X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ef8767128db8fca4832a3fac584f3c66a88b25bd;hb=14193747f3831242bc7dfac12394eb20eb0ba480;hp=b30c5aeb56dd6ef7547fb5c136a54813284c0866;hpb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index b30c5ae..ef87671 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -173,15 +173,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - HiddenColumns hidden, JalviewLite applet, - String title, boolean embedded) + HiddenColumns hidden, JalviewLite applet, String title, + boolean embedded) { this(al, hiddenSeqs, hidden, applet, title, embedded, true); } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - HiddenColumns hidden, JalviewLite applet, - String title, boolean embedded, boolean addToDisplay) + HiddenColumns hidden, JalviewLite applet, String title, + boolean embedded, boolean addToDisplay) { if (applet != null) { @@ -343,7 +343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, createAlignFrameWindow(embedded); validate(); alignPanel.adjustAnnotationHeight(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } public AlignViewport getAlignViewport() @@ -390,8 +390,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { Map colours = alignPanel.seqPanel.seqCanvas .getFeatureRenderer().getFeatureColours(); - boolean relaxedIdMatching = viewport.applet.getDefaultParameter( - "relaxedidmatch", false); + boolean relaxedIdMatching = viewport.applet + .getDefaultParameter("relaxedidmatch", false); featuresFile = new FeaturesFile(file, sourceType).parse( viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) @@ -415,7 +415,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.featureSettings.refreshTable(); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); statusBar.setText(MessageManager .getString("label.successfully_added_features_alignment")); } @@ -428,9 +428,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, ViewportRanges ranges = viewport.getRanges(); if (viewport.cursorMode - && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt - .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt - .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && ((evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 + && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); @@ -573,9 +574,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText(MessageManager.formatMessage( - "label.keyboard_editing_mode", - new String[] { (viewport.cursorMode ? "on" : "off") })); + statusBar.setText(MessageManager + .formatMessage("label.keyboard_editing_mode", new String[] + { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes(); @@ -690,7 +691,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, break; } - alignPanel.paintAlignment(true); + // TODO: repaint flags set only if the keystroke warrants it + alignPanel.paintAlignment(true, true); } /** @@ -708,9 +710,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. - if (viewport.hasSelectedColumns() - || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg - .getEndRes())) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 + && sg.getStartRes() <= sg.getEndRes())) { // now invert the sequence set, if required - empty selection implies // that no hiding is required. @@ -839,16 +840,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { boolean newState = sortAnnBySequence.getState(); sortAnnByLabel.setState(false); - setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL - : SequenceAnnotationOrder.NONE); + setAnnotationSortOrder( + newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL + : SequenceAnnotationOrder.NONE); setViewportAnnotationOrder(); } else if (source == sortAnnByLabel) { boolean newState = sortAnnByLabel.getState(); sortAnnBySequence.setState(false); - setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE - : SequenceAnnotationOrder.NONE); + setAnnotationSortOrder( + newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE + : SequenceAnnotationOrder.NONE); setViewportAnnotationOrder(); } else if (source == showAutoFirst) @@ -915,7 +918,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { applyAutoAnnotationSettings_actionPerformed(); } - alignPanel.paintAlignment(true); + // TODO: repaint flags set only if warranted + alignPanel.paintAlignment(true, true); } /** @@ -1092,7 +1096,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == invertColSel) { viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); viewport.sendSelection(); } else if (source == remove2LeftMenuItem) @@ -1126,34 +1130,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == showColumns) { viewport.showAllHiddenColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } else if (source == showSeqs) { viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); // uncomment if we want to slave sequence selections in split frame // viewport.sendSelection(); } else if (source == hideColumns) { viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } else if (source == hideSequences && viewport.getSelectionGroup() != null) { viewport.hideAllSelectedSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); // uncomment if we want to slave sequence selections in split frame // viewport.sendSelection(); } else if (source == hideAllButSelection) { toggleHiddenRegions(false, false); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } else if (source == hideAllSelection) @@ -1162,14 +1166,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } else if (source == showAllHidden) { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } else if (source == showGroupConsensus) @@ -1208,9 +1212,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cap.setText(contents.toString()); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new String[] { getTitle() }), - 400, 250); + jalview.bin.JalviewLite.addFrame(frame, MessageManager + .formatMessage("label.alignment_properties", new String[] + { getTitle() }), 400, 250); } else if (source == overviewMenuItem) { @@ -1371,15 +1375,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.alignment_output_command", - new Object[] { e.getActionCommand() }), 600, 500); - - FileFormatI fileFormat = FileFormats.getInstance().forName( - e.getActionCommand()); - cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( - fileFormat, viewport.getAlignment(), - viewport.getShowJVSuffix())); + JalviewLite.addFrame(frame, MessageManager + .formatMessage("label.alignment_output_command", new Object[] + { e.getActionCommand() }), 600, 500); + + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); + cap.setText( + new AppletFormatAdapter(alignPanel).formatSequences(fileFormat, + viewport.getAlignment(), viewport.getShowJVSuffix())); } public void loadAnnotations() @@ -1492,8 +1496,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, : "?"; url.append(firstSep); - url.append("open=" - + appendProtocol(viewport.applet.getParameter("file"))); + url.append( + "open=" + appendProtocol(viewport.applet.getParameter("file"))); if (viewport.applet.getParameter("features") != null) { @@ -1504,30 +1508,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.applet.getParameter("annotations") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("annotations"))); + url.append( + appendProtocol(viewport.applet.getParameter("annotations"))); } if (viewport.applet.getParameter("jnetfile") != null || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet - .getParameter("jnetfile") : viewport.applet - .getParameter("jpredfile"))); + url.append(appendProtocol( + viewport.applet.getParameter("jnetfile") != null + ? viewport.applet.getParameter("jnetfile") + : viewport.applet.getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) { - url.append("&colour=" - + removeWhiteSpace(viewport.applet - .getParameter("defaultColour"))); + url.append("&colour=" + removeWhiteSpace( + viewport.applet.getParameter("defaultColour"))); } if (viewport.applet.getParameter("userDefinedColour") != null) { - url.append("&colour=" - + removeWhiteSpace(viewport.applet - .getParameter("userDefinedColour"))); + url.append("&colour=" + removeWhiteSpace( + viewport.applet.getParameter("userDefinedColour"))); } if (viewport.applet.getParameter("tree") != null) { @@ -1599,10 +1603,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { System.exit(0); } - else + + viewport = null; + if (alignPanel != null && alignPanel.overviewPanel != null) { + alignPanel.overviewPanel.dispose(); } - viewport = null; alignPanel = null; this.dispose(); } @@ -1617,9 +1623,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { undoMenuItem.setEnabled(true); CommandI command = viewport.getHistoryList().peek(); - undoMenuItem.setLabel(MessageManager.formatMessage( - "label.undo_command", - new Object[] { command.getDescription() })); + undoMenuItem.setLabel(MessageManager + .formatMessage("label.undo_command", new Object[] + { command.getDescription() })); } else { @@ -1632,9 +1638,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, redoMenuItem.setEnabled(true); CommandI command = viewport.getRedoList().peek(); - redoMenuItem.setLabel(MessageManager.formatMessage( - "label.redo_command", - new Object[] { command.getDescription() })); + redoMenuItem.setLabel(MessageManager + .formatMessage("label.redo_command", new Object[] + { command.getDescription() })); } else { @@ -1686,8 +1692,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // viewport.getColumnSelection().getHiddenColumns() // != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, originalSource - .getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.getAlignment().getSequences()); } /** @@ -1719,8 +1725,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, originalSource - .getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.getAlignment().getSequences()); } AlignmentViewport getOriginatingSource(CommandI command) @@ -1734,8 +1740,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components.get(viewport - .getSequenceSetId()); + Vector comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) @@ -1779,7 +1785,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); /* * Also move cDNA/protein complement sequences @@ -1791,7 +1797,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport, complement); complement.getAlignment().moveSelectedSequencesByOne(mappedSelection, up ? null : complement.getHiddenRepSequences(), up); - getSplitFrame().getComplement(this).alignPanel.paintAlignment(true); + getSplitFrame().getComplement(this).alignPanel.paintAlignment(true, + false); } } @@ -1800,15 +1807,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, List sg = new Vector<>(); if (viewport.cursorMode) { - sg.add(viewport.getAlignment().getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + sg.add(viewport.getAlignment() + .