X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5438ce87ef2cd6e96ecbea76e57d3048df089059;hb=28c2ec20b26a85cc5634238f1261a14930550594;hp=9ad126f9b03b10a68824e68d8a892f214e971213;hpb=1b806c7525927fc937d51b9eab81bd96a1eaa347;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9ad126f..5438ce8 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,68 +20,24 @@ */ package jalview.gui; -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.Rectangle; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -import java.awt.event.MouseAdapter; -import java.awt.event.MouseEvent; -import java.awt.print.PageFormat; -import java.awt.print.PrinterJob; -import java.beans.PropertyChangeEvent; -import java.io.File; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -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; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - -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; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.FeatureSettingsModelI; 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; @@ -93,10 +49,12 @@ 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; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DBRefSource; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; @@ -107,7 +65,6 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; -import jalview.io.FeaturesFile; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; @@ -139,11 +96,58 @@ import jalview.schemes.ZappoColourScheme; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.ws.SequenceFetcher; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + /** * DOCUMENT ME! * @@ -240,7 +244,6 @@ 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 +288,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); init(); } @@ -305,14 +307,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (hiddenSeqs != null && hiddenSeqs.length > 0) { viewport.hideSequence(hiddenSeqs); - viewport.setHasHiddenRows(true); } alignPanel = new AlignmentPanel(this, viewport); addAlignmentPanel(alignPanel, true); init(); } - /** * Make a new AlignFrame from existing alignmentPanels * @@ -335,7 +335,10 @@ 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); @@ -368,10 +371,13 @@ 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); @@ -452,7 +458,13 @@ 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); + } } @@ -549,8 +561,9 @@ 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; @@ -573,8 +586,9 @@ 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; @@ -622,8 +636,8 @@ 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; @@ -791,7 +805,7 @@ 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); @@ -817,6 +831,8 @@ 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); @@ -834,6 +850,7 @@ 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); @@ -891,7 +908,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); rnahelicesColour .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); - setShowProductsEnabled(); + + showProducts.setEnabled(canShowProducts()); + updateEditMenuBar(); } @@ -947,7 +966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void fetchSequence_actionPerformed(ActionEvent e) { - new SequenceFetcher(this); + new jalview.gui.SequenceFetcher(this); } @Override @@ -1026,7 +1045,8 @@ 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 @@ -1067,7 +1087,8 @@ 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); @@ -1125,8 +1146,8 @@ 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 @@ -1135,14 +1156,23 @@ 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(); - FormatAdapter f = new FormatAdapter(viewport); - 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(), @@ -1165,8 +1195,7 @@ 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; @@ -1178,8 +1207,8 @@ 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); } @@ -1187,7 +1216,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return success; } - private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) @@ -1213,20 +1241,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void outputText_actionPerformed(ActionEvent e) { - ExportData exportData = getAlignmentForExport(); + AlignmentExportData exportData = getAlignmentForExport( + e.getActionCommand(), viewport, null); + if (exportData.getSettings().isCancelled()) + { + return; + } CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - try { - cap.setText(new FormatAdapter(viewport).formatSequences( - e.getActionCommand(), - exportData.getAlignment(), - exportData.getOmitHidden(), exportData.getStartEndPostions(), - viewport.getColumnSelection())); + cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) + .