X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=0878cbb1cbeaaa328887a9a8e5beb96d79bce69e;hb=496ecb05d48de1ca8471658fd32824f808bb8823;hp=afd324212dd67fab39603d7fb3f01028069b7c83;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index afd3242..0878cbb 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -21,17 +21,22 @@ package jalview.gui; import jalview.api.AlignViewportI; +import jalview.bin.Cache; import jalview.commands.EditCommand; 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.SearchResults.Match; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; 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; @@ -41,6 +46,7 @@ import jalview.structure.VamsasSource; import jalview.util.Comparison; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; @@ -53,11 +59,12 @@ import java.awt.event.MouseListener; 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.Vector; -import javax.swing.JOptionPane; import javax.swing.JPanel; +import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** @@ -120,7 +127,7 @@ public class SeqPanel extends JPanel implements MouseListener, private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(); + StringBuilder tooltipText = new StringBuilder(); String tmpString; @@ -128,6 +135,8 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; + SearchResultsI lastSearchResults; + /** * Creates a new SeqPanel object. * @@ -167,7 +176,14 @@ public class SeqPanel extends JPanel implements MouseListener, int wrappedBlock = -1; - int findRes(MouseEvent evt) + /** + * Returns the aligned sequence position (base 0) at the mouse position, or + * the closest visible one + * + * @param evt + * @return + */ + int findColumn(MouseEvent evt) { int res = 0; int x = evt.getX(); @@ -182,8 +198,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; @@ -196,25 +211,31 @@ public class SeqPanel extends JPanel implements MouseListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getStartRes() / cwidth; + wrappedBlock += av.getRanges().getStartRes() / cwidth; res = wrappedBlock * cwidth + x / av.getCharWidth(); } else { - if (x > seqCanvas.getWidth() + seqCanvas.getWidth()) + if (x > seqCanvas.getX() + seqCanvas.getWidth()) { // make sure we calculate relative to visible alignment, rather than // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } - res = (x / av.getCharWidth()) + av.getStartRes(); + res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + if (res > av.getRanges().getEndRes()) + { + // moused off right + res = av.getRanges().getEndRes(); + } } if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(res); } return res; @@ -235,8 +256,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -245,7 +265,9 @@ 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); } @@ -319,20 +341,23 @@ 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; } @@ -364,37 +389,12 @@ 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, + av); } setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); @@ -496,6 +496,7 @@ public class SeqPanel extends JPanel implements MouseListener, void insertNucAtCursor(boolean group, String nuc) { + // TODO not called - delete? groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; @@ -563,12 +564,20 @@ 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; + if (evt.isPopupTrigger()) // Windows: mouseReleased + { + showPopupMenu(evt); + evt.consume(); + return; + } + if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -586,19 +595,20 @@ public class SeqPanel extends JPanel implements MouseListener, { lastMousePress = evt.getPoint(); - if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + if (SwingUtilities.isMiddleMouseButton(evt)) { mouseWheelPressed = true; return; } - if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) + boolean isControlDown = Platform.isControlDown(evt); + if (evt.isShiftDown() || isControlDown) { - if (evt.isAltDown() || evt.isControlDown()) + editingSeqs = true; + if (isControlDown) { groupEditing = true; } - editingSeqs = true; } else { @@ -607,7 +617,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < 0 || res < 0) { @@ -644,15 +654,33 @@ public class SeqPanel extends JPanel implements MouseListener, lastMessage = tmp; } + /** + * Highlight the mapped region described by the search results object (unless + * unchanged). This supports highlight of protein while mousing over linked + * cDNA and vice versa. The status bar is also updated to show the location of + * the start of the highlighted region. + */ @Override - public void highlightSequence(SearchResults results) + public void highlightSequence(SearchResultsI results) { - if (av.followHighlight) + if (results == null || results.equals(lastSearchResults)) + { + return; + } + lastSearchResults = results; + + 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, false)) { seqCanvas.revalidate(); } + ap.setToScrollComplementPanel(true); } setStatusMessage(results); seqCanvas.highlightSearchResults(results); @@ -663,6 +691,7 @@ public class SeqPanel extends JPanel implements MouseListener, { return this.ap == null ? null : this.ap.av; } + @Override public void updateColours(SequenceI seq, int index) { @@ -686,25 +715,27 @@ 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); + /* + * set status bar message, returning residue position in sequence + */ + final int pos = setStatusMessage(sequence, column, seq); if (ssm != null && pos > -1) { - mouseOverSequence(sequence, res, pos); + mouseOverSequence(sequence, column, pos); } tooltipText.setLength(6); // Cuts the buffer back to @@ -714,7 +745,8 @@ 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")) @@ -730,17 +762,14 @@ public class SeqPanel extends JPanel implements MouseListener, } } - // use aa to see if the mouse pointer is on a - if (av.isShowSequenceFeatures()) + if (av.isShowSequenceFeatures() && pos != -1) { - int rpos; - List features = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), - rpos = sequence.findPosition(res)); - seqARep.appendFeatures(tooltipText, rpos, features, + List features = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), pos); + seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; @@ -768,6 +797,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) */ + @Override public Point getToolTipLocation(MouseEvent event) { int x = event.getX(), w = getWidth(); @@ -788,17 +818,35 @@ public class SeqPanel extends JPanel implements MouseListener, String lastTooltip; /** - * Set status message in alignment panel + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + + /** + * set if av.getSelectionGroup() refers to a group that is defined on the + * alignment view, rather than a transient selection + */ + // private boolean editingDefinedGroup = false; // TODO: refactor to + // avcontroller or viewModel + + /** + * 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. * * @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 a gap */ - int setStatusMessage(SequenceI sequence, int res, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seq) { StringBuilder text = new StringBuilder(32); @@ -806,13 +854,14 @@ public class SeqPanel extends JPanel implements MouseListener, * Sequence number (if known), and sequence name. */ String seqno = seq == -1 ? "" : " " + (seq + 1); - text.append("Sequence" + seqno + " ID: " + sequence.getName()); + 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)); + final String displayChar = String.valueOf(sequence.getCharAt(column)); if (av.getAlignment().isNucleotide()) { residue = ResidueProperties.nucleotideName.get(displayChar); @@ -823,8 +872,9 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - residue = "X".equalsIgnoreCase(displayChar) ? "X" - : ResidueProperties.aa2Triplet.get(displayChar); + residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" + .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet + .get(displayChar)); if (residue != null) { text.append(" Residue: ").append(residue); @@ -834,7 +884,7 @@ public class SeqPanel extends JPanel implements MouseListener, int pos = -1; if (residue != null) { - pos = sequence.findPosition(res); + pos = sequence.findPosition(column); text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); @@ -847,49 +897,67 @@ public class SeqPanel extends JPanel implements MouseListener, * * @param results */ - private void setStatusMessage(SearchResults results) + private void setStatusMessage(SearchResultsI results) { - List matches = results.getResults(); - if (!matches.isEmpty()) + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) + { + return; + } + SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + for (SearchResultMatchI m : results.getResults()) { - Match m = matches.get(0); SequenceI seq = m.getSequence(); - int sequenceIndex = this.av.getAlignment().findIndex(seq); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } - /* - * Convert position in sequence (base 1) to sequence character array index - * (base 0) - */ - int start = m.getStart() - 1; - setStatusMessage(seq, start, sequenceIndex); + 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); + return; + } } } /** - * 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++; } @@ -898,24 +966,56 @@ 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()); @@ -932,7 +1032,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - int res = findRes(evt); + int res = findColumn(evt); if (res < 0) { @@ -988,7 +1088,8 @@ public class SeqPanel extends JPanel implements MouseListener, message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand(MessageManager.getString("action.edit_group")); + editCommand = new EditCommand( + MessageManager.getString("action.edit_group")); } } else @@ -1001,7 +1102,8 @@ public class SeqPanel extends JPanel implements MouseListener, } if (editCommand == null) { - editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); + editCommand = new EditCommand(MessageManager.formatMessage( + "label.edit_params", new String[] { label })); } } @@ -1063,8 +1165,10 @@ 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)) @@ -1122,8 +1226,7 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = 0; j < startres - lastres; j++) { - if (!jalview.util.Comparison.isGap(groupSeqs[g] - .getCharAt(fixedRight - j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -1140,8 +1243,8 @@ 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; @@ -1185,7 +1288,7 @@ public class SeqPanel extends JPanel implements MouseListener, continue; } - if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid endEditing(); @@ -1239,14 +1342,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres); + appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, + startres - lastres); } } else @@ -1263,8 +1365,7 @@ public class SeqPanel extends JPanel implements MouseListener, endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1282,8 +1383,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { - appendEdit(Action.DELETE_GAP, new SequenceI[] - { seq }, startres, max); + appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, + startres, max); } } } @@ -1293,14 +1394,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - appendEdit(Action.INSERT_NUC, new SequenceI[] - { seq }, lastres, startres - lastres); + appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, + startres - lastres); } } } @@ -1320,7 +1420,7 @@ public class SeqPanel extends JPanel implements MouseListener, for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { - if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) + if (Comparison.isGap(seq[s].getCharAt(blankColumn))) { // Theres a space, so break and insert the gap break; @@ -1356,8 +1456,7 @@ public class SeqPanel extends JPanel implements MouseListener, final Edit edit = new EditCommand().new Edit(action, seq, pos, count, av.getAlignment().getGapCharacter()); - editCommand.appendEdit(edit, av.getAlignment(), - true, null); + editCommand.appendEdit(edit, av.getAlignment(), true, null); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) @@ -1409,6 +1508,11 @@ 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) { @@ -1423,22 +1527,27 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), - sequence.findPosition(findRes(evt))); + List features = seqCanvas.