X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2884c501cc87f2dc65bed280e3a59041f01ed054;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=14274e27a0db2eb372d060a83d71a06b7c64e4f6;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 14274e2..7abbd7d 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,21 +20,35 @@ */ 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.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; +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; import jalview.structure.SequenceListener; import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.Comparison; +import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.Color; @@ -46,11 +60,11 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; +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; /** @@ -59,20 +73,100 @@ 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!! */ + /* + * a class that holds computed mouse position + * - column of the alignment (0...) + * - sequence offset (0...) + * - annotation row offset (0...) + * where annotation offset is -1 unless the alignment is shown + * in wrapped mode, annotations are shown, and the mouse is + * over an annnotation row + */ + static class MousePos + { + /* + * alignment column position of cursor (0...) + */ + final int column; + + /* + * index in alignment of sequence under cursor, + * or nearest above if cursor is not over a sequence + */ + final int seqIndex; + + /* + * index in annotations array of annotation under the cursor + * (only possible in wrapped mode with annotations shown), + * or -1 if cursor is not over an annotation row + */ + final int annotationIndex; + + MousePos(int col, int seq, int ann) + { + column = col; + seqIndex = seq; + annotationIndex = ann; + } + + boolean isOverAnnotation() + { + return annotationIndex != -1; + } + + @Override + public boolean equals(Object obj) + { + if (obj == null || !(obj instanceof MousePos)) + { + return false; + } + MousePos o = (MousePos) obj; + boolean b = (column == o.column && seqIndex == o.seqIndex + && annotationIndex == o.annotationIndex); + // System.out.println(obj + (b ? "= " : "!= ") + this); + return b; + } + + /** + * A simple hashCode that ensures that instances that satisfy equals() have + * the same hashCode + */ + @Override + public int hashCode() + { + return column + seqIndex + annotationIndex; + } + + /** + * toString method for debug output purposes only + */ + @Override + public String toString() + { + return String.format("c%d:s%d:a%d", column, seqIndex, + annotationIndex); + } + } + + private static final int MAX_TOOLTIP_LENGTH = 300; + public SeqCanvas seqCanvas; - /** DOCUMENT ME!! */ public AlignmentPanel ap; - protected int lastres; + /* + * last position for mouseMoved event + */ + private MousePos lastMousePosition; - protected int startseq; + protected int editLastRes; + + protected int editStartSeq; protected AlignViewport av; @@ -113,7 +207,7 @@ public class SeqPanel extends JPanel implements MouseListener, private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(); + StringBuilder tooltipText = new StringBuilder(); String tmpString; @@ -121,36 +215,36 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; + SearchResultsI lastSearchResults; + /** - * Creates a new SeqPanel object. + * Creates a new SeqPanel object * - * @param avp - * DOCUMENT ME! - * @param p - * DOCUMENT ME! + * @param viewport + * @param alignPanel */ - public SeqPanel(AlignViewport av, AlignmentPanel ap) + public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { linkImageURL = getClass().getResource("/images/link.gif"); seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = av; + this.av = viewport; setBackground(Color.white); - seqCanvas = new SeqCanvas(ap); + seqCanvas = new SeqCanvas(alignPanel); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - this.ap = ap; + this.ap = alignPanel; - if (!av.isDataset()) + if (!viewport.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = av.getStructureSelectionManager(); + ssm = viewport.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -160,155 +254,183 @@ public class SeqPanel extends JPanel implements MouseListener, int wrappedBlock = -1; - int findRes(MouseEvent evt) + /** + * Computes the column and sequence row (and possibly annotation row when in + * wrapped mode) for the given mouse position + * + * @param evt + * @return + */ + MousePos findMousePosition(MouseEvent evt) + { + int col = findColumn(evt); + int seqIndex = -1; + int annIndex = -1; + int y = evt.getY(); + + int charHeight = av.getCharHeight(); + int alignmentHeight = av.getAlignment().getHeight(); + if (av.getWrapAlignment()) + { + seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(), + seqCanvas.getHeight()); + + /* + * yPos modulo height of repeating width + */ + int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx; + + /* + * height of sequences plus space / scale above, + * plus gap between sequences and annotations + */ + int alignmentHeightPixels = seqCanvas.wrappedSpaceAboveAlignment + + alignmentHeight * charHeight + + SeqCanvas.SEQS_ANNOTATION_GAP; + if (yOffsetPx >= alignmentHeightPixels) + { + /* + * mouse is over annotations; find annotation index, also set + * last sequence above (for backwards compatible behaviour) + */ + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + int rowOffsetPx = yOffsetPx - alignmentHeightPixels; + annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns); + seqIndex = alignmentHeight - 1; + } + else + { + /* + * mouse is over sequence (or the space above sequences) + */ + yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment; + if (yOffsetPx >= 0) + { + seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); + } + } + } + else + { + seqIndex = Math.min((y / charHeight) + av.getRanges().getStartSeq(), + alignmentHeight - 1); + } + + return new