X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b484118337b696f7f0093b0c6dfd4eaa7f210954;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=42460dc6b50fbe277cea2936f1ac74ad87757e8c;hpb=afcdc36e5f65333f8ff9ca3229b6cffdb27edca7;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 42460dc..b484118 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,18 +20,23 @@ */ 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.NJTree; +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.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; @@ -43,18 +48,21 @@ 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.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; -import jalview.io.FeaturesFile; +import jalview.io.BioJsHTMLOutput; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; @@ -83,7 +91,9 @@ import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; +import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -91,7 +101,6 @@ import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; import java.awt.Component; -import java.awt.GridLayout; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; @@ -105,6 +114,8 @@ 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; @@ -115,22 +126,21 @@ 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.JButton; import javax.swing.JCheckBoxMenuItem; import javax.swing.JEditorPane; import javax.swing.JInternalFrame; -import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.JProgressBar; import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -145,19 +155,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI { - /** DOCUMENT ME!! */ public static final int DEFAULT_WIDTH = 700; - /** DOCUMENT ME!! */ public static final int DEFAULT_HEIGHT = 500; + /* + * The currently displayed panel (selected tabbed view if more than one) + */ public AlignmentPanel alignPanel; AlignViewport viewport; public AlignViewControllerI avc; - Vector alignPanels = new Vector(); + List alignPanels = new ArrayList(); /** * Last format used to load or save alignments in this window @@ -274,7 +285,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel = new AlignmentPanel(this, viewport); + addAlignmentPanel(alignPanel, true); + init(); + } + + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection hiddenColumns, int width, int height) + { + setSize(width, height); + if (al.getDataset() == null) + { + al.setDataset(null); + } + + viewport = new AlignViewport(al, hiddenColumns); + + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + } + alignPanel = new AlignmentPanel(this, viewport); addAlignmentPanel(alignPanel, true); init(); } @@ -301,6 +332,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -335,8 +371,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); - - if (viewport.wrapAlignment) + + if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); } @@ -348,6 +384,82 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addKeyListener(); + final List selviews = new ArrayList(); + final List origview = new ArrayList(); + final String menuLabel = MessageManager + .getString("label.copy_format_from"); + ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, + new ViewSetProvider() + { + + @Override + public AlignmentPanel[] getAllAlignmentPanels() + { + origview.clear(); + origview.add(alignPanel); + // make an array of all alignment panels except for this one + List aps = new ArrayList( + Arrays.asList(Desktop.getAlignmentPanels(null))); + aps.remove(AlignFrame.this.alignPanel); + return aps.toArray(new AlignmentPanel[aps.size()]); + } + }, selviews, new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + if (origview.size() > 0) + { + final AlignmentPanel ap = origview.get(0); + + /* + * Copy the ViewStyle of the selected panel to 'this one'. + * Don't change value of 'scaleProteinAsCdna' unless copying + * from a SplitFrame. + */ + ViewStyleI vs = selviews.get(0).getAlignViewport() + .getViewStyle(); + boolean fromSplitFrame = selviews.get(0) + .getAlignViewport().getCodingComplement() != null; + if (!fromSplitFrame) + { + vs.setScaleProteinAsCdna(ap.getAlignViewport() + .getViewStyle().isScaleProteinAsCdna()); + } + ap.getAlignViewport().setViewStyle(vs); + + /* + * Also rescale ViewStyle of SplitFrame complement if there is + * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy + * the whole ViewStyle (allow cDNA protein to have different + * fonts) + */ + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + if (complement != null && vs.isScaleProteinAsCdna()) + { + AlignFrame af = Desktop.getAlignFrameFor(complement); + ((SplitFrame) af.getSplitViewContainer()) + .adjustLayout(); + af.setMenusForViewport(); + } + + ap.updateLayout(); + ap.setSelected(true); + ap.alignFrame.setMenusForViewport(); + + } + } + }); + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("devel") > -1 + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("test") > -1) + { + formatMenu.add(vsel); + } + } /** @@ -362,10 +474,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void setFileName(String file, String format) { fileName = file; - currentFileFormat = format; + setFileFormat(format); reload.setEnabled(true); } + /** + * Add a KeyListener with handlers for various KeyPressed and KeyReleased + * events + */ void addKeyListener() { addKeyListener(new KeyAdapter() @@ -439,8 +555,9 @@ 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; @@ -463,8 +580,9 @@ 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; @@ -512,8 +630,8 @@ 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; @@ -539,7 +657,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(true); } @@ -550,7 +668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(false); } @@ -594,7 +712,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); - alignPanels.addElement(ap); + alignPanels.add(ap); PaintRefresher.Register(ap, ap.av.getSequenceSetId()); @@ -637,7 +755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.setVisible(true); - AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); + AlignmentPanel