X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2884c501cc87f2dc65bed280e3a59041f01ed054;hb=c3d92b4b7a6cb00f9e596dbb7cd6c8508da5c252;hp=5d3df1a4484101494ab297d909fafbafcb0f2c93;hpb=53a90a961a55fad88199165bdc4c665ba90c28b3;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 5d3df1a..2884c50 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 2.8.2) - * 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 +20,34 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; +import jalview.commands.EditCommand.Edit; +import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; +import jalview.datamodel.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 +59,12 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; +import java.util.ArrayList; +import java.util.Collections; import java.util.List; -import java.util.Vector; -import javax.swing.JOptionPane; import javax.swing.JPanel; +import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** @@ -113,7 +127,7 @@ public class SeqPanel extends JPanel implements MouseListener, private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(); + StringBuilder tooltipText = new StringBuilder(); String tmpString; @@ -121,6 +135,8 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; + SearchResultsI lastSearchResults; + /** * Creates a new SeqPanel object. * @@ -160,22 +176,29 @@ public class SeqPanel extends JPanel implements MouseListener, int wrappedBlock = -1; - int findRes(MouseEvent evt) + /** + * Returns the aligned sequence position (base 0) at the mouse position, or + * the closest visible one + * + * @param evt + * @return + */ + int findColumn(MouseEvent evt) { int res = 0; int x = evt.getX(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + 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; @@ -188,25 +211,31 @@ public class SeqPanel extends JPanel implements MouseListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getStartRes() / cwidth; + wrappedBlock += av.getRanges().getStartRes() / cwidth; res = wrappedBlock * cwidth + x / av.getCharWidth(); } else { - if (x > seqCanvas.getWidth() + seqCanvas.getWidth()) + if (x > seqCanvas.getX() + seqCanvas.getWidth()) { // make sure we calculate relative to visible alignment, rather than // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } - res = (x / av.getCharWidth()) + av.getStartRes(); + res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + if (res > av.getRanges().getEndRes()) + { + // moused off right + res = av.getRanges().getEndRes(); + } } if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(res); } return res; @@ -218,16 +247,16 @@ public class SeqPanel extends JPanel implements MouseListener, int seq = 0; int y = evt.getY(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + 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(); y -= hgap; @@ -236,68 +265,42 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + seq = Math.min((y / av.getCharHeight()) + + av.getRanges().getStartSeq(), + av .getAlignment().getHeight() - 1); } return seq; } - SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) + /** + * 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() { - Vector tmp = new Vector(); - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (features != null) + try { - for (int i = 0; i < features.length; i++) + if (editCommand != null && editCommand.getSize() > 0) { - if (av.getFeaturesDisplayed() == null - || !av.getFeaturesDisplayed().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]); - } + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, av.getAlignment() + .getSequences()); } - } - - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; - } - - void endEditing() - { - if (editCommand != null && editCommand.getSize() > 0) + } finally { - ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); + /* + * Tidy up come what may... + */ + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; } - - startseq = -1; - lastres = -1; - editingSeqs = false; - groupEditing = false; - keyboardNo1 = null; - keyboardNo2 = null; - editCommand = null; } void setCursorRow() @@ -338,20 +341,23 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; + + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + if (av.hasHiddenColumns() - && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) + while (!hidden.isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !hidden.isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -381,32 +387,33 @@ public class SeqPanel extends JPanel implements MouseListener, } endEditing(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { ap.scrollToWrappedVisible(seqCanvas.cursorX); } else { - while (seqCanvas.cursorY < av.startSeq) + while (seqCanvas.cursorY < av.getRanges().getStartSeq()) { ap.scrollUp(true); } - while (seqCanvas.cursorY + 1 > av.endSeq) + while (seqCanvas.cursorY > av.getRanges().getEndSeq()) { ap.scrollUp(false); } - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { - while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(av.startRes)) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av + .getRanges().getStartRes())) { if (!ap.scrollRight(false)) { break; } } - while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.endRes)) + while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av + .getRanges().getEndRes())) { if (!ap.scrollRight(true)) { @@ -515,6 +522,7 @@ public class SeqPanel extends JPanel implements MouseListener, void insertNucAtCursor(boolean group, String nuc) { + // TODO not called - delete? groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; @@ -585,6 +593,13 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragging = false; mouseWheelPressed = false; + if (evt.isPopupTrigger()) // Windows: mouseReleased + { + showPopupMenu(evt); + evt.consume(); + return; + } + if (!editingSeqs) { doMouseReleasedDefineMode(evt); @@ -605,19 +620,20 @@ public class SeqPanel extends JPanel implements MouseListener, { lastMousePress = evt.getPoint(); - if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + if (SwingUtilities.isMiddleMouseButton(evt)) { mouseWheelPressed = true; return; } - if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) + boolean isControlDown = Platform.isControlDown(evt); + if (evt.isShiftDown() || isControlDown) { - if (evt.isAltDown() || evt.isControlDown()) + editingSeqs = true; + if (isControlDown) { groupEditing = true; } - editingSeqs = true; } else { @@ -626,7 +642,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < 0 || res < 0) { @@ -663,20 +679,46 @@ public class SeqPanel extends JPanel implements MouseListener, lastMessage = tmp; } + /** + * Highlight the mapped region described by the search results object (unless + * unchanged). This supports highlight of protein while mousing over linked + * cDNA and vice versa. The status bar is also updated to show the location of + * the start of the highlighted region. + */ @Override - public void highlightSequence(SearchResults results) + public void highlightSequence(SearchResultsI results) { - if (av.followHighlight) + if (results == null || results.equals(lastSearchResults)) { + return; + } + lastSearchResults = results; + + if (av.isFollowHighlight()) + { + /* + * 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)) { seqCanvas.revalidate(); } } + setStatusMessage(results); seqCanvas.highlightSearchResults(results); } @Override + public VamsasSource getVamsasSource() + { + return this.ap == null ? null : this.ap.av; + } + + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -699,25 +741,27 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragged(evt); } - int res = findRes(evt); + final int column = findColumn(evt); int seq = findSeq(evt); - int pos; - if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { return; } SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (res >= sequence.getLength()) + if (column >= sequence.getLength()) { return; } - pos = setStatusMessage(sequence, res, seq); + /* + * set status bar message, returning residue position in sequence + */ + final int pos = setStatusMessage(sequence, column, seq); if (ssm != null && pos > -1) { - mouseOverSequence(sequence, res, pos); + mouseOverSequence(sequence, column, pos); } tooltipText.setLength(6); // Cuts the buffer back to @@ -727,7 +771,8 @@ 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")) @@ -743,17 +788,14 @@ public class SeqPanel extends JPanel implements MouseListener, } } - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures() && pos != -1) { - 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() + .findFeaturesAtRes(sequence.getDatasetSequence(), pos); + seqARep.appendFeatures(tooltipText, pos, features, + this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; @@ -781,6 +823,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) */ + @Override public Point getToolTipLocation(MouseEvent event) { int x = event.getX(), w = getWidth(); @@ -801,78 +844,146 @@ public class SeqPanel extends JPanel implements MouseListener, String lastTooltip; /** - * Set status message in alignment panel + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + + /** + * set if av.getSelectionGroup() refers to a group that is defined on the + * alignment view, rather than a transient selection + */ + // private boolean editingDefinedGroup = false; // TODO: refactor to + // avcontroller or viewModel + + /** + * Sets the status message in alignment panel, showing the sequence number + * (index) and id, residue and residue position for the given sequence and + * column position. Returns the calculated residue position in the sequence, + * or -1 for a gapped column position. * * @param sequence * aligned sequence object - * @param res + * @param column * alignment column * @param seq * index of sequence in alignment * @return position of res in sequence */ - int setStatusMessage(SequenceI sequence, int res, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seq) { - 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 = seq == -1 ? "" : " " + (seq + 1); + text.append("Sequence").append(seqno).append(" ID: ") + .append(sequence.getName()); - Object obj = null; + String residue = null; + /* + * Try to translate the display character to residue name (null for gap). + */ + final String displayChar = String.valueOf(sequence.getCharAt(column)); if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) - + ""); - if (obj != null) + residue = ResidueProperties.nucleotideName.get(displayChar); + if (residue != null) { - text.append(" Nucleotide: "); + text.append(" Nucleotide: ").append(residue); } } else { - obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - if (obj != null) + residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" + .