X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=55a508b60d498f8001ab98386277c6b0b1614eda;hb=d346ed81a91c4fbed1836379bb794ed908cd9a11;hp=d3ed93a50337eb8d16a1669b832d10d31227e2f8;hpb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index d3ed93a..55a508b 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; @@ -183,7 +196,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param evt * @return */ - int findRes(MouseEvent evt) + int findColumn(MouseEvent evt) { int res = 0; int x = evt.getX(); @@ -202,7 +215,7 @@ public class SeqPanel extends JPanel implements MouseListener, int y = evt.getY(); y -= hgap; - x -= seqCanvas.LABEL_WEST; + x -= seqCanvas.labelWidthWest; int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) @@ -393,8 +406,7 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY, - av); + av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY); } setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); @@ -564,6 +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; @@ -576,7 +589,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -616,7 +629,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < 0 || res < 0) { @@ -681,8 +694,10 @@ public class SeqPanel extends JPanel implements MouseListener, } ap.setToScrollComplementPanel(true); } - setStatusMessage(results); - seqCanvas.highlightSearchResults(results); + if (seqCanvas.highlightSearchResults(results)) + { + setStatusMessage(results); + } } @Override @@ -714,25 +729,38 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragged(evt); } - int res = findRes(evt); + final int column = findColumn(evt); int seq = findSeq(evt); - int pos; - if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + 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); - if (res >= sequence.getLength()) + if (column >= sequence.getLength()) { return; } - pos = setStatusMessage(sequence, res, seq); - if (ssm != null && pos > -1) + /* + * 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 && !isGapped) { - mouseOverSequence(sequence, res, pos); + mouseOverSequence(sequence, column, pos); } tooltipText.setLength(6); // Cuts the buffer back to @@ -742,7 +770,8 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int g = 0; g < groups.length; g++) { - if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res) + if (groups[g].getStartRes() <= column + && groups[g].getEndRes() >= column) { if (!groups[g].getName().startsWith("JTreeGroup") && !groups[g].getName().startsWith("JGroup")) @@ -758,14 +787,16 @@ public class SeqPanel extends JPanel implements MouseListener, } } - // use aa to see if the mouse pointer is on a + /* + * 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()) { - int rpos; List features = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - rpos = sequence.findPosition(res)); - seqARep.appendFeatures(tooltipText, rpos, features, + .findFeaturesAtColumn(sequence, column + 1); + seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // @@ -775,18 +806,15 @@ 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; @@ -832,59 +860,88 @@ public class SeqPanel extends JPanel implements MouseListener, // avcontroller or viewModel /** - * Set status message in alignment panel + * Sets the status message in alignment panel, showing the sequence number + * (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 - * @param res + * @param column * alignment column - * @param seq + * @param seqIndex * index of sequence in alignment - * @return position of res in sequence + * @return sequence position of residue at column, or adjacent residue if at a + * gap + */ + int setStatusMessage(SequenceI sequence, final int column, int seqIndex) + { + char sequenceChar = sequence.getCharAt(column); + int pos = sequence.findPosition(column); + setStatusMessage(sequence, seqIndex, sequenceChar, pos); + + return pos; + } + + /** + * Builds the status message for the current cursor location and writes it to + * the status bar, for example + * + * 
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   *
+ * + * @param sequence + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) */ - int setStatusMessage(SequenceI sequence, int res, int seq) + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ - String seqno = seq == -1 ? "" : " " + (seq + 1); + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") .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(res)); - if (av.getAlignment().isNucleotide()) + boolean isGapped = Comparison.isGap(sequenceChar); + + if (!isGapped) { - residue = ResidueProperties.nucleotideName.get(displayChar); - if (residue != null) + boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); + 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(res); - text.append(" (").append(Integer.toString(pos)).append(")"); + text.append(" (").append(Integer.toString(residuePos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); - return pos; } /** @@ -912,12 +969,9 @@ public class SeqPanel extends JPanel implements MouseListener, if (seq == ds) { - /* - * Convert position in sequence (base 1) to sequence character array - * index (base 0) - */ - int start = m.getStart() - m.getSequence().getStart(); - setStatusMessage(seq, start, sequenceIndex); + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); return; } } @@ -1028,7 +1082,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - int res = findRes(evt); + int res = findColumn(evt); if (res < 0) { @@ -1523,9 +1577,14 @@ 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(findRes(evt))); + .findFeaturesAtColumn(sequence, column + 1); if (!features.isEmpty()) { @@ -1543,7 +1602,7 @@ public class SeqPanel extends JPanel implements MouseListener, */ List seqs = Collections.singletonList(sequence); seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, - ap, null); + ap); seqCanvas.highlightSearchResults(null); } } @@ -1587,7 +1646,7 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void doMousePressedDefineMode(MouseEvent evt) { - final int res = findRes(evt); + final int res = findColumn(evt); final int seq = findSeq(evt); oldSeq = seq; needOverviewUpdate = false; @@ -1646,7 +1705,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.cursorMode) { - seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorX = findColumn(evt); seqCanvas.cursorY = findSeq(evt); seqCanvas.repaint(); return; @@ -1702,13 +1761,12 @@ public class SeqPanel extends JPanel implements MouseListener, */ void showPopupMenu(MouseEvent evt) { - final int res = findRes(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) @@ -1725,12 +1783,15 @@ 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) { @@ -1739,7 +1800,8 @@ 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, @@ -1773,7 +1835,7 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void doMouseDraggedDefineMode(MouseEvent evt) { - int res = findRes(evt); + int res = findColumn(evt); int y = findSeq(evt); if (wrappedBlock != startWrapBlock) @@ -1993,11 +2055,13 @@ public class SeqPanel extends JPanel implements MouseListener, ap.getCalculationDialog().validateCalcTypes(); } - // process further ? - if (!av.followSelection) - { - return; - } + return; + } + + // process further ? + if (!av.followSelection) + { + return; } /*