MousePos(col, seqIndex, annIndex); + } + /** + * 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(); - if (av.wrapAlignment) - { + final int startRes = av.getRanges().getStartRes(); + final int charWidth = av.getCharWidth(); - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + if (av.getWrapAlignment()) + { + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) { - hgap += av.charHeight; + hgap += av.getCharHeight(); } - int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap - + seqCanvas.getAnnotationHeight(); + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); - y -= hgap; - x -= seqCanvas.LABEL_WEST; + y = Math.max(0, y - hgap); + x -= seqCanvas.getLabelWidthWest(); + if (x < 0) + { + // mouse is over left scale + return -1; + } int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) { return 0; } + if (x >= cwidth * charWidth) + { + // mouse is over right scale + return -1; + } 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 / charWidth); } else { - if (x > seqCanvas.getWidth() + 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(); + /* + * make sure we calculate relative to visible alignment, + * rather than right-hand gutter + */ + x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth()); + res = (x / charWidth) + startRes; + res = Math.min(res, av.getRanges().getEndRes()); } if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .visibleToAbsoluteColumn(res); } return res; - } - int findSeq(MouseEvent evt) + /** + * When all of a sequence of edits are complete, put the resulting edit list + * on the history stack (undo list), and reset flags for editing in progress. + */ + void endEditing() { - int seq = 0; - int y = evt.getY(); - - if (av.wrapAlignment) + try { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + if (editCommand != null && editCommand.getSize() > 0) { - hgap += av.charHeight; + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } - - int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap - + seqCanvas.getAnnotationHeight(); - - y -= hgap; - - seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() - .getHeight() - 1); - } - else + } finally { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av - .getAlignment().getHeight() - 1); + /* + * Tidy up come what may... + */ + editStartSeq = -1; + editLastRes = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; } - - return seq; - } - - SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) - { - Vector tmp = new Vector(); - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (features != null) - { - for (int i = 0; i < features.length; i++) - { - if (av.featuresDisplayed == null - || !av.featuresDisplayed.containsKey(features[i].getType())) - { - continue; - } - - if (features[i].featureGroup != null - && seqCanvas.fr.featureGroups != null - && seqCanvas.fr.featureGroups - .containsKey(features[i].featureGroup) - && !((Boolean) seqCanvas.fr.featureGroups - .get(features[i].featureGroup)).booleanValue()) - { - continue; - } - - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) - { - tmp.addElement(features[i]); - } - } - } - - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; - } - - void endEditing() - { - if (editCommand != null && editCommand.getSize() > 0) - { - ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); - } - - startseq = -1; - lastres = -1; - editingSeqs = false; - groupEditing = false; - keyboardNo1 = null; - keyboardNo2 = null; - editCommand = null; } void setCursorRow() { seqCanvas.cursorY = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorColumn() { seqCanvas.cursorX = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorRowAndColumn() @@ -321,7 +443,7 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX = getKeyboardNo1() - 1; seqCanvas.cursorY = getKeyboardNo2() - 1; - scrollToVisible(); + scrollToVisible(true); } } @@ -330,36 +452,59 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; - scrollToVisible(); + scrollToVisible(true); } void moveCursor(int dx, int dy) { 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) + if (!hidden.isVisible(seqCanvas.cursorX)) { - seqCanvas.cursorX += dx; + int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx); + int[] region = hidden.getRegionWithEdgeAtRes(visx); + + if (region != null) // just in case + { + if (dx == 1) + { + // moving right + seqCanvas.cursorX = region[1] + 1; + } + else if (dx == -1) + { + // moving left + seqCanvas.cursorX = region[0] - 1; + } + } + seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !hidden.isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } } - scrollToVisible(); + scrollToVisible(false); } - void scrollToVisible() + /** + * Scroll to make the cursor visible in the viewport. + * + * @param jump + * just jump to the location rather than scrolling + */ + void scrollToVisible(boolean jump) { if (seqCanvas.cursorX < 0) { @@ -380,46 +525,44 @@ public class SeqPanel extends JPanel implements MouseListener, } endEditing(); - if (av.wrapAlignment) + + boolean repaintNeeded = true; + if (jump) { - ap.scrollToWrappedVisible(seqCanvas.cursorX); + // only need to repaint if the viewport did not move, as otherwise it will + // get a repaint + repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX, + seqCanvas.cursorY); } else { - while (seqCanvas.cursorY < av.startSeq) - { - ap.scrollUp(true); - } - while (seqCanvas.cursorY + 1 > av.endSeq) + if (av.getWrapAlignment()) { - ap.scrollUp(false); + // scrollToWrappedVisible expects x-value to have hidden cols subtracted + int x = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(seqCanvas.cursorX); + av.getRanges().scrollToWrappedVisible(x); } - if (!av.wrapAlignment) + else { - 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), + + if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX)) + { + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); + } - seqCanvas.repaint(); + if (repaintNeeded) + { + seqCanvas.repaint(); + } } + void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); @@ -490,15 +633,15 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(sg); } - ap.paintAlignment(false); + ap.paintAlignment(false, false); av.sendSelection(); } void insertGapAtCursor(boolean group) { groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX; editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -506,17 +649,18 @@ public class SeqPanel extends JPanel implements MouseListener, void deleteGapAtCursor(boolean group) { groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX + getKeyboardNo1(); + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX + getKeyboardNo1(); editSequence(false, false, seqCanvas.cursorX); endEditing(); } void insertNucAtCursor(boolean group, String nuc) { + // TODO not called - delete? groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX; editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -581,12 +725,26 @@ public class SeqPanel extends JPanel implements MouseListener, @Override public void mouseReleased(MouseEvent evt) { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } + + boolean didDrag = mouseDragging; // did we come here after a drag mouseDragging = false; mouseWheelPressed = false; + if (evt.isPopupTrigger()) // Windows: mouseReleased + { + showPopupMenu(evt, pos); + evt.consume(); + return; + } + if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -603,45 +761,46 @@ public class SeqPanel extends JPanel implements MouseListener, public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } - 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 { - doMousePressedDefineMode(evt); + doMousePressedDefineMode(evt, pos); return; } - int seq = findSeq(evt); - int res = findRes(evt); - - if (seq < 0 || res < 0) - { - return; - } + int seq = pos.seqIndex; + int res = pos.column; if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) { - startseq = seq; - lastres = res; + editStartSeq = seq; + editLastRes = res; } else { - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; } return; @@ -662,17 +821,49 @@ 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)) { - if (ap.scrollToPosition(results, false)) + return; + } + lastSearchResults = results; + + boolean wasScrolled = false; + + 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); + wasScrolled = ap.scrollToPosition(results); + if (wasScrolled) { seqCanvas.revalidate(); } + ap.setToScrollComplementPanel(true); } - seqCanvas.highlightSearchResults(results); + + boolean noFastPaint = wasScrolled && av.getWrapAlignment(); + if (seqCanvas.highlightSearchResults(results, noFastPaint)) + { + setStatusMessage(results); + } + } + + @Override + public VamsasSource getVamsasSource() + { + return this.ap == null ? null : this.ap.av; } @Override @@ -683,10 +874,12 @@ 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) @@ -698,25 +891,48 @@ 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 MousePos mousePos = findMousePosition(evt); + if (mousePos.equals(lastMousePosition)) + { + /* + * just a pixel move without change of 'cell' + */ + return; + } + lastMousePosition = mousePos; + + if (mousePos.isOverAnnotation()) { + mouseMovedOverAnnotation(mousePos); + return; + } + final int seq = mousePos.seqIndex; + + final int column = mousePos.column; + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + { + lastMousePosition = null; + setToolTipText(null); + lastTooltip = null; + ap.alignFrame.setStatus(""); 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 @@ -726,7 +942,8 @@ 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")) @@ -742,35 +959,68 @@ public class SeqPanel extends JPanel implements MouseListener, } } - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + /* + * 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; - SequenceFeature[] features = findFeaturesAtRes( - sequence.getDatasetSequence(), - rpos = sequence.findPosition(res)); - seqARep.appendFeatures(tooltipText, rpos, features, - this.ap.seqPanel.seqCanvas.fr.minmax); + List features = ap.getFeatureRenderer() + .findFeaturesAtColumn(sequence, column + 1); + seqARep.appendFeatures(tooltipText, pos, features, + this.ap.getSeqPanel().seqCanvas.fr); } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; } else { - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) + if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant + { + tooltipText.setLength(MAX_TOOLTIP_LENGTH); + tooltipText.append("..."); + } + 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; } + } + } + /** + * When the view is in wrapped mode, and the mouse is over an annotation row, + * shows the corresponding tooltip and status message (if any) + * + * @param pos + * @param column + */ + protected void mouseMovedOverAnnotation(MousePos pos) + { + final int column = pos.column; + final int rowIndex = pos.annotationIndex; + + if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation() + || rowIndex < 0) + { + return; } + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + + String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column, + anns); + setToolTipText(tooltip); + lastTooltip = tooltip; + String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, + anns[rowIndex]); + ap.alignFrame.setStatus(msg); } private Point lastp = null; @@ -780,98 +1030,204 @@ 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(); - int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too - // close to edge + if (tooltipText == null || tooltipText.length() <= 6) + { + lastp = null; + return null; + } + + int x = event.getX(); + int w = getWidth(); + // switch sides when tooltip is too close to edge + int wdth = (w - x < 200) ? -(w / 2) : 5; Point p = lastp; if (!event.isShiftDown() || p == null) { - p = (tooltipText != null && tooltipText.length() > 6) ? new Point( - event.getX() + wdth, event.getY() - 