X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a616dc036bfa51791c5468d07bba6814243beb26;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=fbcecbef8a5ba9542a1e90ef814b262fb0382572;hpb=47bbb25ec91be3ee864d7ee5393bcf7a19688f87;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index fbcecbe..a616dc0 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -241,7 +241,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this(al, hiddenColumns, width, height, null); } - /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId @@ -286,7 +285,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); init(); } @@ -312,7 +310,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, init(); } - /** * Make a new AlignFrame from existing alignmentPanels * @@ -371,10 +368,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setGUINucleotide(viewport.getAlignment().isNucleotide()); } + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); - + if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); @@ -558,8 +558,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() - || evt.isShiftDown() || evt.isAltDown()); + alignPanel.getSeqPanel().insertGapAtCursor( + evt.isControlDown() || evt.isShiftDown() + || evt.isAltDown()); } break; @@ -582,8 +583,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() - || evt.isShiftDown() || evt.isAltDown()); + alignPanel.getSeqPanel().deleteGapAtCursor( + evt.isControlDown() || evt.isShiftDown() + || evt.isAltDown()); } break; @@ -631,8 +633,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; statusBar.setText(MessageManager.formatMessage( - "label.keyboard_editing_mode", new String[] - { (viewport.cursorMode ? "on" : "off") })); + "label.keyboard_editing_mode", + new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; @@ -843,6 +845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * operation that affects the data in the current view (selection changed, * etc) to update the menus to reflect the new state. */ + @Override public void setMenusForViewport() { setMenusFromViewport(viewport); @@ -1077,7 +1080,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file")); + chooser.setDialogTitle(MessageManager + .getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -1135,8 +1139,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format })); + "label.successfully_saved_to_file_in_format", new Object[] { + fileName, format })); } else @@ -1160,7 +1164,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } FormatAdapter f = new FormatAdapter(alignPanel, exportData.getSettings()); - String output = f.formatSequences(format, + String output = f.formatSequences( + format, exportData.getAlignment(), // class cast exceptions will // occur in the distant future exportData.getOmitHidden(), exportData.getStartEndPostions(), @@ -1183,8 +1188,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new Object[] - { fileName, format })); + new Object[] { fileName, format })); } catch (Exception ex) { success = false; @@ -1196,8 +1200,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { JOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new Object[] - { fileName }), MessageManager + .formatMessage("label.couldnt_save_file", + new Object[] { fileName }), MessageManager .getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE); } @@ -1205,7 +1209,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return success; } - private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) @@ -1242,14 +1245,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences( - e.getActionCommand(), - exportData.getAlignment(), - exportData.getOmitHidden(), exportData.getStartEndPostions(), - viewport.getColumnSelection())); + .formatSequences(e.getActionCommand(), + exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getColumnSelection())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] - { e.getActionCommand() }), 600, 500); + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); } catch (OutOfMemoryError oom) { new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); @@ -1258,8 +1261,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } - public static AlignmentExportData getAlignmentForExport(String exportFormat, - AlignViewportI viewport, + public static AlignmentExportData getAlignmentForExport( + String exportFormat, AlignViewportI viewport, AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; @@ -1270,16 +1273,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, HiddenSequences hiddenSeqs = viewport.getAlignment() .getHiddenSequences(); - alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = new int[] - { 0, alignmentToExport.getWidth() - 1 }; + alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 }; boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; if (settings == null) { settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFormat); + viewport.hasHiddenColumns(), exportFormat); } // settings.isExportAnnotations(); @@ -1298,8 +1299,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport .getColumnSelection().getHiddenColumns()); } - AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, - settings); + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd, settings); return ed; } @@ -1309,19 +1310,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int startPos = aligmentStartEnd[0]; int endPos = aligmentStartEnd[1]; - int[] lowestRange = new int[2]; - int[] higestRange = new