X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=6fbed49e014db3e2f6e52d614d9c0618e11890e3;hb=bb27d9c1cc4d5c31df6bae6c469178b2b700e119;hp=a435fee02bf9d2b5b60a1de75c1f14e3f7ccc041;hpb=1ae70c4324da0e26611bb2a9272dfacb92b6c234;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index a435fee..6fbed49 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -62,6 +62,7 @@ import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.Collections; import java.util.List; +import java.util.ListIterator; import javax.swing.JPanel; import javax.swing.SwingUtilities; @@ -188,6 +189,7 @@ public class SeqPanel extends JPanel implements MouseListener, int res = 0; int x = evt.getX(); + int startRes = av.getRanges().getStartRes(); if (av.getWrapAlignment()) { @@ -202,7 +204,7 @@ public class SeqPanel extends JPanel implements MouseListener, int y = evt.getY(); y -= hgap; - x -= seqCanvas.LABEL_WEST; + x = Math.max(0, x - seqCanvas.LABEL_WEST); int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) @@ -211,10 +213,11 @@ public class SeqPanel extends JPanel implements MouseListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getRanges().getStartRes() / cwidth; - - res = wrappedBlock * cwidth + x / av.getCharWidth(); - + wrappedBlock += startRes / cwidth; + // allow for wrapped view scrolled right (possible from Overview) + int startOffset = startRes % cwidth; + res = wrappedBlock * cwidth + + Math.min(cwidth - 1, startOffset + x / av.getCharWidth()); } else { @@ -224,7 +227,7 @@ public class SeqPanel extends JPanel implements MouseListener, // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } - res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + res = (x / av.getCharWidth()) + startRes; if (res > av.getRanges().getEndRes()) { // moused off right @@ -389,38 +392,11 @@ 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 +566,7 @@ 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 +579,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -696,17 +673,16 @@ 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); @@ -758,8 +734,9 @@ 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 +765,19 @@ public class SeqPanel extends JPanel implements MouseListener, } } + /* + * 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); + if (isGapped) + { + removeAdjacentFeatures(features, column + 1, sequence); + } seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } @@ -816,6 +802,35 @@ public class SeqPanel extends JPanel implements MouseListener, } + /** + * Removes from the list of features any that start after, or end before, the + * given column position. This allows us to retain only those features + * adjacent to a gapped position that straddle the position. Contact features + * that 'straddle' the position are also removed, since they are not 'at' the + * position. + * + * @param features + * @param column + * alignment column (1..) + * @param sequence + */ + protected void removeAdjacentFeatures(List features, + final int column, SequenceI sequence) + { + // TODO should this be an AlignViewController method (and reused by applet)? + ListIterator it = features.listIterator(); + while (it.hasNext()) + { + SequenceFeature sf = it.next(); + if (sf.isContactFeature() + || sequence.findIndex(sf.getBegin()) > column + || sequence.findIndex(sf.getEnd()) < column) + { + it.remove(); + } + } + } + private Point lastp = null; /* @@ -860,8 +875,10 @@ 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. + * (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 @@ -869,7 +886,8 @@ 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) { @@ -883,36 +901,34 @@ 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; - pos = sequence.findPosition(column); - if (residue != null) - { text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); + return pos; } @@ -1552,9 +1568,20 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } + int column = findColumn(evt); + boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); + + /* + * 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))); + sequence.findPosition(column)); + if (isGapped) + { + removeAdjacentFeatures(features, column, sequence); + } if (!features.isEmpty()) { @@ -1586,23 +1613,23 @@ 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. @@ -1737,7 +1764,7 @@ public class SeqPanel extends JPanel implements MouseListener, List allFeatures = ap.getFeatureRenderer() .findFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(res)); - List links = new ArrayList(); + List links = new ArrayList<>(); for (SequenceFeature sf : allFeatures) { if (sf.links != null) @@ -1754,12 +1781,15 @@ 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) { @@ -1768,7 +1798,8 @@ 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, @@ -1970,23 +2001,23 @@ 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); } } @@ -2022,11 +2053,13 @@ public class SeqPanel extends JPanel implements MouseListener, ap.getCalculationDialog().validateCalcTypes(); } - // process further ? - if (!av.followSelection) - { - return; - } + return; + } + + // process further ? + if (!av.followSelection) + { + return; } /* @@ -2114,8 +2147,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (copycolsel && av.hasHiddenColumns() - && (av.getAlignment().getHiddenColumns() == null || av - .getAlignment().getHiddenColumns().getHiddenRegions() == null)) + && (av.getAlignment().getHiddenColumns() == null)) { System.err.println("Bad things"); }