first = alignPanels.get(0); tabbedPane.addTab(first.av.viewName, first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } @@ -681,7 +799,7 @@ 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); @@ -698,6 +816,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }).start(); } + /** + * Configure menu items that vary according to whether the alignment is + * nucleotide or protein + * + * @param nucleotide + */ public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); @@ -706,16 +830,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); - // Remember AlignFrame always starts as protein - // if (!nucleotide) - // { - // showTr - // calculateMenu.remove(calculateMenu.getItemCount() - 2); - // } + showComplementMenuItem.setText(MessageManager + .getString(nucleotide ? "label.protein" : "label.nucleotide")); + setColourSelected(jalview.bin.Cache.getDefault( + nucleotide ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT, "None")); } /** - * set up menus for the currently viewport. This may be called after any + * set up menus for the current viewport. This may be called after any * operation that affects the data in the current view (selection changed, * etc) to update the menus to reflect the new state. */ @@ -734,17 +857,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); - colourTextMenuItem.setSelected(av.showColourText); + colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); - centreColumnLabelsMenuItem.setState(av.centreColumnLabels); - renderGapsMenuItem.setSelected(av.renderGaps); - wrapMenuItem.setSelected(av.wrapAlignment); - scaleAbove.setVisible(av.wrapAlignment); - scaleLeft.setVisible(av.wrapAlignment); - scaleRight.setVisible(av.wrapAlignment); + centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); + renderGapsMenuItem.setSelected(av.isRenderGaps()); + wrapMenuItem.setSelected(av.getWrapAlignment()); + scaleAbove.setVisible(av.getWrapAlignment()); + scaleLeft.setVisible(av.getWrapAlignment()); + scaleRight.setVisible(av.getWrapAlignment()); annotationPanelMenuItem.setState(av.isShowAnnotation()); /* * Show/hide annotations only enabled if annotation panel is shown @@ -753,8 +876,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); - viewBoxesMenuItem.setSelected(av.showBoxes); - viewTextMenuItem.setSelected(av.showText); + viewBoxesMenuItem.setSelected(av.getShowBoxes()); + viewTextMenuItem.setSelected(av.getShowText()); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); showGroupConsensus.setSelected(av.isShowGroupConsensus()); showGroupConservation.setSelected(av.isShowGroupConservation()); @@ -765,11 +888,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); - showSeqFeatures.setSelected(av.showSequenceFeatures); - hiddenMarkers.setState(av.showHiddenMarkers); + showSeqFeatures.setSelected(av.isShowSequenceFeatures()); + hiddenMarkers.setState(av.getShowHiddenMarkers()); applyToAllGroups.setState(av.getColourAppliesToAllGroups()); - showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); - showDbRefsMenuitem.setSelected(av.isShowDbRefs()); + showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); + showDbRefsMenuitem.setSelected(av.isShowDBRefs()); autoCalculate.setSelected(av.autoCalculateConsensus); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); @@ -780,9 +903,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, updateEditMenuBar(); } - // methods for implementing IProgressIndicator - // need to refactor to a reusable stub class - Hashtable progressBars, progressBarHandlers; + private IProgressIndicator progressBar; /* * (non-Javadoc) @@ -792,78 +913,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void setProgressBar(String message, long id) { - if (progressBars == null) - { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); - } - - JPanel progressPanel; - Long lId = new Long(id); - GridLayout layout = (GridLayout) statusPanel.getLayout(); - if (progressBars.get(lId) != null) - { - progressPanel = (JPanel) progressBars.get(new Long(id)); - statusPanel.remove(progressPanel); - progressBars.remove(lId); - progressPanel = null; - if (message != null) - { - statusBar.setText(message); - } - if (progressBarHandlers.contains(lId)) - { - progressBarHandlers.remove(lId); - } - layout.setRows(layout.getRows() - 1); - } - else - { - progressPanel = new JPanel(new BorderLayout(10, 5)); - - JProgressBar progressBar = new JProgressBar(); - progressBar.setIndeterminate(true); - - progressPanel.add(new JLabel(message), BorderLayout.WEST); - progressPanel.add(progressBar, BorderLayout.CENTER); - - layout.setRows(layout.getRows() + 1); - statusPanel.add(progressPanel); - - progressBars.put(lId, progressPanel); - } - // update GUI - // setMenusForViewport(); - validate(); + progressBar.setProgressBar(message, id); } @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - if (progressBarHandlers == null || !progressBars.contains(new Long(id))) - { - throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); - } - progressBarHandlers.put(new Long(id), handler); - final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); - if (handler.canCancel()) - { - JButton cancel = new JButton( - MessageManager.getString("action.cancel")); - final IProgressIndicator us = this; - cancel.