X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=6fbed49e014db3e2f6e52d614d9c0618e11890e3;hb=b4d2b6a2ed131265ed599db27de9b82aaf010400;hp=36fb052ed0eabc3147587fd0d26d1cb70b176887;hpb=134576f5b34894218bdc4c5ce5e27fa18ad973bd;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 36fb052..6fbed49 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,6 +27,7 @@ import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -35,6 +36,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; +import jalview.renderer.ResidueShaderI; import jalview.schemes.ResidueProperties; import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; @@ -58,9 +60,10 @@ 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; +import java.util.ListIterator; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -181,11 +184,12 @@ 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(); + int startRes = av.getRanges().getStartRes(); if (av.getWrapAlignment()) { @@ -200,7 +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) @@ -209,10 +213,11 @@ public class SeqPanel extends JPanel implements MouseListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.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 { @@ -222,17 +227,18 @@ public class SeqPanel extends JPanel implements MouseListener, // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } - res = (x / av.getCharWidth()) + av.getStartRes(); - if (res > av.getEndRes()) + res = (x / av.getCharWidth()) + startRes; + if (res > av.getRanges().getEndRes()) { // moused off right - res = av.getEndRes(); + res = av.getRanges().getEndRes(); } } if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(res); } return res; @@ -262,7 +268,9 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + seq = Math.min((y / av.getCharHeight()) + + av.getRanges().getStartSeq(), + av .getAlignment().getHeight() - 1); } @@ -336,20 +344,23 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; + + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + if (av.hasHiddenColumns() - && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) + while (!hidden.isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !hidden.isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -381,37 +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.startSeq) - { - ap.scrollUp(true); - } - while (seqCanvas.cursorY + 1 > av.endSeq) - { - ap.scrollUp(false); - } - if (!av.getWrapAlignment()) - { - while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(av.startRes)) - { - if (!ap.scrollRight(false)) - { - break; - } - } - while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.endRes)) - { - if (!ap.scrollRight(true)) - { - break; - } - } - } + av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY); } setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); @@ -581,6 +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; @@ -593,7 +579,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -633,7 +619,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < 0 || res < 0) { @@ -687,17 +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); @@ -732,25 +717,28 @@ 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()) { return; } 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 @@ -760,7 +748,8 @@ 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")) @@ -776,14 +765,20 @@ 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, + .findFeaturesAtRes(sequence.getDatasetSequence(), pos); + if (isGapped) + { + removeAdjacentFeatures(features, column + 1, sequence); + } + seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // @@ -807,6 +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; /* @@ -850,17 +874,22 @@ 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 * 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, int res, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seq) { StringBuilder text = new StringBuilder(32); @@ -872,36 +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(res)); - if (av.getAlignment().isNucleotide()) + final String displayChar = String.valueOf(sequence.getCharAt(column)); + 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(res); text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); + return pos; } @@ -942,30 +969,36 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! + * {@inheritDoc} */ @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) { + boolean inSplitFrame = ap.av.getCodingComplement() != null; + boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna(); + int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt .getX() - lastMousePress.getX())) { + /* + * on drag up or down, decrement or increment font size + */ int fontSize = av.font.getSize(); + boolean fontChanged = false; if (evt.getY() < lastMousePress.getY()) { + fontChanged = true; fontSize--; } else if (evt.getY() > lastMousePress.getY()) { + fontChanged = true; fontSize++; } @@ -974,24 +1007,56 @@ public class SeqPanel extends JPanel implements MouseListener, fontSize = 1; } - av.setFont( - new Font(av.font.getName(), av.font.getStyle(), fontSize), - true); - av.setCharWidth(oldWidth); - ap.fontChanged(); + if (fontChanged) + { + Font newFont = new Font(av.font.getName(), av.font.getStyle(), + fontSize); + av.setFont(newFont, true); + av.setCharWidth(oldWidth); + ap.fontChanged(); + if (copyChanges) + { + ap.av.getCodingComplement().setFont(newFont, true); + SplitFrame splitFrame = (SplitFrame) ap.alignFrame + .getSplitViewContainer(); + splitFrame.adjustLayout(); + splitFrame.repaint(); + } + } } else { + /* + * on drag left or right, decrement or increment character width + */ + int newWidth = 0; if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) { - av.setCharWidth(av.getCharWidth() - 1); + newWidth = av.getCharWidth() - 1; + av.setCharWidth(newWidth); } else if (evt.getX() > lastMousePress.getX()) { - av.setCharWidth(av.getCharWidth() + 1); + newWidth = av.getCharWidth() + 1; + av.setCharWidth(newWidth); + } + if (newWidth > 0) + { + ap.paintAlignment(false); + if (copyChanges) + { + /* + * need to ensure newWidth is set on cdna, regardless of which + * panel the mouse drag happened in; protein will compute its + * character width as 1:1 or 3:1 + */ + av.getCodingComplement().setCharWidth(newWidth); + SplitFrame splitFrame = (SplitFrame) ap.alignFrame + .getSplitViewContainer(); + splitFrame.adjustLayout(); + splitFrame.repaint(); + } } - - ap.paintAlignment(false); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -1008,7 +1073,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - int res = findRes(evt); + int res = findColumn(evt); if (res < 0) { @@ -1141,8 +1206,10 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.hasHiddenColumns()) { fixedColumns = true; - int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); - int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + int y1 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryLeft(startres); + int