X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=14ec6e9508e8bfd2a5793351285ce5364248d79a;hb=c735d0c34c8315c3bd86a7f6bf3c28a21c69b1fb;hp=61cac46b0a3912fea31aec14212487be8ee79839;hpb=3a15fb2458a6c774645d299bd2d3013c608cc8b3;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 61cac46..14ec6e9 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -25,6 +25,7 @@ import jalview.bin.Cache; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; @@ -59,7 +60,6 @@ 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; @@ -76,23 +76,88 @@ import javax.swing.ToolTipManager; public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener, SequenceListener, SelectionListener - { - /** DOCUMENT ME!! */ + /* + * a class that holds computed mouse position + * - column of the alignment (0...) + * - sequence offset (0...) + * - annotation row offset (0...) + * where annotation offset is -1 unless the alignment is shown + * in wrapped mode, annotations are shown, and the mouse is + * over an annnotation row + */ + static class MousePos + { + /* + * alignment column position of cursor (0...) + */ + final int column; + + /* + * index in alignment of sequence under cursor, + * or nearest above if cursor is not over a sequence + */ + final int seqIndex; + + /* + * index in annotations array of annotation under the cursor + * (only possible in wrapped mode with annotations shown), + * or -1 if cursor is not over an annotation row + */ + final int annotationIndex; + + MousePos(int col, int seq, int ann) + { + column = col; + seqIndex = seq; + annotationIndex = ann; + } + + @Override + public boolean equals(Object obj) + { + if (obj == null || !(obj instanceof MousePos)) + { + return false; + } + MousePos o = (MousePos) obj; + boolean b = (column == o.column && seqIndex == o.seqIndex + && annotationIndex == o.annotationIndex); + // System.out.println(obj + (b ? "= " : "!= ") + this); + return b; + } + + /** + * A simple hashCode that ensures that instances that satisfy equals() have + * the same hashCode + */ + @Override + public int hashCode() + { + return column + seqIndex + annotationIndex; + } + + /** + * toString method for debug output purposes only + */ + @Override + public String toString() + { + return String.format("c%d:s%d:a%d", column, seqIndex, + annotationIndex); + } + } + + private static final int MAX_TOOLTIP_LENGTH = 300; + public SeqCanvas seqCanvas; - /** DOCUMENT ME!! */ public AlignmentPanel ap; /* - * last column position for mouseMoved event - */ - private int lastMouseColumn; - - /* - * last sequence offset for mouseMoved event + * last position for mouseMoved event */ - private int lastMouseSeq; + private MousePos lastMousePosition; protected int lastres; @@ -148,41 +213,36 @@ public class SeqPanel extends JPanel SearchResultsI lastSearchResults; /** - * Creates a new SeqPanel object. + * Creates a new SeqPanel object * - * @param avp - * DOCUMENT ME! - * @param p - * DOCUMENT ME! + * @param viewport + * @param alignPanel */ - public SeqPanel(AlignViewport av, AlignmentPanel ap) + public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { linkImageURL = getClass().getResource("/images/link.gif"); seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = av; + this.av = viewport; setBackground(Color.white); - seqCanvas = new SeqCanvas(ap); + seqCanvas = new SeqCanvas(alignPanel); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - this.ap = ap; + this.ap = alignPanel; - if (!av.isDataset()) + if (!viewport.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = av.getStructureSelectionManager(); + ssm = viewport.