20) : null; + p = new Point(event.getX() + wdth, event.getY() - 20); + lastp = p; } /* - * TODO: try to modify position region is not obcured by tooltip + * TODO: try to set position so region is not obscured by tooltip */ - return lastp = p; + return p; } String lastTooltip; /** - * Set status message in alignment panel + * set when the current UI interaction has resulted in a change that requires + * 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 updateOverviewAndStructs = 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, 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, 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) */ - int setStatusMessage(SequenceI sequence, int res, int seq) + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { - int pos = -1; - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " - + sequence.getName()); + StringBuilder text = new StringBuilder(32); + + /* + * Sequence number (if known), and sequence name. + */ + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); + text.append("Sequence").append(seqno).append(" ID: ") + .append(sequence.getName()); + + String residue = null; - Object obj = null; - if (av.getAlignment().isNucleotide()) + /* + * Try to translate the display character to residue name (null for gap). + */ + boolean isGapped = Comparison.isGap(sequenceChar); + + if (!isGapped) { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) - + ""); - if (obj != null) + boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); + if (nucleotide) { - text.append(" Nucleotide: "); + residue = ResidueProperties.nucleotideName.get(displayChar); } - } - else - { - obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - if (obj != null) + else { - text.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); + + text.append(" (").append(Integer.toString(residuePos)).append(")"); } + ap.alignFrame.setStatus(text.toString()); + } - if (obj != null) + /** + * Set the status bar message to highlight the first matched position in + * search results. + * + * @param results + */ + private void setStatusMessage(SearchResultsI results) + { + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) { - pos = sequence.findPosition(res); - if (obj != "") + return; + } + SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + for (SearchResultMatchI m : results.getResults()) + { + SequenceI seq = m.getSequence(); + if (seq.getDatasetSequence() != null) { - text.append(obj + " (" + pos + ")"); + seq = seq.getDatasetSequence(); + } + + if (seq == ds) + { + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); + return; } } - ap.alignFrame.statusBar.setText(text.toString()); - return pos; } /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! + * {@inheritDoc} */ @Override public void mouseDragged(MouseEvent evt) { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.column == -1) + { + return; + } + if (mouseWheelPressed) { - int oldWidth = av.charWidth; + 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++; } @@ -880,26 +1236,60 @@ public class SeqPanel extends JPanel implements MouseListener, fontSize = 1; } - av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); - av.charWidth = 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 { - if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) + /* + * on drag left or right, decrement or increment character width + */ + int newWidth = 0; + if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) { - av.charWidth--; + newWidth = av.getCharWidth() - 1; + av.setCharWidth(newWidth); } else if (evt.getX() > lastMousePress.getX()) { - av.charWidth++; + 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()); - av.validCharWidth = fm.charWidth('M') <= av.charWidth; + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); lastMousePress = evt.getPoint(); @@ -908,23 +1298,23 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseDraggedDefineMode(evt); + dragStretchGroup(evt); return; } - int res = findRes(evt); + int res = pos.column; if (res < 0) { res = 0; } - if ((lastres == -1) || (lastres == res)) + if ((editLastRes == -1) || (editLastRes == res)) { return; } - if ((res < av.getAlignment().getWidth()) && (res < lastres)) + if ((res < av.getAlignment().getWidth()) && (res < editLastRes)) { // dragLeft, delete gap editSequence(false, false, res); @@ -935,22 +1325,46 @@ public class SeqPanel extends JPanel implements MouseListener, } mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } } - // TODO: Make it more clever than many booleans + /** + * Edits the sequence to insert or delete one or more gaps, in response to a + * mouse drag or cursor mode command. The number of inserts/deletes may be + * specified with the cursor command, or else depends on the mouse event + * (normally one column, but potentially more for a fast mouse drag). + *

+ * Delete gaps is limited to the number of gaps left of the cursor position + * (mouse drag), or at or right of the cursor position (cursor mode). + *

+ * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in + * the current selection group. + *