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); @@ -1235,73 +1268,65 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } - public ExportData getAlignmentForExport() + public static AlignmentExportData getAlignmentForExport( + String exportFormat, AlignViewportI viewport, + AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; + AlignExportSettingI settings = exportSettings; String[] omitHidden = null; int[] alignmentStartEnd = new int[2]; - FeatureRenderer fr = new FeatureRenderer(this.alignPanel); - viewport.setFeatureRenderer(fr); + HiddenSequences hiddenSeqs = viewport.getAlignment() .getHiddenSequences(); - alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = new int[] - { 0, alignmentToExport.getWidth() - 1 }; + alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 }; - if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0) + boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; + if (settings == null) { - int reply = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager - .getString("label.alignment_contains_hidden_columns"), - MessageManager - .getString("action.save_omit_hidden_columns"), - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFormat); + } + // settings.isExportAnnotations(); - if (reply == JOptionPane.YES_OPTION) - { - // export only visible region - omitHidden = viewport.getViewAsString(false); - alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport - .getColumnSelection().getHiddenColumns()); - viewport.setIncludeHiddenRegion(false); - } - else - { - // export all region including visible - alignmentToExport = hiddenSeqs.getFullAlignment(); - viewport.setIncludeHiddenRegion(true); - } + if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + { + omitHidden = viewport.getViewAsString(false); } - return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd); + if (hasHiddenSeqs && settings.isExportHiddenSequences()) + { + alignmentToExport = hiddenSeqs.getFullAlignment(); + } + else + { + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport + .getColumnSelection().getHiddenColumns()); + } + 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]; } @@ -1310,36 +1335,29 @@ 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]); } @@ -1352,19 +1370,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - // new HTMLOutput(alignPanel, - // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(), - // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); new HtmlSvgOutput(null, alignPanel); } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { - BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, - alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this); bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1394,10 +1409,12 @@ 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) { @@ -1493,6 +1510,10 @@ 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) @@ -1537,8 +1558,8 @@ 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 { @@ -1552,8 +1573,8 @@ 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 { @@ -1562,6 +1583,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1595,8 +1617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport != null) { - return new AlignmentI[] - { viewport.getAlignment() }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } @@ -1823,10 +1844,14 @@ 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 @@ -1897,17 +1922,17 @@ 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() })); } /** @@ -1962,7 +1987,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - format = new IdentifyFile().Identify(str, "Paste"); + format = new IdentifyFile().identify(str, "Paste"); } catch (OutOfMemoryError er) { @@ -2116,8 +2141,7 @@ 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++) @@ -2235,7 +2259,8 @@ 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. @@ -2294,7 +2319,8 @@ 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. @@ -2356,20 +2382,24 @@ 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()]); @@ -2524,7 +2554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2549,23 +2579,20 @@ 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); @@ -2614,8 +2641,9 @@ 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 @@ -2740,12 +2768,17 @@ 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); @@ -2860,8 +2893,8 @@ 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); } @@ -2940,13 +2973,14 @@ 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); } /** @@ -3030,6 +3064,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); + viewport.sendSelection(); } /* @@ -3047,6 +3082,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /* @@ -3062,6 +3098,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3069,6 +3106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3159,6 +3197,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureSettings featureSettings; @Override + public FeatureSettingsControllerI getFeatureSettingsUI() + { + return featureSettings; + } + + @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) @@ -3245,14 +3289,13 @@ 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); } /** @@ -3273,8 +3316,8 @@ 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() @@ -3465,117 +3508,35 @@ 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); } @@ -4082,7 +4043,8 @@ 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() { @@ -4201,8 +4163,7 @@ 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()); @@ -4351,8 +4312,7 @@ 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! @@ -4510,8 +4470,8 @@ 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 @@ -4698,67 +4658,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - /* - * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser - * chooser = new JalviewFileChooser(jalview.bin.Cache. - * getProperty("LAST_DIRECTORY")); - * - * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export - * to Vamsas file"); chooser.setToolTipText("Export"); - * - * int value = chooser.showSaveDialog(this); - * - * if (value == JalviewFileChooser.APPROVE_OPTION) { - * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( - * chooser.getSelectedFile().getAbsolutePath(), this); } } - */ /** - * prototype of an automatically enabled/disabled analysis function + * Searches selected sequences for xRef products and builds the Show + * Cross-References menu (formerly called Show Products) * + * @return true if Show Cross-references menu should be enabled. */ - protected void setShowProductsEnabled() + public boolean canShowProducts() { SequenceI[] selection = viewport.getSequenceSelection(); - if (canShowProducts(selection, viewport.getSelectionGroup() != null, - viewport.getAlignment().getDataset())) - { - showProducts.setEnabled(true); - - } - else - { - showProducts.setEnabled(false); - } - } - - /** - * search selection for sequence xRef products and build the show products - * menu. - * - * @param selection - * @param dataset - * @return true if showProducts menu should be enabled. - */ - public boolean canShowProducts(SequenceI[] selection, - boolean isRegionSelection, Alignment dataset) - { + AlignmentI dataset = viewport.getAlignment().getDataset(); boolean showp = false; try { showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); - final Alignment ds = dataset; String[] ptypes = (selection == null || selection.length == 0) ? null : CrossRef.findSequenceXrefTypes(dna, selection, dataset); - // Object[] prods = - // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), - // selection, dataset, true); - final SequenceI[] sel = selection; + for (int t = 0; ptypes != null && t < ptypes.length; t++) { showp = true; - final boolean isRegSel = isRegionSelection; final AlignFrame af = this; final String source = ptypes[t]; JMenuItem xtype = new JMenuItem(ptypes[t]); @@ -4768,9 +4688,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void actionPerformed(ActionEvent e) { - // TODO: new thread for this call with vis-delay - af.showProductsFor(af.viewport.getSequenceSelection(), - isRegSel, dna, source); + showProductsFor(af.viewport.getSequenceSelection(), dna, source); } }); @@ -4781,15 +4699,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception e) { jalview.bin.Cache.log - .warn("canTranslate threw an exception - please report to help@jalview.org", + .warn("canShowProducts threw an exception - please report to help@jalview.org", e); return false; } return showp; } - protected void showProductsFor(final SequenceI[] sel, - final boolean isRegSel, final boolean dna, final String source) + protected void showProductsFor(final SequenceI[] sel, final boolean dna, + final String source) { Runnable foo = new Runnable() { @@ -4799,51 +4717,48 @@ 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 - Alignment ds = AlignFrame.this.getViewport().getAlignment() - .getDataset(); - Alignment prods = CrossRef - .findXrefSequences(sel, dna, source, ds); - if (prods != null) + /* + * 'peer' sequences are any to add to this alignment, for example + * alternative protein products for my protein's gene + */ + List addedPeers = new ArrayList(); + AlignmentI alignment = AlignFrame.this.getViewport() + .getAlignment(); + Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source, + alignment, addedPeers); + if (xrefs != null) { - SequenceI[] sprods = new SequenceI[prods.getHeight()]; - for (int s = 0; s < sprods.length; s++) + /* + * figure out colour scheme if any to apply to features + */ + ASequenceFetcher sftch = new SequenceFetcher(); + List proxies = sftch.getSourceProxy(source); + FeatureSettingsModelI featureColourScheme = null; + for (DbSourceProxy proxy : proxies) { - sprods[s] = (prods.getSequenceAt(s)).deriveSequence(); - if (ds.getSequences() == null - || !ds.getSequences().contains( - sprods[s].getDatasetSequence())) + FeatureSettingsModelI preferredColours = proxy + .getFeatureColourScheme(); + if (preferredColours != null) { - ds.addSequence(sprods[s].getDatasetSequence()); + featureColourScheme = preferredColours; + break; } - sprods[s].updatePDBIds(); } - Alignment al = new Alignment(sprods); - al.setDataset(ds); + Alignment al = makeCrossReferencesAlignment( + alignment.getDataset(), xrefs); - /* - * Copy dna-to-protein mappings