X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5ff7c6cb239edda0b3e9fd73f05c8e54ef3ca8f1;hb=a6b324e3f5edac3df0b968f0037b1cc8b651598e;hp=07ce23c991ba2cc71df70b5fb8577d6b8be70348;hpb=ba0bedafc61f5e83fa5a34f8ddbd0cd5222abe0e;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 07ce23c..5ff7c6c 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,14 +20,13 @@ */ package jalview.gui; -import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; -import jalview.analysis.Conservation; import jalview.analysis.CrossRef; import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignExportSettingI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; @@ -37,6 +36,7 @@ import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -48,6 +48,7 @@ import jalview.commands.TrimRegionCommand; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; @@ -130,7 +131,6 @@ import java.util.Deque; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; -import java.util.Set; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -240,7 +240,6 @@ 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 @@ -285,7 +284,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); init(); } @@ -311,7 +309,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, init(); } - /** * Make a new AlignFrame from existing alignmentPanels * @@ -334,7 +331,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { - progressBar = new ProgressBar(this.statusPanel, this.statusBar); + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); @@ -367,10 +367,13 @@ 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); @@ -451,7 +454,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } }); - formatMenu.add(vsel); + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("devel") > -1 + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("test") > -1) + { + formatMenu.add(vsel); + } } @@ -548,8 +557,9 @@ 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; @@ -572,8 +582,9 @@ 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; @@ -621,8 +632,8 @@ 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; @@ -790,7 +801,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { - System.out.println("deregistering discoverer listener"); + // System.out.println("deregistering discoverer listener"); Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); @@ -816,6 +827,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); + showReverse.setVisible(nucleotide); + showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); @@ -833,6 +846,7 @@ 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); @@ -1025,7 +1039,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); + Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport + .getAlignPanel()); } @Override @@ -1066,7 +1081,8 @@ 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); @@ -1124,8 +1140,8 @@ 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 @@ -1134,14 +1150,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { warningMessage("Cannot save file " + fileName + " using format " + format, "Alignment output format not supported"); - saveAs_actionPerformed(null); - // JBPNote need to have a raise_gui flag here + if (!Jalview.isHeadlessMode()) + { + saveAs_actionPerformed(null); + } return false; } - ExportData exportData = getAlignmentForExport(format); - FormatAdapter f = new FormatAdapter(alignPanel); - String output = f.formatSequences(format, + AlignmentExportData exportData = getAlignmentForExport(format, + viewport, null); + if (exportData.getSettings().isCancelled()) + { + return false; + } + FormatAdapter f = new FormatAdapter(alignPanel, + exportData.getSettings()); + String output = f.formatSequences( + format, exportData.getAlignment(), // class cast exceptions will // occur in the distant future exportData.getOmitHidden(), exportData.getStartEndPostions(), @@ -1164,8 +1189,7 @@ 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; @@ -1177,8 +1201,8 @@ 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); } @@ -1186,7 +1210,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return success; } - private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) @@ -1212,7 +1235,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void outputText_actionPerformed(ActionEvent e) { - ExportData exportData = getAlignmentForExport(e.getActionCommand()); + AlignmentExportData exportData = getAlignmentForExport( + e.getActionCommand(), viewport, null); if (exportData.getSettings().isCancelled()) { return; @@ -1222,14 +1246,14 @@ 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); @@ -1238,24 +1262,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } - public ExportData getAlignmentForExport(String exportFomat) + public static AlignmentExportData getAlignmentForExport( + String exportFormat, AlignViewportI viewport, + AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; + AlignExportSettingI settings = exportSettings; String[] omitHidden = null; int[] alignmentStartEnd = new int[2]; 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; - AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFomat); - settings.isExportAnnotations(); + if (settings == null) + { + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFormat); + } + // settings.isExportAnnotations(); if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) { @@ -1272,30 +1300,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport .getColumnSelection().getHiddenColumns()); } - return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd, - settings); + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd, settings); + return