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } - - lastMouseColumn = -1; - lastMouseSeq = -1; } int startWrapBlock = -1; @@ -190,6 +250,66 @@ public class SeqPanel extends JPanel int wrappedBlock = -1; /** + * Computes the column and sequence row (or possibly annotation row when in + * wrapped mode) for the given mouse position + * + * @param evt + * @return + */ + MousePos findMousePosition(MouseEvent evt) + { + int col = findColumn(evt); + int seq = -1; + int annIndex = -1; + int y = evt.getY(); + + int charHeight = av.getCharHeight(); + int alignmentHeight = av.getAlignment().getHeight(); + if (av.getWrapAlignment()) + { + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + final int alignmentHeightPixels = alignmentHeight * charHeight + hgap; + final int annotationHeight = seqCanvas.getAnnotationHeight(); + final int cHeight = alignmentHeightPixels + annotationHeight; + + int yOffsetPx = y % cHeight; // yPos below repeating width(s) + if (yOffsetPx > alignmentHeightPixels) + { + /* + * mouse is over annotations + */ + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + int rowOffsetPx = yOffsetPx - alignmentHeightPixels; + annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns); + } + else + { + /* + * mouse is over sequence (or the space above sequences) + */ + yOffsetPx -= hgap; + if (yOffsetPx > 0) + { + seq = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); + } + } + } + else + { + seq = Math.min((y / charHeight) + av.getRanges().getStartSeq(), + alignmentHeight - 1); + } + int seqIndex = seq; + + return new MousePos(col, seqIndex, annIndex); + } + /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one * @@ -250,39 +370,56 @@ public class SeqPanel extends JPanel if (av.hasHiddenColumns()) { res = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(res); + .visibleToAbsoluteColumn(res); } return res; } + /** + * Answers the index in the alignment (0...) of the sequence under the mouse + * position. If the mouse is below the alignment (say, over annotations), + * answers the index of the last sequence. + * + * @param evt + * @return + */ int findSeq(MouseEvent evt) { int seq = 0; int y = evt.getY(); + int charHeight = av.getCharHeight(); + int alignmentHeight = av.getAlignment().getHeight(); if (av.getWrapAlignment()) { - int hgap = av.getCharHeight(); + int hgap = charHeight; if (av.getScaleAboveWrapped()) { - hgap += av.getCharHeight(); + hgap += charHeight; } - int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap + seqCanvas.getAnnotationHeight(); + int alignmentHeightPixels = alignmentHeight * charHeight; + int cHeight = alignmentHeightPixels + hgap + + seqCanvas.getAnnotationHeight(); y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), - av.getAlignment().getHeight() - 1); + int yOffsetPx = y % cHeight; // yPos below repeating width(s) +// if (yOffsetPx > alignmentHeightPixels) +// { +// seq = -1; // cursor is over annotation or below alignment entirely +// } +// else + // { + seq = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); +// } } else { - seq = Math.min( - (y / av.getCharHeight()) + av.getRanges().getStartSeq(), - av.getAlignment().getHeight() - 1); + seq = Math.min((y / charHeight) + av.getRanges().getStartSeq(), + alignmentHeight - 1); } return seq; @@ -363,13 +500,25 @@ public class SeqPanel extends JPanel int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - // TODO: once JAL-2759 is ready, change this loop to something more - // efficient - while (!hidden.isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0 - && dx != 0) + if (!hidden.isVisible(seqCanvas.cursorX)) { - seqCanvas.cursorX += dx; + int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx); + int[] region = hidden.getRegionWithEdgeAtRes(visx); + + if (region != null) // just in case + { + if (dx == 1) + { + // moving right + seqCanvas.cursorX = region[1] + 1; + } + else if (dx == -1) + { + // moving left + seqCanvas.cursorX = region[0] - 1; + } + } + seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX; } if (seqCanvas.cursorX >= maxWidth @@ -424,7 +573,7 @@ public class SeqPanel extends JPanel { // scrollToWrappedVisible expects x-value to have hidden cols subtracted int x = av.getAlignment().getHiddenColumns() - .findColumnPosition(seqCanvas.cursorX); + .absoluteToVisibleColumn(seqCanvas.cursorX); av.getRanges().scrollToWrappedVisible(x); } else @@ -769,23 +918,31 @@ public class SeqPanel extends JPanel mouseDragged(evt); } - final int column = findColumn(evt); - final int seq = findSeq(evt); + final MousePos