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport .getAlignment().getHeight()) { - sg = viewport.getSelectionGroup().getSequences( - viewport.getHiddenRepSequences()); + sg = viewport.getSelectionGroup() + .getSequences(viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1828,8 +1835,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); - SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup - .size()]); + SequenceI[] seqs2 = invertGroup + .toArray(new SequenceI[invertGroup.size()]); for (int i = 0; i < invertGroup.size(); i++) { seqs2[i] = invertGroup.elementAt(i); @@ -1838,13 +1845,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SlideSequencesCommand ssc; if (right) { - ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, - size, viewport.getGapCharacter()); + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, + viewport.getGapCharacter()); } else { - ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, - size, viewport.getGapCharacter()); + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, + viewport.getGapCharacter()); } int groupAdjustment = 0; @@ -1884,9 +1891,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { - appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) historyList - .peek()); + appendHistoryItem = ssc.appendSlideCommand( + (SlideSequencesCommand) historyList.peek()); } if (!appendHistoryItem) @@ -1977,14 +1983,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, endRes += seq.getStart() - 1; } - copiedSequences.append(seq.getName() - + "\t" - + startRes - + "\t" - + endRes - + "\t" - + seq.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes + + "\t" + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + + "\n"); } } @@ -2035,8 +2037,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - newtitle = newtitle.concat(MessageManager.formatMessage( - "label.from_msname", new String[] { getTitle() })); + newtitle = newtitle.concat(MessageManager + .formatMessage("label.from_msname", new String[] + { getTitle() })); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), viewport.applet, newtitle, false); @@ -2078,8 +2081,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight()); viewport.getAlignment().getWidth(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2111,15 +2114,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, */ if (sg.getSize() == viewport.getAlignment().getHeight()) { - boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport - .getAlignment().getWidth()) ? true : false; + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + + 1) == viewport.getAlignment().getWidth()) ? true : false; if (isEntireAlignWidth) { String title = MessageManager.getString("label.delete_all"); Panel infoPanel = new Panel(); infoPanel.setLayout(new FlowLayout()); - infoPanel - .add(new Label(MessageManager.getString("warn.delete_all"))); + infoPanel.add( + new Label(MessageManager.getString("warn.delete_all"))); final JVDialog dialog = new JVDialog(this, title, true, 400, 200); dialog.setMainPanel(infoPanel); @@ -2153,8 +2156,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setSelectionGroup(null); viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); if (viewport.getAlignment().getHeight() < 1) { @@ -2228,7 +2231,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -2265,7 +2268,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2285,7 +2288,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2305,7 +2308,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void invertColSel_actionPerformed() { viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2331,8 +2334,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); } else { @@ -2352,10 +2355,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, column, al); } - statusBar.setText(MessageManager.formatMessage( - "label.removed_columns", - new String[] { Integer.valueOf(trimRegion.getSize()) - .toString() })); + statusBar.setText(MessageManager + .formatMessage("label.removed_columns", new String[] + { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); for (SequenceGroup sg : al.getGroups()) @@ -2381,8 +2383,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2397,10 +2399,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", - new String[] { Integer.valueOf(removeGapCols.getSize()) - .toString() })); + statusBar.setText(MessageManager + .formatMessage("label.removed_empty_columns", new String[] + { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence @@ -2426,8 +2427,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2441,8 +2442,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI seq = al.getSequenceAt(0); int startRes = seq.findPosition(ranges.getStartRes()); - addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - al)); + addHistoryItem( + new