ed; } - private static int[] getStartEnd(int[] aligmentStartEnd, + public static int[] getStartEnd(int[] aligmentStartEnd, List hiddenCols) { 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]; } @@ -1304,36 +1329,29 @@ 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]); } @@ -1355,6 +1373,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1384,10 +1403,12 @@ 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) { @@ -1483,6 +1504,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (closeAllTabs) { + /* + * this will raise an INTERNAL_FRAME_CLOSED event and this method will + * be called recursively, with the frame now in 'closed' state + */ this.setClosed(true); } } catch (Exception ex) @@ -1527,8 +1552,8 @@ 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 { @@ -1542,8 +1567,8 @@ 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 { @@ -1552,6 +1577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1585,8 +1611,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport != null) { - return new AlignmentI[] - { viewport.getAlignment() }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } @@ -1813,10 +1838,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getSelectionGroup().getEndRes() + groupAdjustment); } + /* + * just extend the last slide command if compatible; but not if in + * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) + */ boolean appendHistoryItem = false; Deque historyList = viewport.getHistoryList(); - if (historyList != null - && historyList.size() > 0 + boolean inSplitFrame = getSplitViewContainer() != null; + if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc @@ -1887,17 +1916,17 @@ 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() })); } /** @@ -1952,7 +1981,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - format = new IdentifyFile().Identify(str, "Paste"); + format = new IdentifyFile().identify(str, "Paste"); } catch (OutOfMemoryError er) { @@ -2106,8 +2135,7 @@ 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++) @@ -2225,7 +2253,8 @@ 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. @@ -2284,7 +2313,8 @@ 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. @@ -2346,20 +2376,24 @@ 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()]); @@ -2514,7 +2548,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2539,23 +2573,20 @@ 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); @@ -2604,8 +2635,9 @@ 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 @@ -2730,12 +2762,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* - * Views share the same edits, undo and redo stacks, mappings. + * Views share the same edits undo and redo stacks */ newap.av.setHistoryList(viewport.getHistoryList()); newap.av.setRedoList(viewport.getRedoList()); - newap.av.getAlignment().setCodonFrames( - viewport.getAlignment().getCodonFrames()); + + /* + * Views share the same mappings; need to deregister any new mappings + * created by copyAlignPanel, and register the new reference to the shared + * mappings + */ + newap.av.replaceMappings(viewport.getAlignment()); newap.av.viewName = getNewViewName(viewTitle); @@ -2850,8 +2887,8 @@ 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); } @@ -2930,13 +2967,14 @@ 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); } /** @@ -3020,6 +3058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); + viewport.sendSelection(); } /* @@ -3037,6 +3076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /* @@ -3052,6 +3092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3059,6 +3100,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3241,14 +3283,13 @@ 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); } /** @@ -3269,8 +3310,8 @@ 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() @@ -3461,117 +3502,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param cs * DOCUMENT ME! */ + @Override public void changeColour(ColourSchemeI cs) { - // TODO: compare with applet and pull up to model method - int threshold = 0; + // TODO: pull up to controller method if (cs != null) { + // Make sure viewport is up to date w.r.t. any sliders if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus()); - } - else - { - cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); + viewport.setThreshold(threshold); } if (viewport.getConservationSelected()) { - - Alignment al = (Alignment) viewport.getAlignment(); - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); - - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - - cs.setConservation(c); - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } - else + if (cs instanceof TCoffeeColourScheme) { - cs.setConservation(null); + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); } - - cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); - if (viewport.getColourAppliesToAllGroups()) - { - - for (SequenceGroup sg : viewport.getAlignment().getGroups()) - { - if (cs == null) - { - sg.cs = null; - continue; - } - - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme(sg, - viewport.getHiddenRepSequences()); - } - else if (cs instanceof UserColourScheme) - { - sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours()); - } - else - { - try - { - sg.cs = cs.getClass().newInstance(); - } catch (Exception ex) - { - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus()); - - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - } - else - { - sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(viewport - .getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1); - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - } - } - } - - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - alignPanel.paintAlignment(true); } @@ -4078,7 +4037,8 @@ 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() { @@ -4197,8 +4157,7 @@ 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()); @@ -4347,8 +4306,7 @@ 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! @@ -4506,8 +4464,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final List legacyItems = new ArrayList(); try { - System.err.println("Building ws menu again " - + Thread.currentThread()); + // System.err.println("Building ws menu again " + // + Thread.currentThread()); // TODO: add support for context dependent disabling of services based // on // alignment and current selection @@ -4795,8 +4753,8 @@ 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 @@ -4827,19 +4785,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // TODO 1: no mappings are set up for EMBL product // TODO 2: if they were, should add them to protein alignment, not // dna - Set cf = prods.getCodonFrames(); + List cf = prods.getCodonFrames(); for (AlignedCodonFrame acf : cf) { al.addCodonFrame(acf); } - AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, + AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides") - + " for " + ((isRegSel) ? "selected region of " : "") + String newtitle = "" + (dna ? "Proteins" : "Nucleotides") + + " for " + (isRegSel ? "selected region of " : "") + getTitle(); - naf.setTitle(newtitle); + newFrame.setTitle(newtitle); - // temporary flag until SplitFrame is released boolean asSplitFrame = Cache.getDefault( Preferences.ENABLE_SPLIT_FRAME, true); if (asSplitFrame) @@ -4853,13 +4810,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSequenceSelection(); if (dna) { - copyAlignment = AlignmentUtils.makeExonAlignment( + copyAlignment = AlignmentUtils.makeCdsAlignment( sequenceSelection, cf); al.getCodonFrames().clear(); al.getCodonFrames().addAll(cf); final StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); - ssm.addMappings(cf); + ssm.registerMappings(cf); } else { @@ -4870,9 +4827,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); copyThis.setTitle(AlignFrame.this.getTitle()); // SplitFrame with dna above, protein below - SplitFrame sf = new SplitFrame(dna ? copyThis : naf, - dna ? naf : copyThis); - naf.setVisible(true); + boolean showSequenceFeatures = viewport + .isShowSequenceFeatures(); + newFrame.setShowSeqFeatures(showSequenceFeatures); + copyThis.setShowSeqFeatures(showSequenceFeatures); + SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame, + dna ? newFrame : copyThis); + newFrame.setVisible(true); copyThis.setVisible(true); String linkedTitle = MessageManager .getString("label.linked_view_title"); @@ -4880,7 +4841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, + Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } } @@ -4903,9 +4864,7 @@ 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); } }; @@ -4949,10 +4908,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "Exception during translation. Please report this !", ex); final String msg = MessageManager .getString("label.error_when_translating_sequences_submit_bug_report"); - final String title = MessageManager + final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, title, + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JOptionPane.ERROR_MESSAGE); return; } @@ -4960,9 +4919,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final String msg = MessageManager .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); - final String title = MessageManager + final String errorTitle = MessageManager .getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, title, + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JOptionPane.WARNING_MESSAGE); } else @@ -4970,14 +4929,13 @@ 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)) { final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); - viewport.openSplitFrame(af, new Alignment(seqs), - al.getCodonFrames()); + viewport.openSplitFrame(af, new Alignment(seqs)); } else { @@ -5010,7 +4968,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return avc.parseFeaturesFile(file, type, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); - + } @Override @@ -5025,8 +4983,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures.setSelected(true); } - } + @Override public void dragEnter(DropTargetDragEvent evt) { @@ -5148,7 +5106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String type = null; try { - type = new IdentifyFile().Identify(file, protocol); + type = new IdentifyFile().identify(file, protocol); } catch (Exception ex) { type = null; @@ -5157,8 +5115,7 @@ 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; } } @@ -5177,10 +5134,10 @@ 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"), @@ -5217,14 +5174,16 @@ 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)) @@ -5246,7 +5205,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Attempt to load a "dropped" file or URL string: First by testing whether - * it's and Annotation file, then a JNet file, and finally a features file. If + * it's an Annotation file, then a JNet file, and finally a features file. If * all are false then the user may have dropped an alignment file onto this * AlignFrame. * @@ -5260,15 +5219,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (protocol == null) { - protocol = jalview.io.FormatAdapter.checkProtocol(file); + protocol = FormatAdapter.checkProtocol(file); } // if the file isn't identified, or not