to new alignment - */ - // 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(); - 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 " : "") - + getTitle(); - naf.setTitle(newtitle); + String newtitle = String.format("%s %s %s", + MessageManager.getString(dna ? "label.proteins" + : "label.nucleotides"), MessageManager + .getString("label.for"), getTitle()); + newFrame.setTitle(newtitle); - // temporary flag until SplitFrame is released boolean asSplitFrame = Cache.getDefault( Preferences.ENABLE_SPLIT_FRAME, true); if (asSplitFrame) @@ -4855,36 +4770,106 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentI copyAlignment = null; final SequenceI[] sequenceSelection = AlignFrame.this.viewport .getSequenceSelection(); + List cf = xrefs.getCodonFrames(); if (dna) { - copyAlignment = AlignmentUtils.makeExonAlignment( - sequenceSelection, cf); + copyAlignment = AlignmentUtils.makeCdsAlignment( + sequenceSelection, cf, alignment); + if (copyAlignment.getHeight() == 0) + { + System.err.println("Failed to make CDS alignment"); + } al.getCodonFrames().clear(); al.getCodonFrames().addAll(cf); - final StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - ssm.addMappings(cf); } else { copyAlignment = new Alignment(new Alignment( sequenceSelection)); + copyAlignment.getCodonFrames().addAll(cf); + } + copyAlignment.setGapCharacter(AlignFrame.this.viewport + .getGapCharacter()); + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(cf); + + /* + * add in any extra 'peer' sequences discovered + * (e.g. alternative protein products) + */ + for (SequenceI peer : addedPeers) + { + copyAlignment.addSequence(peer); + } + + if (copyAlignment.getHeight() > 0) + { + /* + * align protein to dna + */ + // FIXME what if the dna is not aligned :-O + if (dna) + { + al.alignAs(copyAlignment); + } + else + { + /* + * align cdna to protein - currently only if + * fetching and aligning Ensembl transcripts! + */ + if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)) + { + copyAlignment.alignAs(al); + } + } + + AlignFrame copyThis = new AlignFrame(copyAlignment, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyThis.setTitle(AlignFrame.this.getTitle()); + + boolean showSequenceFeatures = viewport + .isShowSequenceFeatures(); + newFrame.setShowSeqFeatures(showSequenceFeatures); + copyThis.setShowSeqFeatures(showSequenceFeatures); + FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); + + /* + * copy feature rendering settings to split frame + */ + newFrame.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer().transferSettings( + myFeatureStyling); + copyThis.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer().transferSettings( + myFeatureStyling); + + /* + * apply 'database source' feature configuration + * if any was found + */ + // TODO is this the feature colouring for the original + // alignment or the fetched xrefs? either could be Ensembl + newFrame.getViewport().applyFeaturesStyle( + featureColourScheme); + copyThis.getViewport().applyFeaturesStyle( + featureColourScheme); + + SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame, + dna ? newFrame : copyThis); + newFrame.setVisible(true); + copyThis.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + Desktop.addInternalFrame(sf, linkedTitle, -1, -1); + sf.adjustDivider(); } - AlignFrame copyThis = new AlignFrame(copyAlignment, - 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); - copyThis.setVisible(true); - String linkedTitle = MessageManager - .getString("label.linked_view_title"); - Desktop.addInternalFrame(sf, linkedTitle, -1, -1); } else { - Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, + Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } } @@ -4907,9 +4892,36 @@ 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); + } + + /** + * Makes an alignment containing the given sequences; the sequences are + * added to the given alignment dataset, and the dataset is set on (shared + * by) the new alignment + * + * @param dataset + * @param seqs + * @return + */ + protected Alignment makeCrossReferencesAlignment(Alignment dataset, + Alignment seqs) + { + SequenceI[] sprods = new SequenceI[seqs.getHeight()]; + for (int s = 0; s < sprods.length; s++) + { + sprods[s] = (seqs.getSequenceAt(s)).deriveSequence(); + if (dataset.getSequences() == null + || !dataset.getSequences().contains( + sprods[s].getDatasetSequence())) + { + dataset.addSequence(sprods[s].getDatasetSequence()); + } + sprods[s].updatePDBIds(); + } + Alignment al = new Alignment(sprods); + al.setDataset(dataset); + return al; } }; @@ -4953,10 +4965,10 @@ 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; } @@ -4964,9 +4976,9 @@ 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 @@ -4974,14 +4986,13 @@ 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 { @@ -5008,39 +5019,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * contents or path to retrieve file * @param type * access mode of file (see jalview.io.AlignFile) - * @return true if features file was parsed corectly. + * @return true if features file was parsed correctly. */ public boolean parseFeaturesFile(String file, String type) { - boolean featuresFile = false; - try - { - featuresFile = new FeaturesFile(file, type).parse(viewport - .