X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=e4e3640a7885c544ed3f8884e71282c3d66e00b3;hb=bb27d9c1cc4d5c31df6bae6c469178b2b700e119;hp=fd4b36435a220689a59b4d06cfe3455d1bb71295;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index fd4b364..e4e3640 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -39,6 +39,7 @@ import jalview.structure.SelectionSource; import jalview.structure.SequenceListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.Comparison; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -53,6 +54,10 @@ import java.awt.event.InputEvent; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.ListIterator; import java.util.Vector; public class SeqPanel extends Panel implements MouseMotionListener, @@ -227,7 +232,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, endEditing(); if (av.getWrapAlignment()) { - ap.scrollToWrappedVisible(seqCanvas.cursorX); + av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); } else { @@ -235,17 +240,17 @@ public class SeqPanel extends Panel implements MouseMotionListener, HiddenColumns hidden = av.getAlignment().getHiddenColumns(); while (seqCanvas.cursorY < ranges.getStartSeq()) { - ap.scrollUp(true); + ranges.scrollUp(true); } - while (seqCanvas.cursorY + 1 > ranges.getEndSeq()) + while (seqCanvas.cursorY > ranges.getEndSeq()) { - ap.scrollUp(false); + ranges.scrollUp(false); } while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges .getStartRes())) { - if (!ap.scrollRight(false)) + if (!ranges.scrollRight(false)) { break; } @@ -253,7 +258,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges .getEndRes())) { - if (!ap.scrollRight(true)) + if (!ranges.scrollRight(true)) { break; } @@ -412,13 +417,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, * * @param sequence * aligned sequence object - * @param res + * @param column * alignment column * @param seq * index of sequence in alignment - * @return position of res in sequence + * @return position of column in sequence or -1 if at gap */ - void setStatusMessage(SequenceI sequence, int res, int seq) + void setStatusMessage(SequenceI sequence, int column, int seq) { // TODO remove duplication of identical gui method StringBuilder text = new StringBuilder(32); @@ -429,7 +434,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(res)); + final String displayChar = String.valueOf(sequence.getCharAt(column)); if (av.getAlignment().isNucleotide()) { residue = ResidueProperties.nucleotideName.get(displayChar); @@ -452,7 +457,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, int pos = -1; if (residue != null) { - pos = sequence.findPosition(res); + pos = sequence.findPosition(column); text.append(" (").append(Integer.toString(pos)).append(")"); } @@ -562,20 +567,23 @@ public class SeqPanel extends Panel implements MouseMotionListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes(sequence, - sequence.findPosition(findRes(evt))); + int column = findRes(evt); + boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); + List features = findFeaturesAtRes(sequence, + sequence.findPosition(column)); + if (isGapped) + { + removeAdjacentFeatures(features, column + 1, sequence); + } - if (features != null && features.length > 0) + if (!features.isEmpty()) { SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.length > 0) - { seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, features, false, ap); + Collections.singletonList(sequence), features, false, ap); seqCanvas.highlightSearchResults(null); } @@ -585,13 +593,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, @Override public void mouseReleased(MouseEvent evt) { + boolean didDrag = mouseDragging; // did we come here after a drag mouseDragging = false; mouseWheelPressed = false; - ap.paintAlignment(true); if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -608,6 +616,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, int res = 0; int x = evt.getX(); + int startRes = av.getRanges().getStartRes(); if (av.getWrapAlignment()) { @@ -622,7 +631,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, int y = evt.getY(); y -= hgap; - x -= seqCanvas.LABEL_WEST; + x = Math.max(0, x - seqCanvas.LABEL_WEST); int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width); if (cwidth < 1) @@ -631,14 +640,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getRanges().getStartRes() / cwidth; - - res = wrappedBlock * cwidth + x / av.getCharWidth(); - + wrappedBlock += startRes / cwidth; + int startOffset = startRes % cwidth; // in case start is scrolled right + // from 0 + res = wrappedBlock * cwidth + + Math.min(cwidth - 1, startOffset + x / av.getCharWidth()); } else { - res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + res = (x / av.getCharWidth()) + startRes; } if (av.hasHiddenColumns()) @@ -746,10 +756,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (av.isFollowHighlight()) { + // 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, true)) { ap.alignFrame.repaint(); } + ap.setToScrollComplementPanel(true); } setStatusMessage(results); seqCanvas.highlightSearchResults(results); @@ -772,10 +788,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, @Override public void mouseMoved(MouseEvent evt) { - int res = findRes(evt); + final int column = findRes(evt); int seq = findSeq(evt); - if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0) + if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0) { if (tooltip != null) { @@ -785,7 +801,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (res > sequence.getLength()) + if (column > sequence.getLength()) { if (tooltip != null) { @@ -794,38 +810,34 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } - int respos = sequence.findPosition(res); - if (ssm != null) + final char ch = sequence.getCharAt(column); + boolean isGapped = Comparison.isGap(ch); + // find residue at column (or nearest if at a gap) + int respos = sequence.findPosition(column); + + if (ssm != null && !isGapped) { - mouseOverSequence(sequence, res, respos); + mouseOverSequence(sequence, column, respos); } StringBuilder text = new StringBuilder(); text.append("Sequence ").append(Integer.toString(seq + 1)) .append(" ID: ").append(sequence.getName()); - String obj = null; - final String ch = String.valueOf(sequence.getCharAt(res)); - if (av.getAlignment().isNucleotide()) + if (!isGapped) { - obj = ResidueProperties.nucleotideName.get(ch); - if (obj != null) + if (av.getAlignment().isNucleotide()) { - text.append(" Nucleotide: ").append(obj); + String base = ResidueProperties.nucleotideName.get(ch); + text.append(" Nucleotide: ").append(base == null ? ch : base); } - } - else - { - obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet - .get(ch); - if (obj != null) + else { - text.append(" Residue: ").append(obj); + String residue = (ch == 'x' || ch == 'X') ? "X" + : ResidueProperties.aa2Triplet + .get(String.valueOf(ch)); + text.append(" Residue: ").append(residue == null ? ch : residue); } - } - - if (obj != null) - { text.append(" (").append(Integer.toString(respos)).append(")"); } @@ -837,7 +849,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { 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")) @@ -853,33 +865,37 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } - // use aa to see if the mouse pointer is on a - SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, - sequence.findPosition(res)); - - int index = 0; - while (index < allFeatures.length) + /* + * add feature details to tooltip, including any that straddle + * a gapped position + */ + if (av.isShowSequenceFeatures()) { - SequenceFeature sf = allFeatures[index]; - - tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); - - if (sf.getDescription() != null) + List allFeatures = findFeaturesAtRes(sequence, + sequence.findPosition(column)); + if (isGapped) { - tooltipText.append(" " + sf.getDescription()); + removeAdjacentFeatures(allFeatures, column + 1, sequence); } - - if (sf.getValue("status") != null) + for (SequenceFeature sf : allFeatures) { - String status = sf.getValue("status").toString(); - if (status.length() > 0) + tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); + + if (sf.getDescription() != null) { - tooltipText.append(" (" + sf.getValue("status") + ")"); + tooltipText.append(" " + sf.getDescription()); } - } - tooltipText.append("\n"); - index++; + if (sf.getValue("status") != null) + { + String status = sf.getValue("status").toString(); + if (status.length() > 0) + { + tooltipText.append(" (" + sf.getValue("status") + ")"); + } + } + tooltipText.append("\n"); + } } if (tooltip == null) @@ -892,9 +908,38 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } - SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) + /** + * 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, + int column, SequenceI sequence) + { + // TODO should this be an AlignViewController method (shared by gui)? + 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(); + } + } + } + + List findFeaturesAtRes(SequenceI sequence, int res) { - Vector tmp = new Vector(); + List result = new ArrayList<>(); SequenceFeature[] features = sequence.getSequenceFeatures(); if (features != null) { @@ -917,15 +962,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, if ((features[i].getBegin() <= res) && (features[i].getEnd() >= res)) { - tmp.addElement(features[i]); + result.add(features[i]); } } } - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; + return result; } Tooltip tooltip; @@ -965,7 +1007,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, fontSize = 1; } - av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.setFont( + new Font(av.font.getName(), av.font.getStyle(), fontSize), + true); av.setCharWidth(oldWidth); } else @@ -1449,24 +1493,21 @@ public class SeqPanel extends Panel implements MouseMotionListener, // DETECT RIGHT MOUSE BUTTON IN AWT if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, + List allFeatures = findFeaturesAtRes(sequence, sequence.findPosition(res)); Vector links = null; - if (allFeatures != null) + for (SequenceFeature sf : allFeatures) { - for (int i = 0; i < allFeatures.length; i++) + if (sf.links != null) { - if (allFeatures[i].links != null) + if (links == null) { - if (links == null) - { - links = new Vector(); - } - for (int j = 0; j < allFeatures[i].links.size(); j++) - { - links.addElement(allFeatures[i].links.elementAt(j)); - } + links = new Vector<>(); + } + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); } } } @@ -1510,7 +1551,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } - public void doMouseReleasedDefineMode(MouseEvent evt) + public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag) { if (stretchGroup == null) { @@ -1520,7 +1561,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, // but defer colourscheme update until hidden sequences are passed in boolean vischange = stretchGroup.recalcConservation(true); // here we rely on stretchGroup == av.getSelection() - needOverviewUpdate |= vischange && av.isSelectionDefinedGroup(); + needOverviewUpdate |= vischange && av.isSelectionDefinedGroup() + && afterDrag; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1759,24 +1801,24 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (mouseDragging && evt.getY() < 0 && av.getRanges().getStartSeq() > 0) { - running = ap.scrollUp(true); + running = av.getRanges().scrollUp(true); } if (mouseDragging && evt.getY() >= getSize().height && 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() >= getSize().width) { - running = ap.scrollRight(true); + running = av.getRanges().scrollRight(true); } } @@ -1812,7 +1854,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, * Check for selection in a view of which this one is a dna/protein * complement. */ - if (selectionFromTranslation(seqsel, colsel, source)) + if (selectionFromTranslation(seqsel, colsel, hidden, source)) { return; } @@ -1878,15 +1920,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } repaint |= av.isColSelChanged(true); } if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getAlignment() - .getHiddenColumns().getListOfCols() == null)) + && (av.getColumnSelection() == null)) { System.err.println("Bad things"); } @@ -1946,7 +1988,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, * @param source */ protected boolean selectionFromTranslation(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { if (!(source instanceof AlignViewportI)) { @@ -1969,9 +2012,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, /* * Map column selection */ - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, - av); + // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, + // av); + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); + MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); av.setColumnSelection(cs); + av.getAlignment().setHiddenColumns(hs); ap.scalePanelHolder.repaint(); ap.repaint();