X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=dbbf510bf324101a4f4b32dd53df694f0f8825b4;hb=16eb01c0d83f94f2c1065b6688166d8624529fa2;hp=885aab25810b925766dd9793f5d20221b1e54fc9;hpb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 885aab2..dbbf510 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,13 +27,16 @@ 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; @@ -57,9 +60,9 @@ 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 javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -70,9 +73,9 @@ import javax.swing.ToolTipManager; * @author $author$ * @version $Revision: 1.130 $ */ -public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener, SequenceListener, - SelectionListener +public class SeqPanel extends JPanel + implements MouseListener, MouseMotionListener, MouseWheelListener, + SequenceListener, SelectionListener { /** DOCUMENT ME!! */ @@ -81,6 +84,16 @@ public class SeqPanel extends JPanel implements MouseListener, /** DOCUMENT ME!! */ public AlignmentPanel ap; + /* + * last column position for mouseMoved event + */ + private int lastMouseColumn; + + /* + * last sequence offset for mouseMoved event + */ + private int lastMouseSeq; + protected int lastres; protected int startseq; @@ -132,7 +145,7 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; - SearchResults lastSearchResults; + SearchResultsI lastSearchResults; /** * Creates a new SeqPanel object. @@ -167,6 +180,9 @@ public class SeqPanel extends JPanel implements MouseListener, ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } + + lastMouseColumn = -1; + lastMouseSeq = -1; } int startWrapBlock = -1; @@ -180,11 +196,12 @@ 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()) { @@ -198,8 +215,8 @@ public class SeqPanel extends JPanel implements MouseListener, + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); - y -= hgap; - x -= seqCanvas.LABEL_WEST; + y = Math.max(0, y - hgap); + x = Math.max(0, x - seqCanvas.getLabelWidthWest()); int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) @@ -208,10 +225,11 @@ 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 + startOffset + + +Math.min(cwidth - 1, x / av.getCharWidth()); } else { @@ -221,17 +239,18 @@ 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; @@ -256,13 +275,14 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() - .getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), + av.getAlignment().getHeight() - 1); } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av - .getAlignment().getHeight() - 1); + seq = Math.min( + (y / av.getCharHeight()) + av.getRanges().getStartSeq(), + av.getAlignment().getHeight() - 1); } return seq; @@ -279,8 +299,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (editCommand != null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } } finally { @@ -335,20 +355,25 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; - if (av.hasHiddenColumns() - && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + + if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) + // TODO: once JAL-2759 is ready, change this loop to something more + // efficient + while (!hidden.isVisible(seqCanvas.cursorX) + && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0 + && dx != 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !hidden.isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -380,37 +405,11 @@ 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); @@ -488,7 +487,7 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(sg); } - ap.paintAlignment(false); + ap.paintAlignment(false, false); av.sendSelection(); } @@ -580,6 +579,7 @@ 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; @@ -592,7 +592,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -632,7 +632,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < 0 || res < 0) { @@ -676,7 +676,7 @@ public class SeqPanel extends JPanel implements MouseListener, * the start of the highlighted region. */ @Override - public void highlightSequence(SearchResults results) + public void highlightSequence(SearchResultsI results) { if (results == null || results.equals(lastSearchResults)) { @@ -684,22 +684,28 @@ public class SeqPanel extends JPanel implements MouseListener, } lastSearchResults = results; + boolean wasScrolled = false; + 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); - if (ap.scrollToPosition(results, false)) + // 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); + wasScrolled = ap.scrollToPosition(results, false); + if (wasScrolled) { seqCanvas.revalidate(); } + ap.setToScrollComplementPanel(true); + } + + boolean noFastPaint = wasScrolled && av.getWrapAlignment(); + if (seqCanvas.highlightSearchResults(results, noFastPaint)) + { + setStatusMessage(results); } - setStatusMessage(results); - seqCanvas.highlightSearchResults(results); } @Override @@ -716,10 +722,12 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Action on mouse movement is to update the status bar to show the current + * sequence position, and (if features are shown) to show any features at the + * position in a tooltip. Does nothing if the mouse move does not change + * residue position. * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) @@ -731,25 +739,39 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragged(evt); } - int