y2 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryRight(startres); if ((insertGap && startres > y1 && lastres < y1) || (!insertGap && startres < y2 && lastres > y2)) @@ -1217,8 +1284,8 @@ public class SeqPanel extends JPanel implements MouseListener, { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av - .getColumnSelection().getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av.getAlignment() + .getHiddenColumns().getHiddenBoundaryRight(startres))) { endEditing(); return; @@ -1482,6 +1549,11 @@ public class SeqPanel extends JPanel implements MouseListener, } } + /** + * Handler for double-click on a position with one or more sequence features. + * Opens the Amend Features dialog to allow feature details to be amended, or + * the feature deleted. + */ @Override public void mouseClicked(MouseEvent evt) { @@ -1496,24 +1568,38 @@ 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(findRes(evt))); + sequence.findPosition(column)); + if (isGapped) + { + removeAdjacentFeatures(features, column, sequence); + } - if (features != null && features.size() > 0) + if (!features.isEmpty()) { + /* + * highlight the first feature at the position on the alignment + */ SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.size() > 0) - { - seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, - features.toArray(new SequenceFeature[features.size()]), - false, ap); + /* + * open the Amend Features dialog; clear highlighting afterwards, + * whether changes were made or not + */ + List seqs = Collections.singletonList(sequence); + seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, + ap); seqCanvas.highlightSearchResults(null); } } @@ -1527,23 +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. @@ -1557,7 +1643,7 @@ 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; @@ -1566,10 +1652,10 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -1587,42 +1673,15 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup = av.getSelectionGroup(); - if (stretchGroup == null) + if (stretchGroup == null || !stretchGroup.contains(sequence, res)) { - stretchGroup = av.getAlignment().findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) - && (res < stretchGroup.getEndRes())) + stretchGroup = av.getAlignment().findGroup(sequence, res); + if (stretchGroup != null) { + // only update the current selection if the popup menu has a group to + // focus on av.setSelectionGroup(stretchGroup); } - else - { - stretchGroup = null; - } - } - else if (!stretchGroup.getSequences(null).contains(sequence) - || (stretchGroup.getStartRes() > res) - || (stretchGroup.getEndRes() < res)) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); - - if (allGroups != null) - { - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - stretchGroup = allGroups[i]; - break; - } - } - } - - av.setSelectionGroup(stretchGroup); } if (evt.isPopupTrigger()) // Mac: mousePressed @@ -1643,7 +1702,7 @@ 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; @@ -1663,15 +1722,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); } + // TODO: stretchGroup will always be not null. Is this a merge error ? if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) { // Edit end res position of selected group @@ -1694,17 +1754,17 @@ public class SeqPanel extends JPanel implements MouseListener, * * @param evt * @param res - * @param sequence + * @param sequences */ void showPopupMenu(MouseEvent evt) { - final int res = findRes(evt); + final int res = 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(); + List links = new ArrayList<>(); for (SequenceFeature sf : allFeatures) { if (sf.links != null) @@ -1721,12 +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) { @@ -1735,21 +1798,22 @@ 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, av.getHiddenRepSequences()); + ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme(); + String name = stretchGroup.getName(); if (stretchGroup.cs.conservationApplied()) { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setConservationSlider(ap, groupColourScheme, name); } - else + if (stretchGroup.cs.getThreshold() > 0) { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setPIDSliderSource(ap, groupColourScheme, name); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -1769,7 +1833,7 @@ 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) @@ -1798,9 +1862,9 @@ public class SeqPanel extends JPanel implements MouseListener, changeStartRes = true; } - if (res < av.getStartRes()) + if (res < av.getRanges().getStartRes()) { - res = av.getStartRes(); + res = av.getRanges().getStartRes(); } if (changeEndRes) @@ -1934,24 +1998,26 @@ public class SeqPanel extends JPanel implements MouseListener, { if (evt != null) { - if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0)) + 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.getEndSeq())) + && (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); } } @@ -1970,7 +2036,7 @@ public class SeqPanel extends JPanel implements MouseListener, */ @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, - SelectionSource source) + HiddenColumns hidden, SelectionSource source) { // TODO: fix this hack - source of messages is align viewport, but SeqPanel // handles selection messages... @@ -1978,7 +2044,20 @@ public class SeqPanel extends JPanel implements MouseListener, // shared between viewports. boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))); - if (iSentTheSelection || !av.followSelection) + + if (iSentTheSelection) + { + // respond to our own event by updating dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + + return; + } + + // process further ? + if (!av.followSelection) { return; } @@ -1995,7 +2074,7 @@ public class SeqPanel extends JPanel implements MouseListener, * 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; } @@ -2058,7 +2137,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } av.isColSelChanged(true); @@ -2067,8 +2147,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection() - .getHiddenColumns() == null)) + && (av.getAlignment().getHiddenColumns() == null)) { System.err.println("Bad things"); } @@ -2078,6 +2157,13 @@ public class SeqPanel extends JPanel implements MouseListener, PaintRefresher.Refresh(this, av.getSequenceSetId()); // ap.paintAlignment(false); } + + // lastly, update dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + } /** @@ -2090,7 +2176,8 @@ public class SeqPanel extends JPanel implements MouseListener, * @param source */ protected boolean selectionFromTranslation(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { if (!(source instanceof AlignViewportI)) { @@ -2113,9 +2200,19 @@ public class SeqPanel extends JPanel implements MouseListener, /* * 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); + + // lastly, update any dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } PaintRefresher.Refresh(this, av.getSequenceSetId());