+ * In locked editing mode (with a selection group present), inserts/deletions + * within the selection group are limited to its boundaries (and edits outside + * the group stop at its border). + * + * @param insertGap + * true to insert gaps, false to delete gaps + * @param editSeq + * (unused parameter) + * @param startres + * the column at which to perform the action; the number of columns + * affected depends on this.editLastRes (cursor column + * position) + */ synchronized void editSequence(boolean insertGap, boolean editSeq, - int startres) + final int startres) { int fixedLeft = -1; int fixedRight = -1; boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); - SequenceI seq = av.getAlignment().getSequenceAt(startseq); + final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq); // No group, but the sequence may represent a group if (!groupEditing && av.hasHiddenRows()) @@ -962,27 +1376,38 @@ public class SeqPanel extends JPanel implements MouseListener, } } - StringBuffer message = new StringBuffer(); + StringBuilder message = new StringBuilder(64); // for status bar + + /* + * make a name for the edit action, for + * status bar message and Undo/Redo menu + */ + String label = null; if (groupEditing) - { - message.append("Edit group:"); - if (editCommand == null) - { - editCommand = new EditCommand(MessageManager.getString("action.edit_group")); - } + { + message.append("Edit group:"); + label = MessageManager.getString("action.edit_group"); } else { - message.append("Edit sequence: " + seq.getName()); - String label = seq.getName(); + message.append("Edit sequence: " + seq.getName()); + label = seq.getName(); if (label.length() > 10) { label = label.substring(0, 10); } - if (editCommand == null) - { - editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); - } + label = MessageManager.formatMessage("label.edit_params", + new String[] + { label }); + } + + /* + * initialise the edit command if there is not + * already one being extended + */ + if (editCommand == null) + { + editCommand = new EditCommand(label); } if (insertGap) @@ -994,13 +1419,17 @@ public class SeqPanel extends JPanel implements MouseListener, message.append(" delete "); } - message.append(Math.abs(startres - lastres) + " gaps."); - ap.alignFrame.statusBar.setText(message.toString()); + message.append(Math.abs(startres - editLastRes) + " gaps."); + ap.alignFrame.setStatus(message.toString()); - // Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.getSequences(av.getHiddenRepSequences()) - .contains(seq))) + /* + * is there a selection group containing the sequence being edited? + * if so the boundary of the group is the limit of the edit + * (but the edit may be inside or outside the selection group) + */ + boolean inSelectionGroup = sg != null + && sg.getSequences(av.getHiddenRepSequences()).contains(seq); + if (groupEditing || inSelectionGroup) { fixedColumns = true; @@ -1019,10 +1448,10 @@ public class SeqPanel extends JPanel implements MouseListener, fixedLeft = sg.getStartRes(); fixedRight = sg.getEndRes(); - if ((startres < fixedLeft && lastres >= fixedLeft) - || (startres >= fixedLeft && lastres < fixedLeft) - || (startres > fixedRight && lastres <= fixedRight) - || (startres <= fixedRight && lastres > fixedRight)) + if ((startres < fixedLeft && editLastRes >= fixedLeft) + || (startres >= fixedLeft && editLastRes < fixedLeft) + || (startres > fixedRight && editLastRes <= fixedRight) + || (startres <= fixedRight && editLastRes > fixedRight)) { endEditing(); return; @@ -1043,11 +1472,13 @@ 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() + .getNextHiddenBoundary(true, startres); + int y2 = av.getAlignment().getHiddenColumns() + .getNextHiddenBoundary(false, startres); - if ((insertGap && startres > y1 && lastres < y1) - || (!insertGap && startres < y2 && lastres > y2)) + if ((insertGap && startres > y1 && editLastRes < y1) + || (!insertGap && startres < y2 && editLastRes > y2)) { endEditing(); return; @@ -1068,6 +1499,54 @@ public class SeqPanel extends JPanel implements MouseListener, } } + boolean success = doEditSequence(insertGap, editSeq, startres, + fixedRight, fixedColumns, sg); + + /* + * report what actually happened (might be less than + * what was requested), by inspecting the edit commands added + */ + String msg = getEditStatusMessage(editCommand); + ap.alignFrame.setStatus(msg == null ? " " : msg); + if (!success) + { + endEditing(); + } + + editLastRes = startres; + seqCanvas.repaint(); + } + + /** + * A helper method that performs the requested editing to insert or delete + * gaps (if possible). Answers true if the edit was successful, false if could + * only be performed in part or not at all. Failure may occur in 'locked edit' + * mode, when an insertion requires a matching gapped position (or column) to + * delete, and deletion requires an adjacent gapped position (or column) to + * remove. + * + * @param insertGap + * true if inserting gap(s), false if deleting + * @param editSeq + * (unused parameter, currently always false) + * @param startres + * the column at which to perform the edit + * @param fixedRight + * fixed right boundary column of a locked edit (within or to the + * left of a selection group) + * @param fixedColumns + * true if this is a locked edit + * @param sg + * the sequence group (if group edit is being performed) + * @return + */ + protected boolean doEditSequence(final boolean insertGap, + final boolean editSeq, final int startres, int fixedRight, + final boolean fixedColumns, final SequenceGroup sg) + { + final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq); + SequenceI[] seqs = new SequenceI[] { seq }; + if (groupEditing) { List vseqs = sg.getSequences(av.getHiddenRepSequences()); @@ -1086,7 +1565,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight && sg.