RemoveGapsCommand("Remove Gaps", seqs, start, end, al)); ranges.setStartRes(seq.findIndex(startRes) - 1); @@ -2476,12 +2477,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.getAlignment().getAlignmentAnnotation() != null) { - for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++) + for (int i = 0; i < viewport.getAlignment() + .getAlignmentAnnotation().length; i++) { - if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated) + if (!viewport.getAlignment() + .getAlignmentAnnotation()[i].autoCalculated) { - newal.addAnnotation(viewport.getAlignment() - .getAlignmentAnnotation()[i]); + newal.addAnnotation( + viewport.getAlignment().getAlignmentAnnotation()[i]); } } } @@ -2498,8 +2501,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId()); - Vector comps = (Vector) PaintRefresher.components.get(viewport - .getSequenceSetId()); + Vector comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); int viewSize = -1; for (int i = 0; i < comps.size(); i++) { @@ -2597,19 +2600,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } protected void displayNonconservedMenuItem_actionPerformed() { viewport.setShowUnconserved(displayNonconservedMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } protected void wrapMenuItem_actionPerformed() @@ -2619,7 +2622,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, scaleAbove.setEnabled(wrapMenuItem.getState()); scaleLeft.setEnabled(wrapMenuItem.getState()); scaleRight.setEnabled(wrapMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } public void overviewMenuItem_actionPerformed() @@ -2633,9 +2636,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, final OverviewPanel overview = new OverviewPanel(alignPanel); frame.add(overview); // +50 must allow for applet frame window - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.overview_params", new String[] { this.getTitle() }), - overview.getPreferredSize().width, + jalview.bin.JalviewLite.addFrame(frame, MessageManager + .formatMessage("label.overview_params", new String[] + { this.getTitle() }), overview.getPreferredSize().width, overview.getPreferredSize().height + 50); frame.pack(); @@ -2662,7 +2665,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.setGlobalColourScheme(cs); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } protected void modifyPID_actionPerformed() @@ -2732,21 +2735,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void sortPairwiseMenuItem_actionPerformed() { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0)); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } public void sortIDMenuItem_actionPerformed() { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); + addHistoryItem( + new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } public void sortLengthMenuItem_actionPerformed() @@ -2755,7 +2758,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } public void sortGroupMenuItem_actionPerformed() @@ -2764,7 +2767,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } @@ -2794,7 +2797,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI current; int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + for (int i = 0; i < viewport.getAlignment().getSequences() + .size(); i++) { current = viewport.getAlignment().getSequenceAt(i); @@ -2803,12 +2807,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } if ((viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() < 4 && viewport - .getSelectionGroup().getSize() > 0) + && viewport.getSelectionGroup().getSize() < 4 + && viewport.getSelectionGroup().getSize() > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -2837,15 +2841,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void njTreeBlosumMenuItem_actionPerformed() { - newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance() - .getBlosum62().getName(), + newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, + ScoreModels.getInstance().getBlosum62().getName(), "Neighbour joining tree using BLOSUM62"); } protected void avTreeBlosumMenuItem_actionPerformed() { - newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance() - .getBlosum62().getName(), + newTreePanel(TreeBuilder.AVERAGE_DISTANCE, + ScoreModels.getInstance().getBlosum62().getName(), "Average distance tree using BLOSUM62"); } @@ -2857,7 +2861,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI current; int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + for (int i = 0; i < viewport.getAlignment().getSequences() + .size(); i++) { current = viewport.getAlignment().getSequenceAt(i); @@ -2866,12 +2871,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } - if ((viewport.getSelectionGroup() != null && viewport - .getSelectionGroup().getSize() > 1) + if ((viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 1) || (viewport.getAlignment().getHeight() > 1)) { final TreePanel tp = new TreePanel(alignPanel, type, pwType); @@ -2912,14 +2917,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void sortByTree(TreePanel treePanel, String title) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter - .sortByTree(viewport.getAlignment(), treePanel.getTree()); + AlignmentSorter.sortByTree(viewport.getAlignment(), + treePanel.getTree()); // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); - addHistoryItem(new