessage(results); } + // JAL-3303 feature suppressed for now pending review + return null; // 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 @@ -995,25 +1073,56 @@ 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() == 6) // "" { 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)) { @@ -1124,7 +1233,7 @@ 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; } @@ -1140,7 +1249,7 @@ 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 @@ -1148,7 +1257,7 @@ 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); @@ -1158,7 +1267,7 @@ 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; @@ -1203,7 +1312,8 @@ 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(); @@ -1215,8 +1325,8 @@ 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; } } @@ -1981,7 +2091,7 @@ 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 @@ -2186,11 +2296,11 @@ 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()); + } } /** @@ -2684,7 +2794,7 @@ 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); /*