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet + .get(displayChar)); + if (residue != null) { - text.append(" Residue: "); + text.append(" Residue: ").append(residue); } } - if (obj != null) + int pos = -1; + if (residue != null) { - pos = sequence.findPosition(res); - if (obj != "") - { - text.append(obj + " (" + pos + ")"); - } + pos = sequence.findPosition(column); + text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); return pos; } /** - * DOCUMENT ME! + * Set the status bar message to highlight the first matched position in + * search results. * - * @param evt - * DOCUMENT ME! + * @param results + */ + private void setStatusMessage(SearchResultsI results) + { + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) + { + return; + } + SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + for (SearchResultMatchI m : results.getResults()) + { + SequenceI seq = m.getSequence(); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + + if (seq == ds) + { + /* + * Convert position in sequence (base 1) to sequence character array + * index (base 0) + */ + int start = m.getStart() - m.getSequence().getStart(); + setStatusMessage(seq, start, sequenceIndex); + return; + } + } + } + + /** + * {@inheritDoc} */ @Override public void mouseDragged(MouseEvent evt) { 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())) { + /* + * 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++; } @@ -881,26 +992,60 @@ 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); + 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(); @@ -913,7 +1058,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - int res = findRes(evt); + int res = findColumn(evt); if (res < 0) { @@ -963,13 +1108,14 @@ public class SeqPanel extends JPanel implements MouseListener, } } - StringBuffer message = new StringBuffer(); + StringBuilder message = new StringBuilder(64); if (groupEditing) { message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand(MessageManager.getString("action.edit_group")); + editCommand = new EditCommand( + MessageManager.getString("action.edit_group")); } } else @@ -982,7 +1128,8 @@ public class SeqPanel extends JPanel implements MouseListener, } if (editCommand == null) { - editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); + editCommand = new EditCommand(MessageManager.formatMessage( + "label.edit_params", new String[] { label })); } } @@ -1044,8 +1191,10 @@ 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)) @@ -1103,8 +1252,7 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = 0; j < startres - lastres; j++) { - if (!jalview.util.Comparison.isGap(groupSeqs[g] - .getCharAt(fixedRight - j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -1121,8 +1269,8 @@ 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; @@ -1166,7 +1314,7 @@ public class SeqPanel extends JPanel implements MouseListener, continue; } - if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid endEditing(); @@ -1188,8 +1336,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres + - lastres); } } else @@ -1204,8 +1352,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres + - startres); } } @@ -1220,14 +1368,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, + startres - lastres); } } else @@ -1239,13 +1386,12 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j > startres; j--) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + if (!Comparison.isGap(seq.getCharAt(startres))) { endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1254,7 +1400,7 @@ public class SeqPanel extends JPanel implements MouseListener, int max = 0; for (int m = startres; m < lastres; m++) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + if (!Comparison.isGap(seq.getCharAt(m))) { break; } @@ -1263,9 +1409,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { - editCommand.appendEdit(Action.DELETE_GAP, - new SequenceI[] - { seq }, startres, max, av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, + startres, max); } } } @@ -1275,14 +1420,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, + startres - lastres); } } } @@ -1302,7 +1446,7 @@ 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; @@ -1317,22 +1461,36 @@ public class SeqPanel extends JPanel implements MouseListener, } } - editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, - av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, seq, blankColumn, 1); + + appendEdit(Action.INSERT_GAP, seq, j, 1); - editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, - av.getAlignment(), true); + } + + /** + * Helper method to add and perform one edit action. + * + * @param action + * @param seq + * @param pos + * @param count + */ + protected void appendEdit(Action action, SequenceI[] seq, int pos, + int count) + { + final Edit edit = new EditCommand().new Edit(action, seq, pos, count, + av.getAlignment().getGapCharacter()); + + editCommand.appendEdit(edit, av.getAlignment(), true, null); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, - av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, seq, j, 1); - editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, - av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1); } /** @@ -1376,6 +1534,11 @@ public class SeqPanel extends JPanel implements MouseListener, } } + /** + * Handler for double-click on a position with one or more sequence features. + * Opens the Amend Features dialog to allow feature details to be amended, or + * the feature deleted. + */ @Override public void mouseClicked(MouseEvent evt) { @@ -1390,22 +1553,27 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( - sequence.getDatasetSequence(), - sequence.findPosition(findRes(evt))); + List features = seqCanvas.