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); - } - }); - progressPanel.add(cancel, BorderLayout.EAST); - } + progressBar.registerHandler(id, handler); } /** @@ -873,18 +930,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public boolean operationInProgress() { - if (progressBars != null && progressBars.size() > 0) - { - return true; - } - return false; + return progressBar.operationInProgress(); } @Override public void setStatus(String text) { statusBar.setText(text); - }; + } /* * Added so Castor Mapping file can obtain Jalview Version @@ -981,7 +1034,8 @@ 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 @@ -1022,7 +1076,8 @@ 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); @@ -1030,7 +1085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (value == JalviewFileChooser.APPROVE_OPTION) { currentFileFormat = chooser.getSelectedFormat(); - if (currentFileFormat == null) + while (currentFileFormat == null) { JOptionPane .showInternalMessageDialog( @@ -1040,8 +1095,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager .getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE); + currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); - return; + if (value != JalviewFileChooser.APPROVE_OPTION) + { + return; + } } fileName = chooser.getSelectedFile().getPath(); @@ -1073,11 +1132,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().SaveAlignment(this, file, shortName); + success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new String[] - { fileName, format })); + "label.successfully_saved_to_file_in_format", new Object[] { + fileName, format })); } else @@ -1086,35 +1145,27 @@ 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; } - String[] omitHidden = null; - - if (viewport.hasHiddenColumns()) + AlignmentExportData exportData = getAlignmentForExport(format, + viewport, null); + if (exportData.getSettings().isCancelled()) { - 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); - - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } + return false; } - FormatAdapter f = new FormatAdapter(); - String output = f.formatSequences(format, - viewport.getAlignment(), // class cast exceptions will + FormatAdapter f = new FormatAdapter(alignPanel, + exportData.getSettings()); + String output = f.formatSequences( + format, + exportData.getAlignment(), // class cast exceptions will // occur in the distant future - omitHidden, f.getCacheSuffixDefault(format), + exportData.getOmitHidden(), exportData.getStartEndPostions(), + f.getCacheSuffixDefault(format), viewport.getColumnSelection()); if (output == null) @@ -1133,8 +1184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new String[] - { fileName, format })); + new Object[] { fileName, format })); } catch (Exception ex) { success = false; @@ -1146,8 +1196,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { JOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new String[] - { fileName }), MessageManager + .formatMessage("label.couldnt_save_file", + new Object[] { fileName }), MessageManager .getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE); } @@ -1179,37 +1229,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - String[] omitHidden = null; - if (viewport.hasHiddenColumns()) + AlignmentExportData exportData = getAlignmentForExport( + e.getActionCommand(), viewport, null); + if (exportData.getSettings().isCancelled()) { - 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); - - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } + return; } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - try { - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment(), omitHidden, - 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 String[] - { 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); @@ -1218,6 +1257,102 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } + 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 }; + + boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; + if (settings == null) + { + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFormat); + } + // settings.isExportAnnotations(); + + if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + { + omitHidden = viewport.getViewAsString(false); + } + + 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; + } + + 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]; + + 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) + { + startPos = aligmentStartEnd[0]; + } + else + { + startPos = lowestRange[1] + 1; + } + + if (higestRange[0] == 0 && higestRange[1] == 0) + { + endPos = aligmentStartEnd[1]; + } + else + { + endPos = higestRange[0]; + } + + // System.out.println("Export range : " + minPos + " - " + maxPos); + 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); + // System.out.println("Export range : " + x[0] + " - " + x[1]); + } + /** * DOCUMENT ME! * @@ -1227,12 +1362,16 @@ 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); + bjs.exportJalviewAlignmentAsBioJsHtmlFile(); + } + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1266,6 +1405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { alignPanel.makeSVG(f); } + @Override public void pageSetup_actionPerformed(ActionEvent e) { @@ -1296,11 +1436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel, - viewport.isShowAnnotation() ? viewport.getAlignment() - .getAlignmentAnnotation() : null, viewport - .getAlignment().getGroups(), ((Alignment) viewport - .getAlignment()).alignmentProperties); + new AnnotationExporter().exportAnnotations(alignPanel); } @Override @@ -1352,7 +1488,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // setClosed(true) is called for (int i = 0; i < alignPanels.size(); i++) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); + AlignmentPanel ap = alignPanels.get(i); ap.closePanel(); } } @@ -1365,6 +1501,10 @@ 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) @@ -1374,22 +1514,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * close alignPanel2 and shuffle tabs appropriately. + * Close the specified panel and close up tabs appropriately. * - * @param alignPanel2 + * @param panelToClose */ - public void closeView(AlignmentPanel alignPanel2) + public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); - int closedindex = tabbedPane.indexOfComponent(alignPanel2); - alignPanels.removeElement(alignPanel2); - // Unnecessary - // if (viewport == alignPanel2.av) - // { - // viewport = null; - // } - alignPanel2.closePanel(); - alignPanel2 = null; + int closedindex = tabbedPane.indexOfComponent(panelToClose); + alignPanels.remove(panelToClose); + panelToClose.closePanel(); + panelToClose = null; tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); @@ -1409,13 +1544,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, void updateEditMenuBar() { - if (viewport.historyList.size() > 0) + if (viewport.getHistoryList().size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = viewport.historyList.peek(); + CommandI command = viewport.getHistoryList().peek(); undoMenuItem.setText(MessageManager.formatMessage( - "label.undo_command", new String[] - { command.getDescription() })); + "label.undo_command", + new Object[] { command.getDescription() })); } else { @@ -1423,14 +1558,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, undoMenuItem.setText(MessageManager.getString("action.undo")); } - if (viewport.redoList.size() > 0) + if (viewport.getRedoList().size() > 0) { redoMenuItem.setEnabled(true); - CommandI command = viewport.redoList.peek(); + CommandI command = viewport.getRedoList().peek(); redoMenuItem.setText(MessageManager.formatMessage( - "label.redo_command", new String[] - { command.getDescription() })); + "label.redo_command", + new Object[] { command.getDescription() })); } else { @@ -1443,8 +1578,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (command.getSize() > 0) { - viewport.historyList.push(command); - viewport.redoList.clear(); + viewport.addToHistoryList(command); + viewport.clearRedoList(); updateEditMenuBar(); viewport.updateHiddenColumns(); // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null @@ -1462,18 +1597,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (alignPanels != null) { - Enumeration e = alignPanels.elements(); AlignmentI[] als = new AlignmentI[alignPanels.size()]; - for (int i = 0; e.hasMoreElements(); i++) + int i = 0; + for (AlignmentPanel ap : alignPanels) { - als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); + als[i++] = ap.av.getAlignment(); } return als; } if (viewport != null) { - return new AlignmentI[] - { viewport.getAlignment() }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } @@ -1487,15 +1621,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { - if (viewport.historyList.empty()) + if (viewport.getHistoryList().isEmpty()) { return; } - CommandI command = viewport.historyList.pop(); - viewport.redoList.push(command); + CommandI command = viewport.getHistoryList().pop(); + viewport.addToRedoList(command); command.undoCommand(getViewAlignments()); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) @@ -1525,16 +1659,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { - if (viewport.redoList.size() < 1) + if (viewport.getRedoList().size() < 1) { return; } - CommandI command = viewport.redoList.pop(); - viewport.historyList.push(command); + CommandI command = viewport.getRedoList().pop(); + viewport.addToHistoryList(command); command.doCommand(getViewAlignments()); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) @@ -1556,9 +1690,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - AlignViewport getOriginatingSource(CommandI command) + AlignmentViewport getOriginatingSource(CommandI command) { - AlignViewport originalSource = null; + AlignmentViewport originalSource = null; // For sequence removal and addition, we need to fire // the property change event FROM the viewport where the // original alignment was altered @@ -1567,16 +1701,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components.get(viewport + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - for (int i = 0; i < comps.size(); i++) + for (Component comp : comps) { - if (comps.elementAt(i) instanceof AlignmentPanel) + if (comp instanceof AlignmentPanel) { - if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) + if (al == ((AlignmentPanel) comp).av.getAlignment()) { - originalSource = ((AlignmentPanel) comps.elementAt(i)).av; + originalSource = ((AlignmentPanel) comp).av; break; } } @@ -1619,7 +1753,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, synchronized void slideSequences(boolean right, int size) { - List sg = new Vector(); + List sg = new ArrayList(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( @@ -1638,13 +1772,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector invertGroup = new Vector(); + List invertGroup = new ArrayList(); - for (int i = 0; i < viewport.getAlignment().getHeight(); i++) + for (SequenceI seq : viewport.getAlignment().getSequences()) { - if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + if (!sg.contains(seq)) { - invertGroup.add(viewport.getAlignment().getSequenceAt(i)); + invertGroup.add(seq); } } @@ -1653,7 +1787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) { - seqs2[i] = (SequenceI) invertGroup.elementAt(i); + seqs2[i] = invertGroup.get(i); } SlideSequencesCommand ssc; @@ -1700,12 +1834,18 @@ 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; - if (viewport.historyList != null && viewport.historyList.size() > 0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) + Deque historyList = viewport.getHistoryList(); + boolean inSplitFrame = getSplitViewContainer() != null; + if (!inSplitFrame && historyList != null && historyList.size() > 0 + && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .appendSlideCommand((SlideSequencesCommand) historyList .peek()); } @@ -1742,7 +1882,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + omitHidden, null); StringSelection ss = new StringSelection(output); @@ -1762,30 +1902,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector hiddenColumns = null; + ArrayList hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new Vector(); + hiddenColumns = new ArrayList(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { - hiddenColumns.addElement(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 String[] - { Integer.valueOf(seqs.length).toString() })); + "label.copied_sequences_to_clipboard", new Object[] { Integer + .valueOf(seqs.length).toString() })); } /** @@ -1994,8 +2131,7 @@ 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++) @@ -2082,7 +2218,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignment.getSequences()); if (alignPanels != null) { - for (AlignmentPanel ap : ((Vector) alignPanels)) + for (AlignmentPanel ap : alignPanels) { ap.validateAnnotationDimensions(false); } @@ -2102,10 +2238,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int[] region : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } @@ -2114,7 +2249,8 @@ 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. @@ -2162,10 +2298,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int region[] : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } @@ -2174,7 +2309,8 @@ 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. @@ -2231,15 +2367,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - List seqs = new ArrayList(sg.getSize()); - SequenceI seq; - for (int i = 0; i < sg.getSize(); i++) - { - seq = sg.getSequenceAt(i); - seqs.add(seq); - } - - // If the cut affects all sequences, warn, remove highlighted columns + /* + * If the cut affects all sequences, warn, remove highlighted columns + */ if (sg.getSize() == viewport.getAlignment().getHeight()) { int confirm = JOptionPane.showConfirmDialog(this, @@ -2256,15 +2386,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.getEndRes() + 1); } - SequenceI[] cut = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - cut[i] = seqs.get(i); - } + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); - /* - * //ADD HISTORY ITEM - */ addHistoryItem(new EditCommand( MessageManager.getString("label.cut_sequences"), Action.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, @@ -2456,8 +2580,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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); @@ -2506,8 +2631,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", new String[] - { 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 @@ -2577,16 +2703,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSequences()); } - // else - { - // if (justifySeqs>0) - { - // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); - } - } - - // } - /** * DOCUMENT ME! * @@ -2599,74 +2715,85 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new Finder(); } - @Override - public void newView_actionPerformed(ActionEvent e) - { - newView(true); - } - - /** - * - * @param copyAnnotation - * if true then duplicate all annnotation, groups and settings - * @return new alignment panel, already displayed. - */ - public AlignmentPanel newView(boolean copyAnnotation) - { - return newView(null, copyAnnotation); - } - /** - * - * @param viewTitle - * title of newly created view - * @return new alignment panel, already displayed. + * Create a new view of the current alignment. */ - public AlignmentPanel newView(String viewTitle) + @Override + public void newView_actionPerformed(ActionEvent e) { - return newView(viewTitle, true); + newView(null, true); } /** + * Creates and shows a new view of the current alignment. * * @param viewTitle - * title of newly created view + * title of newly created view; if null, one will be generated * @param copyAnnotation * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. */ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) { + /* + * Create a new AlignmentPanel (with its own, new Viewport) + */ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, true); if (!copyAnnotation) { - // just remove all the current annotation except for the automatic stuff + /* + * remove all groups and annotation except for the automatic stuff + */ newap.av.getAlignment().deleteAllGroups(); - for (AlignmentAnnotation alan : newap.av.getAlignment() - .getAlignmentAnnotation()) - { - if (!alan.autoCalculated) - { - newap.av.getAlignment().deleteAnnotation(alan); - } - ; - } + newap.av.getAlignment().deleteAllAnnotations(false); } - newap.av.gatherViewsHere = false; + newap.av.setGatherViewsHere(false); if (viewport.viewName == null) { - viewport.viewName = "Original"; + viewport.viewName = MessageManager + .getString("label.view_name_original"); } - newap.av.historyList = viewport.historyList; - newap.av.redoList = viewport.redoList; + /* + * Views share the same edits undo and redo stacks + */ + newap.av.setHistoryList(viewport.getHistoryList()); + newap.av.setRedoList(viewport.getRedoList()); + + /* + * 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); + + addAlignmentPanel(newap, true); + newap.alignmentChanged(); + + if (alignPanels.size() == 2) + { + viewport.setGatherViewsHere(true); + } + tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; + } + /** + * Make a new name for the view, ensuring it is unique within the current + * sequenceSetId. (This used to be essential for Jalview Project archives, but + * these now use viewId. Unique view names are still desirable for usability.) + * + * @param viewTitle + * @return + */ + protected String getNewViewName(String viewTitle) + { int index = Desktop.getViewCount(viewport.getSequenceSetId()); - // make sure the new view has a unique name - this is essential for Jalview - // 2 archives boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { @@ -2678,45 +2805,55 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, index = 1;// we count from 1 if given a specific name } String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); - Vector comps = (Vector) PaintRefresher.components.get(viewport + + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - Vector existingNames = new Vector(); - for (int i = 0; i < comps.size(); i++) - { - if (comps.elementAt(i) instanceof AlignmentPanel) - { - AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i); - if (!existingNames.contains(ap.av.viewName)) - { - existingNames.addElement(ap.av.viewName); - } - } - } + + List existingNames = getExistingViewNames(comps); while (existingNames.contains(newViewName)) { newViewName = viewTitle + " " + (++index); } + return newViewName; + } - newap.av.viewName = newViewName; - - addAlignmentPanel(newap, true); - newap.alignmentChanged(); - - if (alignPanels.size() == 2) + /** + * Returns a list of distinct view names found in the given list of + * components. View names are held on the viewport of an AlignmentPanel. + * + * @param comps + * @return + */ + protected List