int[2]; + int[] lowestRange = new int[] { -1, -1 }; + int[] higestRange = new int[] { -1, -1 }; for (int[] hiddenCol : hiddenCols) { - // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]); lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; } - // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]); - // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]); - if (lowestRange[0] == 0 && lowestRange[1] == 0) + if (lowestRange[0] == -1 && lowestRange[1] == -1) { startPos = aligmentStartEnd[0]; } @@ -1330,36 +1328,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, startPos = lowestRange[1] + 1; } - if (higestRange[0] == 0 && higestRange[1] == 0) + if (higestRange[0] == -1 && higestRange[1] == -1) { endPos = aligmentStartEnd[1]; } else { - endPos = higestRange[0]; + endPos = higestRange[0] - 1; } - // System.out.println("Export range : " + minPos + " - " + maxPos); - return new int[] - { startPos, endPos }; + // System.out.println("Export range : " + startPos + " - " + endPos); + return new int[] { startPos, endPos }; } public static void main(String[] args) { ArrayList hiddenCols = new ArrayList(); - hiddenCols.add(new int[] - { 0, 4 }); - hiddenCols.add(new int[] - { 6, 9 }); - hiddenCols.add(new int[] - { 11, 12 }); - hiddenCols.add(new int[] - { 33, 33 }); - hiddenCols.add(new int[] - { 45, 50 }); - - int[] x = getStartEnd(new int[] - { 0, 50 }, hiddenCols); + hiddenCols.add(new int[] { 0, 0 }); + hiddenCols.add(new int[] { 6, 9 }); + hiddenCols.add(new int[] { 11, 12 }); + hiddenCols.add(new int[] { 33, 33 }); + hiddenCols.add(new int[] { 50, 50 }); + + int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols); // System.out.println("Export range : " + x[0] + " - " + x[1]); } @@ -1378,9 +1369,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { - BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this); bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1410,10 +1402,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.makeEPS(f); } + @Override public void createSVG(File f) { alignPanel.makeSVG(f); } + @Override public void pageSetup_actionPerformed(ActionEvent e) { @@ -1557,8 +1551,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, undoMenuItem.setEnabled(true); CommandI command = viewport.getHistoryList().peek(); undoMenuItem.setText(MessageManager.formatMessage( - "label.undo_command", new Object[] - { command.getDescription() })); + "label.undo_command", + new Object[] { command.getDescription() })); } else { @@ -1572,8 +1566,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, CommandI command = viewport.getRedoList().peek(); redoMenuItem.setText(MessageManager.formatMessage( - "label.redo_command", new Object[] - { command.getDescription() })); + "label.redo_command", + new Object[] { command.getDescription() })); } else { @@ -1582,6 +1576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1615,8 +1610,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport != null) { - return new AlignmentI[] - { viewport.getAlignment() }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } @@ -1850,8 +1844,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean appendHistoryItem = false; Deque historyList = viewport.getHistoryList(); boolean inSplitFrame = getSplitViewContainer() != null; - if (!inSplitFrame && historyList != null - && historyList.size() > 0 + if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc @@ -1922,17 +1915,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { - hiddenColumns.add(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); + hiddenColumns.add(new int[] { region[0] - hiddenOffset, + region[1] - hiddenOffset }); } } } - Desktop.jalviewClipboard = new Object[] - { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; + Desktop.jalviewClipboard = new Object[] { seqs, + viewport.getAlignment().getDataset(), hiddenColumns }; statusBar.setText(MessageManager.formatMessage( - "label.copied_sequences_to_clipboard", new Object[] - { Integer.valueOf(seqs.length).toString() })); + "label.copied_sequences_to_clipboard", new Object[] { Integer + .valueOf(seqs.length).toString() })); } /** @@ -2141,8 +2134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // addHistoryItem(new EditCommand( MessageManager.getString("label.add_sequences"), - Action.PASTE, - sequences, 0, alignment.getWidth(), alignment)); + Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences for (int i = 0; i < sequences.length; i++) @@ -2260,7 +2252,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2319,7 +2312,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2381,20 +2375,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ if (sg.getSize() == viewport.getAlignment().getHeight()) { - int confirm = JOptionPane.showConfirmDialog(this, - MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ - MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JOptionPane.OK_CANCEL_OPTION); - - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport + .getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) { - return; + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); + + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } - SequenceI[] cut = sg.getSequences() .toArray(new SequenceI[sg.getSize()]); @@ -2549,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2574,23 +2572,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, TrimRegionCommand trimRegion; if (trimLeft) { - trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); viewport.setStartRes(0); } else { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); } statusBar.setText(MessageManager.formatMessage( - "label.removed_columns", new String[] - { Integer.valueOf(trimRegion.getSize()).toString() })); + "label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()) + .toString() })); addHistoryItem(trimRegion); @@ -2639,8 +2634,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", new Object[] - { Integer.valueOf(removeGapCols.getSize()).toString() })); + "label.removed_empty_columns", + new Object[] { Integer.valueOf(removeGapCols.getSize()) + .toString() })); // This is to maintain viewport position on first residue // of first sequence @@ -2890,8 +2886,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowJVSuffix(seqLimits.isSelected()); - alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel - .calculateIdWidth()); + alignPanel.getIdPanel().getIdCanvas() + .setPreferredSize(alignPanel.calculateIdWidth()); alignPanel.paintAlignment(true); } @@ -2970,13 +2966,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showAllHiddenColumns(); repaint(); + viewport.sendSelection(); } @Override public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); -// alignPanel.paintAlignment(true); + // alignPanel.paintAlignment(true); } /** @@ -3060,6 +3057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); + viewport.sendSelection(); } /* @@ -3077,6 +3075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /* @@ -3092,6 +3091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3099,6 +3099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3281,14 +3282,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); editPane.setText(MessageManager.formatMessage("label.html_content", - new Object[] - { contents.toString() })); + new Object[] { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new Object[] - { getTitle() }), 500, 400); + "label.alignment_properties", new Object[] { getTitle() }), + 500, 400); } /** @@ -3309,8 +3309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.overview_params", new Object[] - { this.getTitle() }), frame.getWidth(), frame.getHeight()); + "label.overview_params", new Object[] { this.getTitle() }), + frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() @@ -3501,6 +3501,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param cs * DOCUMENT ME! */ + @Override public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method @@ -3520,6 +3521,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } + if (cs instanceof TCoffeeColourScheme) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + } } viewport.setGlobalColourScheme(cs); @@ -4030,7 +4036,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title})); + final JMenuItem item = new JMenuItem(MessageManager.formatMessage( + "action.by_title_param", new Object[] { title })); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @@ -4149,8 +4156,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, calculateTree.removeAll(); // build the calculate menu - for (final String type : new String[] - { "NJ", "AV" }) + for (final String type : new String[] { "NJ", "AV" }) { String treecalcnm = MessageManager.getString("label.tree_calc_" + type.toLowerCase()); @@ -4299,8 +4305,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // selection may well be aligned - we preserve 2.0.8 behaviour for moment. if (!viewport.getAlignment().isAligned(false)) { - seqs.setSequences(new SeqCigar[] - { seqs.getSequences()[0] }); + seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); // TODO: if seqs.getSequences().length>1 then should really have warned // user! @@ -4747,8 +4752,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final long sttime = System.currentTimeMillis(); AlignFrame.this.setProgressBar(MessageManager.formatMessage( - "status.searching_for_sequences_from", new Object[] - { source }), sttime); + "status.searching_for_sequences_from", + new Object[] { source }), sttime); try { // update our local dataset reference @@ -4855,9 +4860,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignFrame.this.setProgressBar(MessageManager.formatMessage( "status.finished_searching_for_sequences_from", - new Object[] - { source }), - sttime); + new Object[] { source }), sttime); } }; @@ -4922,8 +4925,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); af.setFileFormat(this.currentFileFormat); final String newTitle = MessageManager.formatMessage( - "label.translation_of_params", new Object[] - { this.getTitle() }); + "label.translation_of_params", + new Object[] { this.getTitle() }); af.setTitle(newTitle); if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { @@ -4961,7 +4964,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return avc.parseFeaturesFile(file, type, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); - + } @Override @@ -4976,8 +4979,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures.setSelected(true); } - } + @Override public void dragEnter(DropTargetDragEvent evt) { @@ -5108,8 +5111,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (type.equalsIgnoreCase("PDB")) { - filesmatched.add(new Object[] - { file, protocol, mtch }); + filesmatched.add(new Object[] { file, protocol, mtch }); continue; } } @@ -5128,10 +5130,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager .formatMessage( "label.automatically_associate_pdb_files_with_sequences_same_name", - new