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(findColumn(evt))); - if (features != null && features.length > 0) + if (!features.isEmpty()) { - SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); + /* + * highlight the first feature at the position on the alignment + */ + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.length > 0) - { - seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + /* + * open the Amend Features dialog; clear highlighting afterwards, + * whether changes were made or not + */ + List seqs = Collections.singletonList(sequence); + seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, + ap); seqCanvas.highlightSearchResults(null); } } @@ -1449,18 +1617,19 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void doMousePressedDefineMode(MouseEvent evt) { - int res = findRes(evt); - int seq = findSeq(evt); + final int res = findColumn(evt); + final int seq = findSeq(evt); oldSeq = seq; + needOverviewUpdate = false; startWrapBlock = wrappedBlock; - if (av.wrapAlignment && seq > av.getAlignment().getHeight()) + if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -1478,69 +1647,36 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup = av.getSelectionGroup(); - if (stretchGroup == null) + if (stretchGroup == null || !stretchGroup.contains(sequence, res)) { - stretchGroup = av.getAlignment().findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) - && (res < stretchGroup.getEndRes())) + stretchGroup = av.getAlignment().findGroup(sequence, res); + if (stretchGroup != null) { + // only update the current selection if the popup menu has a group to + // focus on av.setSelectionGroup(stretchGroup); } - else - { - stretchGroup = null; - } } - else if (!stretchGroup.getSequences(null).contains(sequence) - || (stretchGroup.getStartRes() > res) - || (stretchGroup.getEndRes() < res)) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); - - if (allGroups != null) - { - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - stretchGroup = allGroups[i]; - break; - } - } - } - - av.setSelectionGroup(stretchGroup); + if (evt.isPopupTrigger()) // Mac: mousePressed + { + showPopupMenu(evt); + return; } - if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + /* + * defer right-mouse click handling to mouseReleased on Windows + * (where isPopupTrigger() will answer true) + * NB isRightMouseButton is also true for Cmd-click on Mac + */ + if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac()) { - 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.cursorX = findColumn(evt); seqCanvas.cursorY = findSeq(evt); seqCanvas.repaint(); return; @@ -1556,20 +1692,20 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); - stretchGroup = sg; if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); } + // TODO: stretchGroup will always be not null. Is this a merge error ? if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) { // Edit end res position of selected group @@ -1588,6 +1724,37 @@ public class SeqPanel extends JPanel implements MouseListener, } /** + * Build and show a pop-up menu at the right-click mouse position + * + * @param evt + * @param res + * @param sequences + */ + void showPopupMenu(MouseEvent evt) + { + final int res = findColumn(evt); + final int seq = findSeq(evt); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + List allFeatures = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + List links = new ArrayList(); + for (SequenceFeature sf : allFeatures) + { + if (sf.links != null) + { + for (String link : sf.links) + { + links.add(link); + } + } + } + + PopupMenu pop = new PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); + } + + /** * DOCUMENT ME! * * @param evt @@ -1599,28 +1766,29 @@ public class SeqPanel extends JPanel implements MouseListener, { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // always do this - annotation has own state + // but defer colourscheme update until hidden sequences are passed in + boolean vischange = stretchGroup.recalcConservation(true); + needOverviewUpdate |= vischange && av.isSelectionDefinedGroup(); if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, av.getHiddenRepSequences()); + ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme(); + String name = stretchGroup.getName(); if (stretchGroup.cs.conservationApplied()) { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setConservationSlider(ap, groupColourScheme, name); } - else + if (stretchGroup.cs.getThreshold() > 0) { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setPIDSliderSource(ap, groupColourScheme, name); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(true); - + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1635,7 +1803,7 @@ 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) @@ -1664,9 +1832,9 @@ 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) @@ -1674,6 +1842,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1681,6 +1850,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1714,6 +1884,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } else { @@ -1723,6 +1894,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1796,13 +1968,15 @@ public class SeqPanel extends JPanel implements MouseListener, { if (evt != null) { - if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging && (evt.getY() < 0) + && (av.getRanges().getStartSeq() > 0)) { running = ap.scrollUp(true); } if (mouseDragging && (evt.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getRanges() + .getEndSeq())) { running = ap.scrollUp(false); } @@ -1832,63 +2006,89 @@ 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(); + } + + // 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) { - 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) - { - 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) { @@ -1905,24 +2105,86 @@ 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)) + && (av.getAlignment().getHiddenColumns() == null || av + .getAlignment().getHiddenColumns().getHiddenRegions() == 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); + av.getAlignment().setHiddenColumns(hs); + + // lastly, update any dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + + PaintRefresher.Refresh(this, av.getSequenceSetId()); + + return true; } }