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); + sg.setEndRes( + av.getAlignment().getWidth() + startres - editLastRes); fixedRight = sg.getEndRes(); } @@ -1094,16 +1574,16 @@ 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 > editLastRes; fixedRight--) { blank = true; for (g = 0; g < groupSize; g++) { - for (int j = 0; j < startres - lastres; j++) + for (int j = 0; j < startres - editLastRes; j++) { - if (!jalview.util.Comparison.isGap(groupSeqs[g] - .getCharAt(fixedRight - j))) + if (!Comparison + .isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -1120,11 +1600,11 @@ 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() + .getNextHiddenBoundary(false, startres))) { - endEditing(); - return; + return false; } int alWidth = av.getAlignment().getWidth(); @@ -1139,13 +1619,12 @@ public class SeqPanel extends JPanel implements MouseListener, } // We can still insert gaps if the selectionGroup // contains all the sequences - sg.setEndRes(sg.getEndRes() + startres - lastres); - fixedRight = alWidth + startres - lastres; + sg.setEndRes(sg.getEndRes() + startres - editLastRes); + fixedRight = alWidth + startres - editLastRes; } else { - endEditing(); - return; + return false; } } } @@ -1158,18 +1637,17 @@ public class SeqPanel extends JPanel implements MouseListener, for (g = 0; g < groupSize; g++) { - for (int j = startres; j < lastres; j++) + for (int j = startres; j < editLastRes; j++) { if (groupSeqs[g].getLength() <= j) { 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(); - return; + return false; } } } @@ -1180,15 +1658,15 @@ public class SeqPanel extends JPanel implements MouseListener, // dragging to the right if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, groupSeqs, fixedRight); + insertGap(j, groupSeqs, fixedRight); } } else { - editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, groupSeqs, startres, + startres - editLastRes, false); } } else @@ -1196,37 +1674,44 @@ public class SeqPanel extends JPanel implements MouseListener, // dragging to the left if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j > startres; j--) + for (int j = editLastRes; j > startres; j--) { deleteChar(startres, groupSeqs, fixedRight); } } else { - editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, groupSeqs, startres, + editLastRes - startres, false); } - } } else - // ///Editing a single sequence/////////// { + /* + * editing a single sequence + */ if (insertGap) { // dragging to the right if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + if (!insertGap(j, seqs, fixedRight)) + { + /* + * e.g. cursor mode command specified + * more inserts than are possible + */ + return false; + } } } else { - editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, seqs, editLastRes, + startres - editLastRes, false); } } else @@ -1236,35 +1721,30 @@ public class SeqPanel extends JPanel implements MouseListener, // dragging to the left if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j > startres; j--) + for (int j = editLastRes; j > startres; j--) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + if (!Comparison.isGap(seq.getCharAt(startres))) { - endEditing(); - break; + return false; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, seqs, fixedRight); } } else { // could be a keyboard edit trying to delete none gaps int max = 0; - for (int m = startres; m < lastres; m++) + for (int m = startres; m < editLastRes; m++) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + if (!Comparison.isGap(seq.getCharAt(m))) { break; } max++; } - if (max > 0) { - editCommand.appendEdit(Action.DELETE_GAP, - new SequenceI[] - { seq }, startres, max, av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, seqs, startres, max, false); } } } @@ -1272,26 +1752,82 @@ public class SeqPanel extends JPanel implements MouseListener, {// insertGap==false AND editSeq==TRUE; if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertGap(j, seqs, fixedRight); } } else { - editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_NUC, seqs, editLastRes, + startres - editLastRes, false); } } } } - lastres = startres; - seqCanvas.repaint(); + return true; + } + + /** + * Constructs an informative status bar message while dragging to insert or + * delete gaps. Answers null if inserts and deletes cancel out. + * + * @param editCommand + * a command containing the list of individual edits + * @return + */ + protected static String getEditStatusMessage(EditCommand editCommand) + { + if (editCommand == null) + { + return null; + } + + /* + * add any inserts, and subtract any deletes, + * not counting those auto-inserted when doing a 'locked edit' + * (so only counting edits 'under the cursor') + */ + int count = 0; + for (Edit cmd : editCommand.getEdits()) + { + if (!cmd.isSystemGenerated()) + { + count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber() + : -cmd.getNumber(); + } + } + + if (count == 0) + { + /* + * inserts and deletes cancel out + */ + return null; + } + + String msgKey = count > 1 ? "label.insert_gaps" + : (count == 1 ? "label.insert_gap" + : (count == -1 ? "label.delete_gap" + : "label.delete_gaps")); + count = Math.abs(count); + + return MessageManager.formatMessage(msgKey, String.valueOf(count)); } - void insertChar(int j, SequenceI[] seq, int fixedColumn) + /** + * Inserts one gap at column j, deleting the right-most gapped column up to + * (and including) fixedColumn. Returns true if the edit is successful, false + * if no blank column is available to allow the insertion to be balanced by a + * deletion. + * + * @param j + * @param seq + * @param fixedColumn + * @return + */ + boolean insertGap(int j, SequenceI[] seq, int fixedColumn) { int blankColumn = fixedColumn; for (int s = 0; s < seq.length; s++) @@ -1301,7 +1837,7 @@ 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; @@ -1312,26 +1848,53 @@ public class SeqPanel extends JPanel implements MouseListener, { blankColumn = fixedColumn; endEditing(); - return; + return false; } } - editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, - av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, true); - editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, - av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, seq, j, 1, false); + return true; } - void deleteChar(int j, SequenceI[] seq, int fixedColumn) + /** + * Helper method to add and perform one edit action + * + * @param action + * @param seq + * @param pos + * @param count + * @param systemGenerated + * true if the edit is a 'balancing' delete (or insert) to match a + * user's insert (or delete) in a locked editing region + */ + protected void appendEdit(Action action, SequenceI[] seq, int pos, + int count, boolean