X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=8e6584089d16d4cf5f2969a7128913acc9be5b19;hb=73f4373f0ad3d76ca36a32201d3ed53c255180c5;hp=20e585a1da82f5f154bf34d3e2345f411b153a5e;hpb=1499d3297cf70ff34df05362449dbf36873c5bc1;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 20e585a..8e65840 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -84,6 +84,16 @@ public class SeqPanel extends JPanel implements MouseListener, /** DOCUMENT ME!! */ public AlignmentPanel ap; + /* + * last column position for mouseMoved event + */ + private int lastMouseColumn; + + /* + * last sequence offset for mouseMoved event + */ + private int lastMouseSeq; + protected int lastres; protected int startseq; @@ -170,6 +180,9 @@ public class SeqPanel extends JPanel implements MouseListener, ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } + + lastMouseColumn = -1; + lastMouseSeq = -1; } int startWrapBlock = -1; @@ -389,38 +402,11 @@ public class SeqPanel extends JPanel implements MouseListener, endEditing(); if (av.getWrapAlignment()) { - ap.scrollToWrappedVisible(seqCanvas.cursorX); + av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); } else { - while (seqCanvas.cursorY < av.getRanges().getStartSeq()) - { - ap.scrollUp(true); - } - while (seqCanvas.cursorY > av.getRanges().getEndSeq()) - { - ap.scrollUp(false); - } - if (!av.getWrapAlignment()) - { - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av - .getRanges().getStartRes())) - { - if (!ap.scrollRight(false)) - { - break; - } - } - while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av - .getRanges().getEndRes())) - { - if (!ap.scrollRight(true)) - { - break; - } - } - } + av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY); } setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); @@ -590,6 +576,7 @@ public class SeqPanel extends JPanel implements MouseListener, @Override public void mouseReleased(MouseEvent evt) { + boolean didDrag = mouseDragging; // did we come here after a drag mouseDragging = false; mouseWheelPressed = false; @@ -602,7 +589,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -696,17 +683,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.isFollowHighlight()) { - /* - * if scrollToPosition requires a scroll adjustment, this flag prevents - * another scroll event being propagated back to the originator - * - * @see AlignmentPanel#adjustmentValueChanged - */ - ap.setDontScrollComplement(true); + // don't allow highlight of protein/cDNA to also scroll a complementary + // panel,as this sets up a feedback loop (scrolling panel 1 causes moused + // over residue to change abruptly, causing highlighted residue in panel 2 + // to change, causing a scroll in panel 1 etc) + ap.setToScrollComplementPanel(false); if (ap.scrollToPosition(results, false)) { seqCanvas.revalidate(); } + ap.setToScrollComplementPanel(true); } setStatusMessage(results); seqCanvas.highlightSearchResults(results); @@ -745,8 +731,18 @@ public class SeqPanel extends JPanel implements MouseListener, int seq = findSeq(evt); if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { + lastMouseSeq = -1; + return; + } + if (column == lastMouseColumn && seq == lastMouseSeq) + { + /* + * just a pixel move without change of residue + */ return; } + lastMouseColumn = column; + lastMouseSeq = seq; SequenceI sequence = av.getAlignment().getSequenceAt(seq); @@ -758,8 +754,9 @@ public class SeqPanel extends JPanel implements MouseListener, /* * set status bar message, returning residue position in sequence */ + boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); final int pos = setStatusMessage(sequence, column, seq); - if (ssm != null && pos > -1) + if (ssm != null && !isGapped) { mouseOverSequence(sequence, column, pos); } @@ -788,10 +785,15 @@ public class SeqPanel extends JPanel implements MouseListener, } } - if (av.isShowSequenceFeatures() && pos != -1) + /* + * add any features at the position to the tooltip; if over a gap, only + * add features that straddle the gap (pos may be the residue before or + * after the gap) + */ + if (av.isShowSequenceFeatures()) { List features = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), pos); + .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } @@ -802,18 +804,15 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) + String textString = tooltipText.toString(); + if (lastTooltip == null || !lastTooltip.equals(textString)) { - String formatedTooltipText = JvSwingUtils.wrapTooltip(true, - tooltipText.toString()); - // String formatedTooltipText = tooltipText.toString(); - setToolTipText(formatedTooltipText); - lastTooltip = tooltipText.toString(); + String formattedTooltipText = JvSwingUtils.wrapTooltip(true, + textString); + setToolTipText(formattedTooltipText); + lastTooltip = textString; } - } - } private Point lastp = null; @@ -860,9 +859,10 @@ public class SeqPanel extends JPanel implements MouseListener, /** * Sets the status message in alignment panel, showing the sequence number - * (index) and id, residue and residue position for the given sequence and - * column position. Returns the calculated residue position in the sequence, - * or -1 for a gapped column position. + * (index) and id, and residue and