res = findRes(evt); - int seq = findSeq(evt); - int pos; - if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + final int column = findColumn(evt); + final int seq = findSeq(evt); + + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { + lastMouseSeq = -1; return; } + if (column == lastMouseColumn && seq == lastMouseSeq) + { + /* + * just a pixel move without change of residue + */ + return; + } + lastMouseColumn = column; + lastMouseSeq = seq; SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (res >= sequence.getLength()) + if (column >= sequence.getLength()) { return; } - pos = setStatusMessage(sequence, res, seq); - if (ssm != null && pos > -1) + /* + * set status bar message, returning residue position in sequence + */ + boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); + final int pos = setStatusMessage(sequence, column, seq); + if (ssm != null && !isGapped) { - mouseOverSequence(sequence, res, pos); + mouseOverSequence(sequence, column, pos); } tooltipText.setLength(6); // Cuts the buffer back to @@ -759,7 +781,8 @@ 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")) @@ -775,35 +798,34 @@ public class SeqPanel extends JPanel implements MouseListener, } } - // use aa to see if the mouse pointer is on a + /* + * add any features at the position to the tooltip; if over a gap, only + * add features that straddle the gap (pos may be the residue before or + * after the gap) + */ if (av.isShowSequenceFeatures()) { - int rpos; List features = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - rpos = sequence.findPosition(res)); - seqARep.appendFeatures(tooltipText, rpos, features, + .findFeaturesAtColumn(sequence, column + 1); + seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; } else { - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) + String textString = tooltipText.toString(); + if (lastTooltip == null || !lastTooltip.equals(textString)) { - String formatedTooltipText = JvSwingUtils.wrapTooltip(true, - tooltipText.toString()); - // String formatedTooltipText = tooltipText.toString(); - setToolTipText(formatedTooltipText); - lastTooltip = tooltipText.toString(); + String formattedTooltipText = JvSwingUtils.wrapTooltip(true, + textString); + setToolTipText(formattedTooltipText); + lastTooltip = textString; } - } - } private Point lastp = null; @@ -822,8 +844,9 @@ public class SeqPanel extends JPanel implements MouseListener, Point p = lastp; if (!event.isShiftDown() || p == null) { - p = (tooltipText != null && tooltipText.length() > 6) ? new Point( - event.getX() + wdth, event.getY() - 20) : null; + p = (tooltipText != null && tooltipText.length() > 6) + ? new Point(event.getX() + wdth, event.getY() - 20) + : null; } /* * TODO: try to modify position region is not obcured by tooltip @@ -835,11 +858,12 @@ public class SeqPanel extends JPanel implements MouseListener, /** * 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 + * shading in overviews and structures to be recalculated. this could be + * changed to a something more expressive that indicates what actually has + * changed, so selective redraws can be applied (ie. only structures, only + * overview, etc) */ - private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller /** * set if av.getSelectionGroup() refers to a group that is defined on the @@ -849,59 +873,88 @@ public class SeqPanel extends JPanel implements MouseListener, // avcontroller or viewModel /** - * Set status message in alignment panel + * Sets the status message in alignment panel, showing the sequence number + * (index) and id, and residue and residue position if not at a gap, for the + * given sequence and column position. Returns the residue position returned + * by Sequence.findPosition. Note this may be for the nearest adjacent residue + * if at a gapped position. * * @param sequence * aligned sequence object - * @param res + * @param column * alignment column - * @param seq + * @param seqIndex * index of sequence in alignment - * @return position of res in sequence + * @return sequence position of residue at column, or adjacent residue if at a + * gap */ - int setStatusMessage(SequenceI sequence, int res, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seqIndex) + { + char sequenceChar = sequence.getCharAt(column); + int pos = sequence.findPosition(column); + setStatusMessage(sequence, seqIndex, sequenceChar, pos); + + return pos; + } + + /** + * Builds the status message for the current cursor location and writes it to + * the status bar, for example + * + * 
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   *