positively identified as some // other filetype (PFAM is default unidentified alignment file type) then // 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) { @@ -5322,7 +5280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse it as a features file if (format == null) { - format = new IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); } if (format.equalsIgnoreCase("JnetFile")) { @@ -5338,42 +5296,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setColumnSelection(cs); isAnnotation = true; } - else + else if (IdentifyFile.FeaturesFile.equals(format)) { - /* - * if (format.equalsIgnoreCase("PDB")) { - * - * String pdbfn = ""; // try to match up filename with sequence id - * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = - * new File(file); pdbfn = fl.getName(); } else if (protocol == - * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = - * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == - * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport - * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { - * // attempt to find a match in the alignment SequenceI mtch = - * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while - * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > - * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch - * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and - * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() - * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) - * { System.err.println("Associated file : " + file + " with " + - * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // - * TODO: maybe need to load as normal otherwise return; } } - */ - // try to parse it as a features file - boolean isGroupsFile = parseFeaturesFile(file, protocol); - // if it wasn't a features file then we just treat it as a general - // alignment file to load into the current view. - if (!isGroupsFile) + if (parseFeaturesFile(file, protocol)) { - new FileLoader().LoadFile(viewport, file, protocol, format); + alignPanel.paintAlignment(true); } + } else { - alignPanel.paintAlignment(true); + new FileLoader().LoadFile(viewport, file, protocol, format); } - } } } if (isAnnotation) @@ -5395,7 +5328,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception x) { } - ; new OOMWarning( "loading data " + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." @@ -5582,8 +5514,14 @@ 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(); @@ -5652,16 +5590,24 @@ 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++; } @@ -5672,8 +5618,8 @@ 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 @@ -5685,20 +5631,33 @@ 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; @@ -5711,11 +5670,11 @@ 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() { @@ -5728,9 +5687,14 @@ 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(); @@ -5738,7 +5702,9 @@ 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())) @@ -5793,6 +5759,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, al); } + @Override public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(b); @@ -5902,10 +5869,12 @@ 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(); @@ -5941,7 +5910,9 @@ 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 @@ -5982,7 +5953,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, aa.visible = visible; } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); alignPanel.alignmentChanged(); } @@ -6004,8 +5975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) - : alignPanels; + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; } /** @@ -6016,14 +5986,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // TODO no longer a menu action - refactor as required final AlignmentI alignment = getViewport().getAlignment(); - Set mappings = alignment.getCodonFrames(); + List mappings = alignment.getCodonFrames(); if (mappings == null) { 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) { @@ -6051,8 +6023,7 @@ 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); } /** @@ -6065,71 +6036,32 @@ 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); } } - public class ExportData + /** + * Generate the reverse (optionally complemented) of the selected sequences, + * and add them to the alignment + */ + @Override + protected void showReverse_actionPerformed(boolean complement) { - private AlignmentI alignment; - - private String[] omitHidden; - - private int[] startEnd; - - private AlignExportSettings settings; - - public ExportData(AlignmentI align, String[] ommit, int[] startEnd, - AlignExportSettings settings) - { - this.alignment = align; - this.omitHidden = ommit; - this.startEnd = startEnd; - this.settings = settings; - } - - public AlignmentI getAlignment() - { - return alignment; - } - - public void setAlignment(AlignmentI alignment) - { - this.alignment = alignment; - } - - public String[] getOmitHidden() - { - return omitHidden; - } - - public void setOmitHidden(String[] omitHidden) - { - this.omitHidden = omitHidden; - } - - public int[] getStartEndPostions() - { - return startEnd; - } - - public void setStartEndPostions(int[] startEnd) - { - this.startEnd = startEnd; - } - - public AlignExportSettings getSettings() + AlignmentI al = null; + try { - return settings; - } + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - public void setSettings(AlignExportSettings settings) + al = dna.reverseCdna(complement); + viewport.addAlignment(al, ""); + } catch (Exception ex) { - this.settings = settings; + System.err.println(ex.getMessage()); + return; } } - } class PrintThread extends Thread