systemGenerated) { - editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, - av.getAlignment(), true); + final Edit edit = new EditCommand().new Edit(action, seq, pos, count, + av.getAlignment().getGapCharacter()); + edit.setSystemGenerated(systemGenerated); + + editCommand.appendEdit(edit, av.getAlignment(), true, null); + } + + /** + * Deletes the character at column j, and inserts a gap at fixedColumn, in + * each of the given sequences. The caller should ensure that all sequences + * are gapped in column j. + * + * @param j + * @param seqs + * @param fixedColumn + */ + void deleteChar(int j, SequenceI[] seqs, int fixedColumn) + { + appendEdit(Action.DELETE_GAP, seqs, j, 1, false); - editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, - av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, seqs, fixedColumn, 1, true); } /** @@ -1348,9 +1911,9 @@ public class SeqPanel extends JPanel implements MouseListener, oldSeq = 0; } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } } @@ -1364,22 +1927,33 @@ public class SeqPanel extends JPanel implements MouseListener, @Override public void mouseExited(MouseEvent e) { + ap.alignFrame.setStatus(" "); if (av.getWrapAlignment()) { 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) { SequenceGroup sg = null; - SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } + if (evt.getClickCount() > 1) { sg = av.getSelectionGroup(); @@ -1389,23 +1963,35 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( - sequence.getDatasetSequence(), - sequence.findPosition(findRes(evt))); + int column = pos.column; - if (features != null && features.length > 0) - { - SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); - seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.length > 0) + /* + * find features at the position (if not gapped), or straddling + * the position (if at a gap) + */ + SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex); + List features = seqCanvas.getFeatureRenderer() + .findFeaturesAtColumn(sequence, column + 1); + + if (!features.isEmpty()) { - seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + /* + * 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, 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 } } } @@ -1414,59 +2000,58 @@ public class SeqPanel extends JPanel implements MouseListener, public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { if (e.isShiftDown()) { - ap.scrollRight(true); + av.getRanges().scrollRight(true); } else { - ap.scrollUp(false); + av.getRanges().scrollUp(false); } } - else + else if (wheelRotation < 0) { 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); } /** * DOCUMENT ME! * - * @param evt + * @param pos * DOCUMENT ME! */ - public void doMousePressedDefineMode(MouseEvent evt) + protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos) { - int res = findRes(evt); - int seq = findSeq(evt); - oldSeq = seq; - - startWrapBlock = wrappedBlock; - - if (av.wrapAlignment && seq > av.getAlignment().getHeight()) + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.cannot_edit_annotations_in_wrapped_view"), - MessageManager.getString("label.wrapped_view_no_edit"), - JOptionPane.WARNING_MESSAGE); return; } - if (seq < 0 || res < 0) - { - return; - } + final int res = pos.column; + final int seq = pos.seqIndex; + oldSeq = seq; + updateOverviewAndStructs = false; + + startWrapBlock = wrappedBlock; SequenceI sequence = av.getAlignment().getSequenceAt(seq); @@ -1477,149 +2062,159 @@ 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, pos); + 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()) { - SequenceFeature[] allFeatures = findFeaturesAtRes( - sequence.getDatasetSequence(), sequence.findPosition(res)); - Vector links = new Vector(); - for (int i = 0; i < allFeatures.length; i++) - { - if (allFeatures[i].links != null) - { - for (int j = 0; j < allFeatures[i].links.size(); j++) - { - links.addElement(allFeatures[i].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.cursorY = findSeq(evt); + seqCanvas.cursorX = res; + seqCanvas.cursorY = seq; seqCanvas.repaint(); return; } 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); + if (stretchGroup != null) + { + stretchGroup.addPropertyChangeListener(seqCanvas); + } - stretchGroup = sg; + seqCanvas.repaint(); + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); - } + 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.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(); + 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(); + } /** - * DOCUMENT ME! + * Build and show a pop-up menu at the right-click mouse position + * + * @param evt + * @param pos + */ + void showPopupMenu(MouseEvent evt, MousePos pos) + { + final int column = pos.column; + final int seq = pos.seqIndex; + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + List features = ap.getFeatureRenderer() + .findFeaturesAtColumn(sequence, column + 1); + + PopupMenu pop = new PopupMenu(ap, null, features); + pop.show(this, evt.getX(), evt.getY()); + } + + /** + * 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) + protected void doMouseReleasedDefineMode(MouseEvent evt, + boolean afterDrag) { if (stretchGroup == null) { return; } - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + 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); + updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup() + && afterDrag; if (stretchGroup.cs != null) { - stretchGroup.cs.alignmentChanged(stretchGroup, - av.getHiddenRepSequences()); + if (afterDrag) + { + 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); - + // 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; @@ -1627,22 +2222,28 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Resizes the borders of a selection group depending on the direction of + * mouse drag * * @param evt - * DOCUMENT ME! */ - public void doMouseDraggedDefineMode(MouseEvent evt) + protected void dragStretchGroup(MouseEvent