Object[] - { Integer.valueOf( - filesmatched - .size()) + new Object[] { Integer + .valueOf( + filesmatched + .size()) .toString() }), MessageManager .getString("label.automatically_associate_pdb_files_by_name"), @@ -5168,14 +5170,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane .showConfirmDialog( this, - ""+MessageManager - .formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] - { Integer.valueOf( - filesnotmatched - .size()) - .toString() })+"", + "" + + MessageManager + .formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] { Integer + .valueOf( + filesnotmatched + .size()) + .toString() }) + + "", MessageManager .getString("label.ignore_unmatched_dropped_files"), JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) @@ -5218,8 +5222,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse as annotation. boolean isAnnotation = (format == null || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, protocol) - : false; + .annotateAlignmentView(viewport, file, protocol) : false; if (!isAnnotation) { @@ -5533,8 +5536,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame) + .getSequenceSelection(), + alignPanel.alignFrame, null, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); @@ -5603,16 +5612,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), - alignPanel.alignFrame, dassource) + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); } }); - fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()}))); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from", + new Object[] { src.getDbName() }))); dfetch.add(fetchr); comp++; } @@ -5623,8 +5640,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // fetch all entry DbSourceProxy src = otherdb.get(0); fetchr = new JMenuItem(MessageManager.formatMessage( - "label.fetch_all_param", new Object[] - { src.getDbSource() })); + "label.fetch_all_param", + new Object[] { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override @@ -5636,20 +5653,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), - alignPanel.alignFrame, dassource) + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); } }); - fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()}))); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from_all_sources", + new Object[] { + Integer.valueOf(otherdb.size()) + .toString(), src.getDbSource(), + src.getDbName() }))); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus - ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()})); + ifetch = new JMenu(MessageManager.formatMessage( + "label.source_from_db_source", + new Object[] { src.getDbSource() })); icomp = 0; String imname = null; int i = 0; @@ -5662,11 +5692,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 0, 10) + "..." : dbname; if (imname == null) { - imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname}); + imname = MessageManager.formatMessage( + "label.from_msname", new Object[] { sname }); } fetchr = new JMenuItem(msname); - final DbSourceProxy[] dassrc = - { sproxy }; + final DbSourceProxy[] dassrc = { sproxy }; fetchr.addActionListener(new ActionListener() { @@ -5679,9 +5709,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), - alignPanel.alignFrame, dassrc) + alignPanel.alignFrame, dassrc, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); @@ -5689,7 +5724,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText("" - + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname})); + + MessageManager.formatMessage( + "label.fetch_retrieve_from", new Object[] + { dbname })); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) @@ -5744,6 +5781,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, al); } + @Override public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(b); @@ -5853,10 +5891,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } } + public void clearAlignmentSeqRep() { // TODO refactor alignmentseqrep to controller - if (viewport.getAlignment().hasSeqrep()) { + if (viewport.getAlignment().hasSeqrep()) + { viewport.getAlignment().setSeqrep(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); @@ -5892,7 +5932,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!viewport.getSequenceSetId().equals( alignmentPanel.av.getSequenceSetId())) { - throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame")); + throw new Error( + MessageManager + .getString("error.implementation_error_cannot_show_view_alignment_frame")); } if (tabbedPane != null && tabbedPane.getTabCount() > 0 @@ -5955,8 +5997,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) - : alignPanels; + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; } /** @@ -5973,8 +6014,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } List cdnaSeqs = new ArrayList(); - for (SequenceI aaSeq : alignment.getSequences()) { - for (AlignedCodonFrame acf : mappings) { + for (SequenceI aaSeq : alignment.getSequences()) + { + for (AlignedCodonFrame acf : mappings) + { SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); if (dnaSeq != null) { @@ -6002,8 +6045,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + this.title; Desktop.addInternalFrame(alignFrame, newtitle, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } /** @@ -6016,7 +6058,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showComplement_actionPerformed(boolean show) { SplitContainerI sf = getSplitViewContainer(); - if (sf != null) { + if (sf != null) + { sf.setComplementVisible(this, show); } }