residue position if not at a gap, for the + * given sequence and column position. Returns the residue position returned + * by Sequence.findPosition. Note this may be for the nearest adjacent residue + * if at a gapped position. * * @param sequence * aligned sequence object @@ -870,7 +870,8 @@ public class SeqPanel extends JPanel implements MouseListener, * alignment column * @param seq * index of sequence in alignment - * @return position of column in sequence or -1 if at a gap + * @return sequence position of residue at column, or adjacent residue if at a + * gap */ int setStatusMessage(SequenceI sequence, final int column, int seq) { @@ -884,36 +885,34 @@ public class SeqPanel extends JPanel implements MouseListener, .append(sequence.getName()); String residue = null; + /* * Try to translate the display character to residue name (null for gap). */ final String displayChar = String.valueOf(sequence.getCharAt(column)); - if (av.getAlignment().isNucleotide()) + boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); + int pos = sequence.findPosition(column); + + if (!isGapped) { - residue = ResidueProperties.nucleotideName.get(displayChar); - if (residue != null) + boolean nucleotide = av.getAlignment().isNucleotide(); + if (nucleotide) { - text.append(" Nucleotide: ").append(residue); + residue = ResidueProperties.nucleotideName.get(displayChar); } - } - else - { - residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" - .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet - .get(displayChar)); - if (residue != null) + else { - text.append(" Residue: ").append(residue); + residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" + .equals(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar)); } - } + text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") + .append(": ").append(residue == null ? displayChar : residue); - int pos = -1; - if (residue != null) - { - pos = sequence.findPosition(column); text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); + return pos; } @@ -1553,9 +1552,14 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } + int column = findColumn(evt); + + /* + * find features at the position (if not gapped), or straddling + * the position (if at a gap) + */ List features = seqCanvas.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(findColumn(evt))); + .findFeaturesAtColumn(sequence, column + 1); if (!features.isEmpty()) { @@ -1587,23 +1591,23 @@ public class SeqPanel extends JPanel implements MouseListener, { if (e.isShiftDown()) { - ap.scrollRight(true); + av.getRanges().scrollRight(true); } else { - ap.scrollUp(false); + av.getRanges().scrollUp(false); } } else { if (e.isShiftDown()) { - ap.scrollRight(false); + av.getRanges().scrollRight(false); } else { - ap.scrollUp(true); + av.getRanges().scrollUp(true); } } // TODO Update tooltip for new position. @@ -1732,13 +1736,12 @@ public class SeqPanel extends JPanel implements MouseListener, */ void showPopupMenu(MouseEvent evt) { - final int res = findColumn(evt); + final int column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); List allFeatures = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); - List links = new ArrayList(); + .findFeaturesAtColumn(sequence, column + 1); + List links = new ArrayList<>(); for (SequenceFeature sf : allFeatures) { if (sf.links != null) @@ -1755,12 +1758,15 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Update the display after mouse up on a selection or group * * @param evt - * DOCUMENT ME! + * mouse released event details + * @param afterDrag + * true if this event is happening after a mouse drag (rather than a + * mouse down) */ - public void doMouseReleasedDefineMode(MouseEvent evt) + public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag) { if (stretchGroup == null) { @@ -1769,7 +1775,8 @@ public class SeqPanel extends JPanel implements MouseListener, // always do this - annotation has own state // but defer colourscheme update until hidden sequences are passed in boolean vischange = stretchGroup.recalcConservation(true); - needOverviewUpdate |= vischange && av.isSelectionDefinedGroup(); + needOverviewUpdate |= vischange && av.isSelectionDefinedGroup() + && afterDrag; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1971,23 +1978,23 @@ public class SeqPanel extends JPanel implements MouseListener, if (mouseDragging && (evt.getY() < 0) && (av.getRanges().getStartSeq() > 0)) { - running = ap.scrollUp(true); + running = av.getRanges().scrollUp(true); } if (mouseDragging && (evt.getY() >= getHeight()) && (av.getAlignment().getHeight() > av.getRanges() .getEndSeq())) { - running = ap.scrollUp(false); + running = av.getRanges().scrollUp(false); } if (mouseDragging && (evt.getX() < 0)) { - running = ap.scrollRight(false); + running = av.getRanges().scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = ap.scrollRight(true); + running = av.getRanges().scrollRight(true); } } @@ -2023,11 +2030,13 @@ public class SeqPanel extends JPanel implements MouseListener, ap.getCalculationDialog().validateCalcTypes(); } - // process further ? - if (!av.followSelection) - { - return; - } + return; + } + + // process further ? + if (!av.followSelection) + { + return; } /*