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(findColumn(evt))); - if (features != null && features.size()> 0) + if (!features.isEmpty()) { - SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features.get(0).getBegin(), - features.get(0).getEnd()); + /* + * 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); } } @@ -1452,23 +1561,23 @@ 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. @@ -1482,18 +1591,19 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void doMousePressedDefineMode(MouseEvent evt) { - int res = findRes(evt); - int seq = findSeq(evt); + final int res = findColumn(evt); + final int seq = findSeq(evt); oldSeq = seq; + needOverviewUpdate = false; startWrapBlock = wrappedBlock; 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; } @@ -1511,69 +1621,36 @@ 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 + { + showPopupMenu(evt); + return; } - if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + /* + * defer right-mouse click handling to mouseReleased on Windows + * (where isPopupTrigger() will answer true) + * NB isRightMouseButton is also true for Cmd-click on Mac + */ + if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac()) { - List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), sequence.findPosition(res)); - Vector links = new Vector(); - for (SequenceFeature sf:allFeatures) - { - if (sf.links != null) - { - for (int j = 0; j < sf.links.size(); j++) - { - links.addElement(sf.links.elementAt(j)); - } - } - } - - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); - pop.show(this, evt.getX(), evt.getY()); return; } if (av.cursorMode) { - seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorX = findColumn(evt); seqCanvas.cursorY = findSeq(evt); seqCanvas.repaint(); return; @@ -1589,20 +1666,20 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); - stretchGroup = sg; 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 @@ -1621,39 +1698,75 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Build and show a pop-up menu at the right-click mouse position * * @param evt - * DOCUMENT ME! + * @param res + * @param sequences */ - public void doMouseReleasedDefineMode(MouseEvent evt) + void showPopupMenu(MouseEvent 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<>(); + for (SequenceFeature sf : allFeatures) + { + if (sf.links != null) + { + for (String link : sf.links) + { + links.add(link); + } + } + } + + PopupMenu pop = new PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); + } + + /** + * Update the display after mouse up on a selection or group + * + * @param evt + * 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, boolean afterDrag) { if (stretchGroup == null) { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // 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() + && 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()); - ap.paintAlignment(true); - + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1668,7 +1781,7 @@ 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) @@ -1697,9 +1810,9 @@ 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) @@ -1707,6 +1820,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1714,6 +1828,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1747,6 +1862,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } else { @@ -1756,6 +1872,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1829,24 +1946,26 @@ 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); } } @@ -1865,16 +1984,28 @@ 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... // TODO: extend config options to allow user to control if selections may be // shared between viewports. - boolean iSentTheSelection = (av == source - || (source instanceof AlignViewport && ((AlignmentViewport) source) + 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; } @@ -1891,35 +2022,35 @@ 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; } // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - // rules are: colsel is copied if there is a real intersection between - // sequence selection + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ boolean repaint = false; - boolean copycolsel = true; + boolean copycolsel = false; SequenceGroup sgroup = null; if (seqsel != null && seqsel.getSize() > 0) { if (av.getAlignment() == null) { - jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" - + av.getSequenceSetId() + " ViewId=" + av.getViewId() + Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + + " ViewId=" + av.getViewId() + " 's alignment is NULL! returning immediately."); return; } sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - || (colsel == null || colsel.size() == 0)) + if ((sgroup != null && sgroup.getSize() > 0)) { - // don't copy columns if the region didn't intersect. - copycolsel = false; + copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) @@ -1937,7 +2068,7 @@ public class SeqPanel extends JPanel implements MouseListener, { // the current selection is unset or from a previous message // so import the new colsel. - if (colsel == null || colsel.size() == 0) + if (colsel == null || colsel.isEmpty()) { if (av.getColumnSelection() != null) { @@ -1954,7 +2085,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } av.isColSelChanged(true); @@ -1963,8 +2095,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection() - .getHiddenColumns() == null)) + && (av.getAlignment().getHiddenColumns() == null || av + .getAlignment().getHiddenColumns().getHiddenRegions() == null)) { System.err.println("Bad things"); } @@ -1974,6 +2106,13 @@ 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(); + } + } /** @@ -1986,13 +2125,16 @@ 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)) { + if (!(source instanceof AlignViewportI)) + { return false; } final AlignViewportI sourceAv = (AlignViewportI) source; - if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv) + if (sourceAv.getCodingComplement() != av + && av.getCodingComplement() != sourceAv) { return false; } @@ -2007,10 +2149,19 @@ 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.isColSelChanged(true); + av.getAlignment().setHiddenColumns(hs); + + // lastly, update any dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } PaintRefresher.Refresh(this, av.getSequenceSetId());