+ * + * @param sequence + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) + */ + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ - String seqno = seq == -1 ? "" : " " + (seq + 1); + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") .append(sequence.getName()); String residue = null; + /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(res)); - if (av.getAlignment().isNucleotide()) + boolean isGapped = Comparison.isGap(sequenceChar); + + if (!isGapped) { - residue = ResidueProperties.nucleotideName.get(displayChar); - if (residue != null) + boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); + if (nucleotide) { - text.append(" Nucleotide: ").append(residue); + residue = ResidueProperties.nucleotideName.get(displayChar); } - } - else - { - residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" - .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet - .get(displayChar)); - if (residue != null) + else { - text.append(" Residue: ").append(residue); + residue = "X".equalsIgnoreCase(displayChar) ? "X" + : ("*".equals(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar)); } - } + text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") + .append(": ").append(residue == null ? displayChar : residue); - int pos = -1; - if (residue != null) - { - pos = sequence.findPosition(res); - text.append(" (").append(Integer.toString(pos)).append(")"); + text.append(" (").append(Integer.toString(residuePos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); - return pos; } /** @@ -910,7 +963,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @param results */ - private void setStatusMessage(SearchResults results) + private void setStatusMessage(SearchResultsI results) { AlignmentI al = this.av.getAlignment(); int sequenceIndex = al.findIndex(results); @@ -919,7 +972,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); - for (Match m : results.getResults()) + for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); if (seq.getDatasetSequence() != null) @@ -929,42 +982,45 @@ public class SeqPanel extends JPanel implements MouseListener, if (seq == ds) { - /* - * Convert position in sequence (base 1) to sequence character array - * index (base 0) - */ - int start = m.getStart() - m.getSequence().getStart(); - setStatusMessage(seq, start, sequenceIndex); + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); return; } } } /** - * 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())) + 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++; } @@ -973,24 +1029,56 @@ 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, 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()); @@ -1007,7 +1095,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - int res = findRes(evt); + int res = findColumn(evt); if (res < 0) { @@ -1030,7 +1118,7 @@ public class SeqPanel extends JPanel implements MouseListener, } mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } @@ -1077,8 +1165,9 @@ 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 })); } } @@ -1095,9 +1184,8 @@ public class SeqPanel extends JPanel implements MouseListener, ap.alignFrame.statusBar.setText(message.toString()); // Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.getSequences(av.getHiddenRepSequences()) - .contains(seq))) + if (groupEditing || (sg != null + && sg.getSequences(av.getHiddenRepSequences()).contains(seq))) { fixedColumns = true; @@ -1140,8 +1228,10 @@ 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)) @@ -1191,7 +1281,7 @@ public class SeqPanel extends JPanel implements MouseListener, // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--) + for (; fixedRight > lastres; fixedRight--) { blank = true; @@ -1216,8 +1306,8 @@ 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; @@ -1283,8 +1373,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres - - lastres); + appendEdit(Action.INSERT_GAP, groupSeqs, startres, + startres - lastres); } } else @@ -1299,8 +1389,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres - - startres); + appendEdit(Action.DELETE_GAP, groupSeqs, startres, + lastres - startres); } } @@ -1454,9 +1544,9 @@ public class SeqPanel extends JPanel implements MouseListener, oldSeq = 0; } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } } @@ -1475,12 +1565,17 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - if (mouseDragging) + if (mouseDragging && scrollThread == null) { scrollThread = new ScrollThread(); } } + /** + * 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) { @@ -1495,25 +1590,34 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } + int column = findColumn(evt); + + /* + * find features at the position (if not gapped), or straddling + * the position (if at a gap) + */ List features = seqCanvas.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(findRes(evt))); + .findFeaturesAtColumn(sequence, column + 1); - if (features != null && features.size() > 0) + if (!features.isEmpty()) { - SearchResults highlight = new SearchResults(); + /* + * 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); + seqCanvas.highlightSearchResults(highlight, false); - seqCanvas.highlightSearchResults(null); + /* + * 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); + av.setSearchResults(null); // clear highlighting + seqCanvas.repaint(); // draw new/amended features } } } @@ -1526,26 +1630,32 @@ 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. + + /* + * update status bar and tooltip for new position + * (need to synthesize a mouse movement to refresh tooltip) + */ + mouseMoved(e); + ToolTipManager.sharedInstance().mouseMoved(e); } /** @@ -1556,19 +1666,20 @@ 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; + updateOverviewAndStructs = false; startWrapBlock = wrappedBlock; if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.cannot_edit_annotations_in_wrapped_view"), + 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; } @@ -1586,42 +1697,15 @@ 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 @@ -1642,7 +1726,7 @@ 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; @@ -1650,42 +1734,53 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup == null) { - // Only if left mouse button do we want to change group sizes + createStretchGroup(res, sequence); + } - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + if (stretchGroup != null) + { + stretchGroup.addPropertyChangeListener(seqCanvas); + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); - } + seqCanvas.repaint(); + } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); - } - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if ((stretchGroup != null) - && (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } - stretchGroup.getWidth(); + private void createStretchGroup(int res, SequenceI sequence) + { + // Only if left mouse button do we want to change group sizes + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } - seqCanvas.repaint(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); + } + // TODO: stretchGroup will always be not null. Is this a merge error ? + // or is there a threading issue here? + if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); + } /** @@ -1693,17 +1788,16 @@ 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 column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); List allFeatures = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); - List links = new ArrayList(); + .findFeaturesAtColumn(sequence, column + 1); + List links = new ArrayList<>(); for (SequenceFeature sf : allFeatures) { if (sf.links != null) @@ -1720,40 +1814,50 @@ 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) { return; } + + stretchGroup.removePropertyChangeListener(seqCanvas); + // 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(); + updateOverviewAndStructs |= 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(needOverviewUpdate); - needOverviewUpdate = false; + // TODO: structure colours only need updating if stretchGroup used to or now + // does contain sequences with structure views + ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs); + updateOverviewAndStructs = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1768,7 +1872,7 @@ 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) @@ -1797,9 +1901,9 @@ 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) @@ -1807,7 +1911,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1815,7 +1919,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1849,7 +1953,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } else { @@ -1859,7 +1963,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1870,21 +1974,19 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } - - seqCanvas.repaint(); } void scrollCanvas(MouseEvent evt) { if (evt == null) { - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } mouseDragging = false; @@ -1907,7 +2009,7 @@ public class SeqPanel extends JPanel implements MouseListener, { MouseEvent evt; - boolean running = false; + private volatile boolean threadRunning = true; public ScrollThread() { @@ -1921,36 +2023,40 @@ public class SeqPanel extends JPanel implements MouseListener, public void stopScrolling() { - running = false; + threadRunning = false; + } + + public boolean isRunning() + { + return threadRunning; } @Override public void run() { - running = true; - - while (running) + while (threadRunning) { if (evt != null) { - if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging && (evt.getY() < 0) + && (av.getRanges().getStartSeq() > 0)) { - running = ap.scrollUp(true); + av.getRanges().scrollUp(true); } - if (mouseDragging && (evt.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + if (mouseDragging && (evt.getY() >= getHeight()) && (av + .getAlignment().getHeight() > av.getRanges().getEndSeq())) { - running = ap.scrollUp(false); + av.getRanges().scrollUp(false); } if (mouseDragging && (evt.getX() < 0)) { - running = ap.scrollRight(false); + av.getRanges().scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = ap.scrollRight(true); + av.getRanges().scrollRight(true); } } @@ -1969,15 +2075,30 @@ 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) - .getSequenceSetId().equals(av.getSequenceSetId()))); - if (iSentTheSelection || !av.followSelection) + boolean iSentTheSelection = (av == source + || (source instanceof AlignViewport + && ((AlignmentViewport) source).getSequenceSetId() + .equals(av.getSequenceSetId()))); + + 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; } @@ -1994,7 +2115,7 @@ 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; } @@ -2057,17 +2178,16 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } av.isColSelChanged(true); repaint = true; } - if (copycolsel - && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection() - .getHiddenColumns() == null)) + if (copycolsel && av.hasHiddenColumns() + && (av.getAlignment().getHiddenColumns() == null)) { System.err.println("Bad things"); } @@ -2077,6 +2197,13 @@ 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(); + } + } /** @@ -2089,7 +2216,8 @@ 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)) { @@ -2112,9 +2240,19 @@ 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());