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer().getFeatureColours(), false, - jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); - } catch (Exception ex) - { - ex.printStackTrace(); - } + return avc.parseFeaturesFile(file, type, + jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); - if (featuresFile) + } + + @Override + public void refreshFeatureUI(boolean enableIfNecessary) + { + // note - currently this is only still here rather than in the controller + // because of the featureSettings hard reference that is yet to be + // abstracted + if (enableIfNecessary) { viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); - if (alignPanel.getSeqPanel().seqCanvas.fr != null) - { - // update the min/max ranges where necessary - alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true); - } - if (featureSettings != null) - { - featureSettings.setTableData(); - } - alignPanel.paintAlignment(true); } - return featuresFile; } @Override @@ -5164,7 +5163,7 @@ 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; @@ -5173,8 +5172,7 @@ 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; } } @@ -5193,10 +5191,10 @@ 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"), @@ -5233,14 +5231,16 @@ 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)) @@ -5262,7 +5262,7 @@ 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. * @@ -5276,15 +5276,14 @@ 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) { @@ -5338,7 +5337,7 @@ 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")) { @@ -5354,42 +5353,17 @@ 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) - { - new FileLoader().LoadFile(viewport, file, protocol, format); - } - else + if (parseFeaturesFile(file, protocol)) { alignPanel.paintAlignment(true); } } + else + { + new FileLoader().LoadFile(viewport, file, protocol, format); + } } } if (isAnnotation) @@ -5411,7 +5385,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception x) { } - ; new OOMWarning( "loading data " + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." @@ -5598,8 +5571,11 @@ 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(); @@ -5614,7 +5590,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - final jalview.ws.SequenceFetcher sf = SequenceFetcher + final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher .getSequenceFetcherSingleton(me); javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -5668,16 +5644,23 @@ 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) - .fetchDBRefs(false); + 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++; } @@ -5688,8 +5671,8 @@ 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 @@ -5701,20 +5684,32 @@ 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) - .fetchDBRefs(false); + 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; @@ -5727,11 +5722,11 @@ 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() { @@ -5744,17 +5739,23 @@ 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) - .fetchDBRefs(false); + alignPanel.alignFrame, dassrc, + alignPanel.alignFrame.featureSettings, + isNuclueotide).fetchDBRefs(false); } }).start(); } }); 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())) @@ -5809,6 +5810,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, al); } + @Override public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(b); @@ -5918,10 +5920,12 @@ 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(); @@ -5957,7 +5961,9 @@ 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 @@ -5998,7 +6004,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, aa.visible = visible; } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); alignPanel.alignmentChanged(); } @@ -6020,8 +6026,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) - : alignPanels; + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; } /** @@ -6032,14 +6037,16 @@ 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) { @@ -6067,8 +6074,7 @@ 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); } /** @@ -6081,57 +6087,32 @@ 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; - - public ExportData(AlignmentI align, String[] ommit, int[] startEnd) - { - this.alignment = align; - this.omitHidden = ommit; - this.startEnd = startEnd; - } - - 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() + AlignmentI al = null; + try { - return startEnd; - } + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - public void setStartEndPostions(int[] startEnd) + al = dna.reverseCdna(complement); + viewport.addAlignment(al, ""); + } catch (Exception ex) { - this.startEnd = startEnd; + System.err.println(ex.getMessage()); + return; } } - } class PrintThread extends Thread