OrderCommand(MessageManager.formatMessage( - "label.order_by_params", new String[] { title }), oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); + addHistoryItem(new OrderCommand(MessageManager + .formatMessage("label.order_by_params", new String[] + { title }), oldOrder, viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } /** @@ -2977,7 +2982,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); return true; } @@ -3014,39 +3019,37 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // TODO: update this text for each release or centrally store it for // lite and application g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString(MessageManager.formatMessage( - "label.jalviewLite_release", new String[] { version }), x, - y += fh); + g.drawString(MessageManager + .formatMessage("label.jalviewLite_release", new String[] + { version }), x, y += fh); g.setFont(new Font("Helvetica", Font.BOLD, 12)); - g.drawString(MessageManager.formatMessage( - "label.jaview_build_date", new String[] { builddate }), x, - y += fh); + g.drawString(MessageManager.formatMessage("label.jaview_build_date", + new String[] + { builddate }), x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString(MessageManager.getString("label.jalview_authors_1"), - x, y += fh * 1.5); + g.drawString(MessageManager.getString("label.jalview_authors_1"), x, + y += fh * 1.5); g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh + 8); - g.drawString( - MessageManager.getString("label.jalview_dev_managers"), x, - y += fh); + g.drawString(MessageManager.getString("label.jalview_dev_managers"), + x, y += fh); g.drawString(MessageManager .getString("label.jalview_distribution_lists"), x, y += fh); g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8); g.drawString( - MessageManager.getString("label.jalview_cite_1_authors"), - x, y += fh); - g.drawString( - MessageManager.getString("label.jalview_cite_1_title"), x, + MessageManager.getString("label.jalview_cite_1_authors"), x, y += fh); + g.drawString(MessageManager.getString("label.jalview_cite_1_title"), + x, y += fh); g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), x, y += fh); } } Frame frame = new Frame(); - frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite - .getBuildDate())); + frame.add(new AboutPanel(JalviewLite.getVersion(), + JalviewLite.getBuildDate())); jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220); @@ -3319,20 +3322,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, pasteNew.addActionListener(this); pasteThis.setLabel(MessageManager.getString("label.to_this_alignment")); pasteThis.addActionListener(this); - remove2LeftMenuItem.setLabel(MessageManager - .getString("action.remove_left")); + remove2LeftMenuItem + .setLabel(MessageManager.getString("action.remove_left")); remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel(MessageManager - .getString("action.remove_right")); + remove2RightMenuItem + .setLabel(MessageManager.getString("action.remove_right")); remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel(MessageManager - .getString("action.remove_empty_columns")); + removeGappedColumnMenuItem.setLabel( + MessageManager.getString("action.remove_empty_columns")); removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel(MessageManager - .getString("action.remove_all_gaps")); + removeAllGapsMenuItem + .setLabel(MessageManager.getString("action.remove_all_gaps")); removeAllGapsMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel(MessageManager - .getString("action.remove_redundancy")); + removeRedundancyMenuItem + .setLabel(MessageManager.getString("action.remove_redundancy")); removeRedundancyMenuItem.addActionListener(this); /* @@ -3342,25 +3345,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, findMenuItem.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.setLabel(MessageManager - .getString("action.invert_sequence_selection")); + invertSequenceMenuItem.setLabel( + MessageManager.getString("action.invert_sequence_selection")); invertSequenceMenuItem.addActionListener(this); - invertColSel.setLabel(MessageManager - .getString("action.invert_column_selection")); + invertColSel.setLabel( + MessageManager.getString("action.invert_column_selection")); invertColSel.addActionListener(this); - deleteGroups.setLabel(MessageManager - .getString("action.undefine_groups")); + deleteGroups + .setLabel(MessageManager.getString("action.undefine_groups")); deleteGroups.addActionListener(this); - grpsFromSelection.setLabel(MessageManager - .getString("action.make_groups_selection")); + grpsFromSelection.setLabel( + MessageManager.getString("action.make_groups_selection")); grpsFromSelection.addActionListener(this); createGroup.setLabel(MessageManager.getString("action.create_group")); createGroup.addActionListener(this); unGroup.setLabel(MessageManager.getString("action.remove_group")); unGroup.addActionListener(this); - annotationColumnSelection.setLabel(MessageManager - .getString("action.select_by_annotation")); + annotationColumnSelection.setLabel( + MessageManager.getString("action.select_by_annotation")); annotationColumnSelection.addActionListener(this); /* @@ -3374,14 +3377,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Menu hideMenu = new Menu(MessageManager.getString("action.hide")); hideColumns .setLabel(MessageManager.getString("label.selected_columns")); - hideSequences.setLabel(MessageManager - .getString("label.selected_sequences")); - hideAllButSelection.setLabel(MessageManager - .getString("label.all_but_selected_region")); - hideAllSelection.setLabel(MessageManager - .getString("label.selected_region")); - showAllHidden.setLabel(MessageManager - .getString("label.all_sequences_columns")); + hideSequences + .setLabel(MessageManager.getString("label.selected_sequences")); + hideAllButSelection.setLabel( + MessageManager.getString("label.all_but_selected_region")); + hideAllSelection + .setLabel(MessageManager.getString("label.selected_region")); + showAllHidden.setLabel( + MessageManager.getString("label.all_sequences_columns")); showColumns.addActionListener(this); showSeqs.addActionListener(this); hideColumns.addActionListener(this); @@ -3389,39 +3392,39 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hideAllButSelection.addActionListener(this); hideAllSelection.addActionListener(this); showAllHidden.addActionListener(this); - featureSettings.setLabel(MessageManager - .getString("action.feature_settings")); + featureSettings + .setLabel(MessageManager.getString("action.feature_settings")); featureSettings.addActionListener(this); - sequenceFeatures.setLabel(MessageManager - .getString("label.show_sequence_features")); + sequenceFeatures.setLabel( + MessageManager.getString("label.show_sequence_features")); sequenceFeatures.addItemListener(this); sequenceFeatures.setState(false); - followMouseOverFlag.setLabel(MessageManager - .getString("label.automatic_scrolling")); + followMouseOverFlag.setLabel( + MessageManager.getString("label.automatic_scrolling")); followMouseOverFlag.addItemListener(this); alProperties.addActionListener(this); - overviewMenuItem.setLabel(MessageManager - .getString("label.overview_window")); + overviewMenuItem + .setLabel(MessageManager.getString("label.overview_window")); overviewMenuItem.addActionListener(this); /* * Configure Annotations menu items and actions */ - annotationPanelMenuItem.setLabel(MessageManager - .getString("label.show_annotations")); + annotationPanelMenuItem + .setLabel(MessageManager.getString("label.show_annotations")); annotationPanelMenuItem.addItemListener(this); - showGroupConsensus.setLabel(MessageManager - .getString("label.group_consensus")); - showGroupConservation.setLabel(MessageManager - .getString("label.group_conservation")); - showConsensusHistogram.setLabel(MessageManager - .getString("label.show_consensus_histogram")); - showSequenceLogo.setLabel(MessageManager - .getString("label.show_consensus_logo")); - normSequenceLogo.setLabel(MessageManager - .getString("label.norm_consensus_logo")); - applyAutoAnnotationSettings.setLabel(MessageManager - .getString("label.apply_all_groups")); + showGroupConsensus + .setLabel(MessageManager.getString("label.group_consensus")); + showGroupConservation + .setLabel(MessageManager.getString("label.group_conservation")); + showConsensusHistogram.setLabel( + MessageManager.getString("label.show_consensus_histogram")); + showSequenceLogo.setLabel( + MessageManager.getString("label.show_consensus_logo")); + normSequenceLogo.setLabel( + MessageManager.getString("label.norm_consensus_logo")); + applyAutoAnnotationSettings + .setLabel(MessageManager.getString("label.apply_all_groups")); applyAutoAnnotationSettings.setState(true); Menu autoAnnMenu = new Menu( MessageManager.getString("label.autocalculated_annotation")); @@ -3476,44 +3479,44 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewTextMenuItem.setLabel(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); viewTextMenuItem.addItemListener(this); - colourTextMenuItem.setLabel(MessageManager - .getString("label.colour_text")); + colourTextMenuItem + .setLabel(MessageManager.getString("label.colour_text")); colourTextMenuItem.addItemListener(this); - displayNonconservedMenuItem.setLabel(MessageManager - .getString("label.show_non_conserved")); + displayNonconservedMenuItem + .setLabel(MessageManager.getString("label.show_non_conserved")); displayNonconservedMenuItem.addItemListener(this); wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel(MessageManager - .getString("action.show_gaps")); + renderGapsMenuItem + .setLabel(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); renderGapsMenuItem.addItemListener(this); - centreColumnLabelFlag.setLabel(MessageManager - .getString("label.centre_column_labels")); + centreColumnLabelFlag.setLabel( + MessageManager.getString("label.centre_column_labels")); centreColumnLabelFlag.addItemListener(this); seqLimits.setState(true); - seqLimits.setLabel(MessageManager - .getString("label.show_sequence_limits")); + seqLimits.setLabel( + MessageManager.getString("label.show_sequence_limits")); seqLimits.addItemListener(this); /* * Configure Colour menu items and actions */ - applyToAllGroups.setLabel(MessageManager - .getString("label.apply_colour_to_all_groups")); + applyToAllGroups.setLabel( + MessageManager.getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); - clustalColour.setLabel(MessageManager - .getString("label.colourScheme_clustal")); + clustalColour.setLabel( + MessageManager.getString("label.colourScheme_clustal")); clustalColour.addActionListener(this); - zappoColour.setLabel(MessageManager - .getString("label.colourScheme_zappo")); + zappoColour + .setLabel(MessageManager.getString("label.colourScheme_zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel(MessageManager - .getString("label.colourScheme_taylor")); + taylorColour.setLabel( + MessageManager.getString("label.colourScheme_taylor")); taylorColour.addActionListener(this); - hydrophobicityColour.setLabel(MessageManager - .getString("label.colourScheme_hydrophobic")); + hydrophobicityColour.setLabel( + MessageManager.getString("label.colourScheme_hydrophobic")); hydrophobicityColour.addActionListener(this); helixColour.setLabel(MessageManager .getString("label.colourScheme_helix_propensity")); @@ -3521,11 +3524,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, strandColour.setLabel(MessageManager .getString("label.colourScheme_strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel(MessageManager - .getString("label.colourScheme_turn_propensity")); + turnColour.setLabel( + MessageManager.getString("label.colourScheme_turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel(MessageManager - .getString("label.colourScheme_buried_index")); + buriedColour.setLabel( + MessageManager.getString("label.colourScheme_buried_index")); buriedColour.addActionListener(this); purinePyrimidineColour.setLabel(MessageManager .getString("label.colourScheme_purine/pyrimidine")); @@ -3533,81 +3536,82 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // RNAInteractionColour.setLabel(MessageManager // .getString("label.rna_interaction")); // RNAInteractionColour.addActionListener(this); - RNAHelixColour.setLabel(MessageManager - .getString("label.colourScheme_rna_helices")); + RNAHelixColour.setLabel( + MessageManager.getString("label.colourScheme_rna_helices")); RNAHelixColour.addActionListener(this); - userDefinedColour.setLabel(MessageManager - .getString("action.user_defined")); + userDefinedColour + .setLabel(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel(MessageManager - .getString("label.colourScheme_%_identity")); + PIDColour.setLabel( + MessageManager.getString("label.colourScheme_%_identity")); PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel(MessageManager - .getString("label.colourScheme_blosum62")); + BLOSUM62Colour.setLabel( + MessageManager.getString("label.colourScheme_blosum62")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour.setLabel(MessageManager - .getString("label.colourScheme_t-coffee_scores")); + tcoffeeColour.setLabel( + MessageManager.getString("label.colourScheme_t-coffee_scores")); // it will be enabled only if a score file is provided tcoffeeColour.setEnabled(false); tcoffeeColour.addActionListener(this); - conservationMenuItem.setLabel(MessageManager - .getString("action.by_conservation")); + conservationMenuItem + .setLabel(MessageManager.getString("action.by_conservation")); conservationMenuItem.addItemListener(this); noColourmenuItem.setLabel(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(this); - abovePIDThreshold.setLabel(MessageManager - .getString("label.above_identity_threshold")); + abovePIDThreshold.setLabel( + MessageManager.getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel(MessageManager - .getString("label.colourScheme_nucleotide")); + nucleotideColour.setLabel( + MessageManager.getString("label.colourScheme_nucleotide")); nucleotideColour.addActionListener(this); - modifyPID.setLabel(MessageManager - .getString("label.modify_identity_threshold")); + modifyPID.setLabel( + MessageManager.getString("label.modify_identity_threshold")); modifyPID.setEnabled(abovePIDThreshold.getState()); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager .getString("label.modify_conservation_threshold")); modifyConservation.setEnabled(conservationMenuItem.getState()); modifyConservation.addActionListener(this); - annotationColour.setLabel(MessageManager - .getString("action.by_annotation")); + annotationColour + .setLabel(MessageManager.getString("action.by_annotation")); annotationColour.addActionListener(this); /* * Configure Calculate menu items and actions */ - sortPairwiseMenuItem.setLabel(MessageManager - .getString("action.by_pairwise_id")); + sortPairwiseMenuItem + .setLabel(MessageManager.getString("action.by_pairwise_id")); sortPairwiseMenuItem.addActionListener(this); sortIDMenuItem.setLabel(MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(this); - sortLengthMenuItem.setLabel(MessageManager - .getString("action.by_length")); + sortLengthMenuItem + .setLabel(MessageManager.getString("action.by_length")); sortLengthMenuItem.addActionListener(this); sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel(MessageManager - .getString("action.pairwise_alignment")); + pairwiseAlignmentMenuItem.setLabel( + MessageManager.getString("action.pairwise_alignment")); pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel(MessageManager - .getString("label.principal_component_analysis")); + PCAMenuItem.setLabel( + MessageManager.getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(this); autoCalculate = new CheckboxMenuItem( - MessageManager.getString("label.autocalculate_consensus"), true); - averageDistanceTreeMenuItem.setLabel(MessageManager - .getString("label.average_distance_identity")); + MessageManager.getString("label.autocalculate_consensus"), + true); + averageDistanceTreeMenuItem.setLabel( + MessageManager.getString("label.average_distance_identity")); averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel(MessageManager - .getString("label.neighbour_joining_identity")); + neighbourTreeMenuItem.setLabel( + MessageManager.getString("label.neighbour_joining_identity")); neighbourTreeMenuItem.addActionListener(this); - avDistanceTreeBlosumMenuItem.setLabel(MessageManager - .getString("label.average_distance_blosum62")); + avDistanceTreeBlosumMenuItem.setLabel( + MessageManager.getString("label.average_distance_blosum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel(MessageManager - .getString("label.neighbour_blosum62")); + njTreeBlosumMenuItem + .setLabel(MessageManager.getString("label.neighbour_blosum62")); njTreeBlosumMenuItem.addActionListener(this); - sortByTreeMenu.setLabel(MessageManager - .getString("action.by_tree_order")); + sortByTreeMenu + .setLabel(MessageManager.getString("action.by_tree_order")); Menu sortMenu = new Menu(MessageManager.getString("action.sort")); Menu calculateTreeMenu = new Menu( MessageManager.getString("action.calculate_tree")); @@ -3924,9 +3928,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, theApplet.add(embeddedMenu, BorderLayout.NORTH); theApplet.add(statusBar, BorderLayout.SOUTH); // TODO should size be left to the layout manager? - alignPanel.setSize(theApplet.getSize().width, - theApplet.getSize().height - embeddedMenu.getHeight() - - statusBar.getHeight()); + alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height + - embeddedMenu.getHeight() - statusBar.getHeight()); theApplet.add(alignPanel, BorderLayout.CENTER); final AlignFrame me = this; theApplet.addFocusListener(new FocusListener() @@ -3972,8 +3975,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewer = (Viewer) jmolviewer; } catch (ClassCastException ex) { - System.err.println("Unsupported viewer object :" - + jmolviewer.getClass()); + System.err.println( + "Unsupported viewer object :" + jmolviewer.getClass()); } if (viewer == null) { @@ -4068,8 +4071,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // resolve data source // TODO: this code should be a refactored to an io package - DataSourceType protocol = AppletFormatAdapter.resolveProtocol( - pdbFile, FileFormat.PDB); + DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile, + FileFormat.PDB); if (protocol == null) { return false; @@ -4094,8 +4097,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (seqs[i] != null) { - sequences.addElement(new Object[] { seqs[i], - (chains != null) ? chains[i] : null }); + sequences + .addElement(new Object[] + { seqs[i], (chains != null) ? chains[i] : null }); } } seqs = new SequenceI[sequences.size()]; @@ -4121,8 +4125,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, chains = (String[]) sqch[1]; if (seqs == null || seqs.length == 0) { - System.err - .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); + System.err.println( + "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } if (protocol == null) { @@ -4145,7 +4149,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // register the association(s) and quit, don't create any windows. if (StructureSelectionManager.getStructureSelectionManager(applet) - .setMapping(seqs, chains, pdb.getFile(), protocol) == null) + .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null) { System.err.println("Failed to map " + pdb.getFile() + " (" + protocol + ") to any sequences"); @@ -4169,8 +4173,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (ajm != null) { - System.err - .println("Incremental adding and aligning structure to existing Jmol view not yet implemented."); + System.err.println( + "Incremental adding and aligning structure to existing Jmol view not yet implemented."); // try and add the pdb structure // ajm.addS ajm = null; @@ -4179,8 +4183,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // otherwise, create a new window if (applet.jmolAvailable) { - new AppletJmol(pdb, seqs, chains, alignPanel, - protocol); + new AppletJmol(pdb, seqs, chains, alignPanel, protocol); applet.lastFrameX += 40; applet.lastFrameY += 40; } @@ -4263,12 +4266,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, */ AlignmentI aln; if ((aln = viewport.getAlignment()) != null - && (aln.getHeight() != file.getHeight() || aln.getWidth() != file - .getWidth())) + && (aln.getHeight() != file.getHeight() + || aln.getWidth() != file.getWidth())) { // TODO: raise a dialog box here rather than bomb out. - System.err - .println("The scores matrix does not match the alignment dimensions"); + System.err.println( + "The scores matrix does not match the alignment dimensions"); }