mousePos = findMousePosition(evt); + if (mousePos.equals(lastMousePosition)) + { + /* + * just a pixel move without change of 'cell' + */ + return; + } + lastMousePosition = mousePos; - if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + if (mousePos.annotationIndex != -1) { - lastMouseSeq = -1; + mouseMovedOverAnnotation(mousePos); return; } - if (column == lastMouseColumn && seq == lastMouseSeq) + final int seq = mousePos.seqIndex;// findSeq(evt); + + final int column = mousePos.column; + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { - /* - * just a pixel move without change of residue - */ + lastMousePosition = null; + setToolTipText(null); + ap.alignFrame.statusBar.setText(""); return; } - lastMouseColumn = column; - lastMouseSeq = seq; SequenceI sequence = av.getAlignment().getSequenceAt(seq); @@ -838,7 +995,7 @@ public class SeqPanel extends JPanel List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, - this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); + this.ap.getSeqPanel().seqCanvas.fr); } if (tooltipText.length() == 6) // { @@ -847,6 +1004,11 @@ public class SeqPanel extends JPanel } else { + if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant + { + tooltipText.setLength(MAX_TOOLTIP_LENGTH); + tooltipText.append("..."); + } String textString = tooltipText.toString(); if (lastTooltip == null || !lastTooltip.equals(textString)) { @@ -858,6 +1020,34 @@ public class SeqPanel extends JPanel } } + /** + * When the view is in wrapped mode, and the mouse is over an annotation row, + * shows the corresponding tooltip and status message (if any) + * + * @param pos + * @param column + */ + protected void mouseMovedOverAnnotation(MousePos pos) + { + final int column = pos.column; + final int rowIndex = pos.annotationIndex; + + if (!av.getWrapAlignment() || !av.isShowAnnotation() || rowIndex < 0) + { + return; + } + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + + String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column, + anns); + setToolTipText(tooltip); + lastTooltip = tooltip; + + String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, + anns[rowIndex]); + ap.alignFrame.statusBar.setText(msg); + } + private Point lastp = null; /* @@ -1259,9 +1449,9 @@ public class SeqPanel extends JPanel { fixedColumns = true; int y1 = av.getAlignment().getHiddenColumns() - .getHiddenBoundaryLeft(startres); + .getNextHiddenBoundary(true, startres); int y2 = av.getAlignment().getHiddenColumns() - .getHiddenBoundaryRight(startres); + .getNextHiddenBoundary(false, startres); if ((insertGap && startres > y1 && lastres < y1) || (!insertGap && startres < y2 && lastres > y2)) @@ -1337,7 +1527,8 @@ public class SeqPanel extends JPanel if (sg.getSize() == av.getAlignment().getHeight()) { if ((av.hasHiddenColumns() && startres < av.getAlignment() - .getHiddenColumns().getHiddenBoundaryRight(startres))) + .getHiddenColumns() + .getNextHiddenBoundary(false, startres))) { endEditing(); return; @@ -1656,7 +1847,8 @@ public class SeqPanel extends JPanel public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { if (e.isShiftDown()) { @@ -1668,7 +1860,7 @@ public class SeqPanel extends JPanel av.getRanges().scrollUp(false); } } - else + else if (wheelRotation < 0) { if (e.isShiftDown()) { @@ -1825,21 +2017,10 @@ public class SeqPanel extends JPanel final int column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); - List allFeatures = ap.getFeatureRenderer() + List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - List links = new ArrayList<>(); - for (SequenceFeature sf : allFeatures) - { - if (sf.links != null) - { - for (String link : sf.links) - { - links.add(link); - } - } - } - PopupMenu pop = new PopupMenu(ap, null, links); + PopupMenu pop = new PopupMenu(ap, null, features); pop.show(this, evt.getX(), evt.getY()); } @@ -2288,4 +2469,13 @@ public class SeqPanel extends JPanel return true; } + + /** + * + * @return null or last search results handled by this panel + */ + public SearchResultsI getLastSearchResults() + { + return lastSearchResults; + } }