evt) { - int res = findRes(evt); - int y = findSeq(evt); + if (stretchGroup == null) + { + return; + } - if (wrappedBlock != startWrapBlock) + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1) { return; } - if (stretchGroup == null) + int res = pos.column; + int y = pos.seqIndex; + + if (wrappedBlock != startWrapBlock) { return; } @@ -1663,9 +2264,9 @@ 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) @@ -1673,6 +2274,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1680,6 +2282,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1713,6 +2316,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } else { @@ -1722,6 +2326,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1732,21 +2337,45 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } - seqCanvas.repaint(); + /* + * construct a status message showing the range of the selection + */ + StringBuilder status = new StringBuilder(64); + List seqs = stretchGroup.getSequences(); + String name = seqs.get(0).getName(); + if (name.length() > 20) + { + name = name.substring(0, 20); + } + status.append(name).append(" - "); + name = seqs.get(seqs.size() - 1).getName(); + if (name.length() > 20) + { + name = name.substring(0, 20); + } + status.append(name).append(" "); + int startRes = stretchGroup.getStartRes(); + status.append(" cols ").append(String.valueOf(startRes + 1)) + .append("-"); + int endRes = stretchGroup.getEndRes(); + status.append(String.valueOf(endRes + 1)); + status.append(" (").append(String.valueOf(seqs.size())).append(" x ") + .append(String.valueOf(endRes - startRes + 1)).append(")"); + ap.alignFrame.setStatus(status.toString()); } void scrollCanvas(MouseEvent evt) { if (evt == null) { - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } mouseDragging = false; @@ -1769,7 +2398,7 @@ public class SeqPanel extends JPanel implements MouseListener, { MouseEvent evt; - boolean running = false; + private volatile boolean threadRunning = true; public ScrollThread() { @@ -1783,36 +2412,40 @@ 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); } } @@ -1831,63 +2464,93 @@ 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. - if (av == source - || !av.followSelection - || (av.isSelectionGroupChanged(false) || av - .isColSelChanged(false)) - || (source instanceof AlignViewport && ((AlignViewport) source) - .getSequenceSetId().equals(av.getSequenceSetId()))) + 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; + } + + /* + * Ignore the selection if there is one of our own pending. + */ + if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + { + return; + } + + /* + * Check for selection in a view of which this one is a dna/protein + * complement. + */ + 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 - boolean repaint = false, copycolsel = true; - // if (!av.isSelectionGroupChanged(false)) + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ + boolean repaint = false; + boolean copycolsel = false; + + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize() > 0) { - 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() - + " 's alignment is NULL! returning immediatly."); - return; - } - sgroup = seqsel.intersect(av.getAlignment(), - (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - || (colsel == null || colsel.size() == 0)) - { - // don't copy columns if the region didn't intersect. - copycolsel = false; - } - } - if (sgroup != null && sgroup.getSize() > 0) + if (av.getAlignment() == null) { - av.setSelectionGroup(sgroup); + Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + + " ViewId=" + av.getViewId() + + " 's alignment is NULL! returning immediately."); + return; } - else + sgroup = seqsel.intersect(av.getAlignment(), + (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); + if ((sgroup != null && sgroup.getSize() > 0)) { - av.setSelectionGroup(null); + copycolsel = true; } - av.isSelectionGroupChanged(true); - repaint = true; } + if (sgroup != null && sgroup.getSize() > 0) + { + av.setSelectionGroup(sgroup); + } + else + { + av.setSelectionGroup(null); + } + av.isSelectionGroupChanged(true); + repaint = true; + if (copycolsel) { // 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) { @@ -1904,24 +2567,97 @@ 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"); } - if (repaint) + if (repaint) // always true! { // probably finessing with multiple redraws here PaintRefresher.Refresh(this, av.getSequenceSetId()); // ap.paintAlignment(false); } + + // lastly, update dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + + } + + /** + * If this panel is a cdna/protein translation view of the selection source, + * tries to map the source selection to a local one, and returns true. Else + * returns false. + * + * @param seqsel + * @param colsel + * @param source + */ + protected boolean selectionFromTranslation(SequenceGroup seqsel, + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) + { + if (!(source instanceof AlignViewportI)) + { + return false; + } + final AlignViewportI sourceAv = (AlignViewportI) source; + if (sourceAv.getCodingComplement() != av + && av.getCodingComplement() != sourceAv) + { + return false; + } + + /* + * Map sequence selection + */ + SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av); + av.setSelectionGroup(sg); + av.isSelectionGroupChanged(true); + + /* + * Map column selection + */ + // 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); + boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs); + + // lastly, update any dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + + /* + * repaint alignment, and also Overview or Structure + * if hidden column selection has changed + */ + ap.paintAlignment(hiddenChanged, hiddenChanged); + + return true; + } + + /** + * + * @return null or last search results handled by this panel + */ + public SearchResultsI getLastSearchResults() + { + return lastSearchResults; } }