getExistingViewNames(List comps) + { + List existingNames = new ArrayList(); + for (Component comp : comps) { - viewport.gatherViewsHere = true; + if (comp instanceof AlignmentPanel) + { + AlignmentPanel ap = (AlignmentPanel) comp; + if (!existingNames.contains(ap.av.viewName)) + { + existingNames.add(ap.av.viewName); + } + } } - tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); - return newap; + return existingNames; } + /** + * Explode tabbed views into separate windows. + */ @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } + /** + * Gather views in separate windows back into a tabbed presentation. + */ @Override public void gatherViews_actionPerformed(ActionEvent e) { @@ -2746,8 +2883,8 @@ 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); } @@ -2761,7 +2898,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { - viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); + viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); alignPanel.paintAlignment(true); } @@ -2773,7 +2910,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void followHighlight_actionPerformed() { - if (viewport.followHighlight = this.followHighlightMenuItem.getState()) + /* + * Set the 'follow' flag on the Viewport (and scroll to position if now + * true). + */ + final boolean state = this.followHighlightMenuItem.getState(); + viewport.setFollowHighlight(state); + if (state) { alignPanel.scrollToPosition( alignPanel.getSeqPanel().seqCanvas.searchResults, false); @@ -2806,7 +2949,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, scaleLeft.setVisible(wrapMenuItem.isSelected()); scaleRight.setVisible(wrapMenuItem.isSelected()); viewport.setWrapAlignment(wrapMenuItem.isSelected()); - alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); + alignPanel.updateLayout(); } @Override @@ -2826,7 +2969,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - alignPanel.paintAlignment(true); + // alignPanel.paintAlignment(true); } /** @@ -3039,6 +3182,12 @@ 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) @@ -3083,7 +3232,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight .isSelected()); - if (viewport.getShowSequenceFeaturesHeight()) + if (viewport.isShowSequenceFeaturesHeight()) { // ensure we're actually displaying features viewport.setShowSequenceFeatures(true); @@ -3110,11 +3259,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final boolean setVisible = annotationPanelMenuItem.isSelected(); viewport.setShowAnnotation(setVisible); - alignPanel.setAnnotationVisible(setVisible); this.showAllSeqAnnotations.setEnabled(setVisible); this.hideAllSeqAnnotations.setEnabled(setVisible); this.showAllAlAnnotations.setEnabled(setVisible); this.hideAllAlAnnotations.setEnabled(setVisible); + alignPanel.updateLayout(); } @Override @@ -3125,14 +3274,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); editPane.setText(MessageManager.formatMessage("label.html_content", - new String[] - { contents.toString() })); + new Object[] { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new String[] - { getTitle() }), 500, 400); + Desktop.addInternalFrame(frame, MessageManager.formatMessage( + "label.alignment_properties", new Object[] { getTitle() }), + 500, 400); } /** @@ -3153,8 +3301,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.overview_params", new String[] - { 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() @@ -3316,6 +3464,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void annotationColumn_actionPerformed(ActionEvent e) + { + new AnnotationColumnChooser(viewport, alignPanel); + } + + @Override public void rnahelicesColour_actionPerformed(ActionEvent e) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -3341,115 +3495,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ 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.getIgnoreGapsConsensus()); - } - else - { - cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + 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 - { - cs.setConservation(null); - } - - 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.getIgnoreGapsConsensus()); - - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - 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); } @@ -3554,8 +3620,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { Component[] menuItems = colourMenu.getMenuComponents(); - int i, iSize = menuItems.length; - for (i = 0; i < iSize; i++) + int iSize = menuItems.length; + for (int i = 0; i < iSize; i++) { if (menuItems[i].getName() != null && menuItems[i].getName().equals("USER_DEFINED")) @@ -3816,7 +3882,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "PID", "Average distance tree using PID"); + newTreePanel("AV", "PID", "Average distance tree using PID"); } /** @@ -3828,7 +3894,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + newTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } /** @@ -3840,7 +3906,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } /** @@ -3852,7 +3918,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + newTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } /** @@ -3865,7 +3931,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param title * DOCUMENT ME! */ - void NewTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String pwType, String title) { TreePanel tp; @@ -3956,7 +4022,8 @@ 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 String[]{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() { @@ -4075,12 +4142,11 @@ 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()); - for (final Object pwtype : ResidueProperties.scoreMatrices.keySet()) + for (final String pwtype : ResidueProperties.scoreMatrices.keySet()) { JMenuItem tm = new JMenuItem(); ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); @@ -4096,7 +4162,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void actionPerformed(ActionEvent e) { - NewTreePanel(type, (String) pwtype, title); + newTreePanel(type, pwtype, title); } }); calculateTree.add(tm); @@ -4106,21 +4172,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } sortByTreeMenu.removeAll(); - Vector comps = (Vector) PaintRefresher.components.get(viewport + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - Vector treePanels = new Vector(); - int i, iSize = comps.size(); - for (i = 0; i < iSize; i++) + List treePanels = new ArrayList(); + for (Component comp : comps) { - if (comps.elementAt(i) instanceof TreePanel) + if (comp instanceof TreePanel) { - treePanels.add(comps.elementAt(i)); + treePanels.add((TreePanel) comp); } } - iSize = treePanels.size(); - - if (iSize < 1) + if (treePanels.size() < 1) { sortByTreeMenu.setVisible(false); return; @@ -4128,17 +4191,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortByTreeMenu.setVisible(true); - for (i = 0; i < treePanels.size(); i++) + for (final TreePanel tp : treePanels) { - final TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); - final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { - tp.sortByTree_actionPerformed(null); + tp.sortByTree_actionPerformed(); addHistoryItem(tp.sortAlignmentIn(alignPanel)); } @@ -4188,28 +4249,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() == 1) { - int option = JOptionPane - .showConfirmDialog( -this, - "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.", - "Invalid selection", - JOptionPane.OK_CANCEL_OPTION); + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); if (option == JOptionPane.OK_OPTION) { msa = viewport.getAlignmentView(false); } - } else { - /* - * Vector seqs = viewport.getAlignment().getSequences(); - * - * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * - * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) - * seqs.elementAt(i); } } - */ msa = viewport.getAlignmentView(false); } return msa; @@ -4241,8 +4291,7 @@ this, // 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! @@ -4257,7 +4306,7 @@ this, * DOCUMENT ME! */ @Override - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( @@ -4389,7 +4438,6 @@ this, } catch (Exception e) { } - ; } final AlignFrame me = this; buildingMenu = true; @@ -4401,8 +4449,8 @@ this, 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 @@ -4544,14 +4592,11 @@ this, .debug("Exception during web service menu building process.", e); } - ; } }); } catch (Exception e) { } - ; - buildingMenu = false; } }).start(); @@ -4663,7 +4708,7 @@ this, public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay - af.showProductsFor(af.viewport.getSequenceSelection(), ds, + af.showProductsFor(af.viewport.getSequenceSelection(), isRegSel, dna, source); } @@ -4682,14 +4727,9 @@ this, return showp; } - protected void showProductsFor(SequenceI[] sel, Alignment ds, - boolean isRegSel, boolean dna, String source) + protected void showProductsFor(final SequenceI[] sel, + final boolean isRegSel, final boolean dna, final String source) { - final boolean fisRegSel = isRegSel; - final boolean fdna = dna; - final String fsrc = source; - final AlignFrame ths = this; - final SequenceI[] fsel = sel; Runnable foo = new Runnable() { @@ -4697,15 +4737,16 @@ this, public void run() { final long sttime = System.currentTimeMillis(); - ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime); + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.searching_for_sequences_from", + new Object[] { source }), sttime); try { - Alignment ds = ths.getViewport().getAlignment().getDataset(); // update - // our local - // dataset - // reference + // update our local dataset reference + Alignment ds = AlignFrame.this.getViewport().getAlignment() + .getDataset(); Alignment prods = CrossRef - .findXrefSequences(fsel, fdna, fsrc, ds); + .findXrefSequences(sel, dna, source, ds); if (prods != null) { SequenceI[] sprods = new SequenceI[prods.getHeight()]; @@ -4721,25 +4762,75 @@ this, sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); - AlignedCodonFrame[] cf = prods.getCodonFrames(); al.setDataset(ds); - for (int s = 0; cf != null && s < cf.length; s++) + + /* + * 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(cf[s]); - cf[s] = null; + al.addCodonFrame(acf); } AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ") - + " for " + ((fisRegSel) ? "selected region of " : "") + String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides") + + " for " + ((isRegSel) ? "selected region of " : "") + getTitle(); - Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + naf.setTitle(newtitle); + + // temporary flag until SplitFrame is released + boolean asSplitFrame = Cache.getDefault( + Preferences.ENABLE_SPLIT_FRAME, true); + if (asSplitFrame) + { + /* + * Make a copy of this alignment (sharing the same dataset + * sequences). If we are DNA, drop introns and update mappings + */ + AlignmentI copyAlignment = null; + final SequenceI[] sequenceSelection = AlignFrame.this.viewport + .getSequenceSelection(); + if (dna) + { + copyAlignment = AlignmentUtils.makeExonAlignment( + sequenceSelection, cf); + al.getCodonFrames().clear(); + al.getCodonFrames().addAll(cf); + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(cf); + } + else + { + copyAlignment = new Alignment(new Alignment( + sequenceSelection)); + } + 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, + DEFAULT_HEIGHT); + } } else { System.err.println("No Sequences generated for xRef type " - + fsrc); + + source); } } catch (Exception e) { @@ -4753,8 +4844,9 @@ this, jalview.bin.Cache.log.error("Error when finding crossreferences", e); } - ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}), - sttime); + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.finished_searching_for_sequences_from", + new Object[] { source }), sttime); } }; @@ -4779,135 +4871,100 @@ this, } } - @Override - public void showProducts_actionPerformed(ActionEvent e) - { - // ///////////////////////////// - // Collect Data to be translated/transferred - - SequenceI[] selection = viewport.getSequenceSelection(); - AlignmentI al = null; - try - { - al = jalview.analysis.Dna.CdnaTranslate(selection, viewport - .getViewAsVisibleContigs(true), viewport.getGapCharacter(), - viewport.getAlignment().getDataset()); - } catch (Exception ex) - { - al = null; - jalview.bin.Cache.log.debug("Exception during translation.", ex); - } - if (al == null) - { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), - MessageManager.getString("label.translation_failed"), - JOptionPane.WARNING_MESSAGE); - } - else - { - AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.translation_of_params", new String[] - { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); - } - } - + /** + * Construct and display a new frame containing the translation of this + * frame's DNA sequences to their aligned protein (amino acid) equivalents. + */ @Override public void showTranslation_actionPerformed(ActionEvent e) { - // ///////////////////////////// - // Collect Data to be translated/transferred - - SequenceI[] selection = viewport.getSequenceSelection(); - String[] seqstring = viewport.getViewAsString(true); AlignmentI al = null; try { - al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, - viewport.getViewAsVisibleContigs(true), viewport - .getGapCharacter(), viewport.getAlignment() - .getAlignmentAnnotation(), viewport.getAlignment() - .getWidth(), viewport.getAlignment().getDataset()); + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); + + al = dna.translateCdna(); } catch (Exception ex) { - al = null; jalview.bin.Cache.log.error( "Exception during translation. Please report this !", ex); - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.error_when_translating_sequences_submit_bug_report"), - MessageManager - .getString("label.implementation_error") - + MessageManager - .getString("translation_failed"), - JOptionPane.ERROR_MESSAGE); + final String msg = MessageManager + .getString("label.error_when_translating_sequences_submit_bug_report"); + final String errorTitle = MessageManager + .getString("label.implementation_error") + + MessageManager.getString("translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JOptionPane.ERROR_MESSAGE); return; } - if (al == null) + if (al == null || al.getHeight() == 0) { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), - MessageManager.getString("label.translation_failed"), - JOptionPane.WARNING_MESSAGE); + final String msg = MessageManager + .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); + final String errorTitle = MessageManager + .getString("label.translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.translation_of_params", new String[] - { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); + af.setFileFormat(this.currentFileFormat); + final String newTitle = MessageManager.formatMessage( + "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)); + } + else + { + Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } } } /** + * Set the file format + * + * @param fileFormat + */ + public void setFileFormat(String fileFormat) + { + this.currentFileFormat = fileFormat; + } + + /** * Try to load a features file onto the alignment. * * @param file * 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().featureColours, 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.showSequenceFeatures = true; + 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 @@ -5040,8 +5097,7 @@ this, { if (type.equalsIgnoreCase("PDB")) { - filesmatched.add(new Object[] - { file, protocol, mtch }); + filesmatched.add(new Object[] { file, protocol, mtch }); continue; } } @@ -5060,10 +5116,10 @@ this, MessageManager .formatMessage( "label.automatically_associate_pdb_files_with_sequences_same_name", - new String[] - { Integer.valueOf( - filesmatched - .size()) + new Object[] { Integer + .valueOf( + filesmatched + .size()) .toString() }), MessageManager .getString("label.automatically_associate_pdb_files_by_name"), @@ -5100,14 +5156,16 @@ this, "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane .showConfirmDialog( this, - ""+MessageManager - .formatMessage( - "label.ignore_unmatched_dropped_files_info", - new String[] - { 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)) @@ -5150,8 +5208,7 @@ this, // try to parse as annotation. boolean isAnnotation = (format == null || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .readAnnotationFile(viewport.getAlignment(), file, protocol) - : false; + .annotateAlignmentView(viewport, file, protocol) : false; if (!isAnnotation) { @@ -5211,8 +5268,14 @@ this, { jalview.io.JPredFile predictions = new jalview.io.JPredFile( file, protocol); - new JnetAnnotationMaker().add_annotation(predictions, + new JnetAnnotationMaker(); + JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); + SequenceI repseq = viewport.getAlignment().getSequenceAt(0); + viewport.getAlignment().setSeqrep(repseq); + ColumnSelection cs = new ColumnSelection(); + cs.hideInsertionsFor(repseq); + viewport.setColumnSelection(cs); isAnnotation = true; } else @@ -5283,31 +5346,55 @@ this, } } + /** + * Method invoked by the ChangeListener on the tabbed pane, in other words + * when a different tabbed pane is selected by the user or programmatically. + */ @Override public void tabSelectionChanged(int index) { if (index > -1) { - alignPanel = (AlignmentPanel) alignPanels.elementAt(index); + alignPanel = alignPanels.get(index); viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); } + + /* + * If there is a frame linked to this one in a SplitPane, switch it to the + * same view tab index. No infinite recursion of calls should happen, since + * tabSelectionChanged() should not get invoked on setting the selected + * index to an unchanged value. Guard against setting an invalid index + * before the new view peer tab has been created. + */ + final AlignViewportI peer = viewport.getCodingComplement(); + if (peer != null) + { + AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame; + if (linkedAlignFrame.tabbedPane.getTabCount() > index) + { + linkedAlignFrame.tabbedPane.setSelectedIndex(index); + } + } } + /** + * On right mouse click on view tab, prompt for and set new view name. + */ @Override public void tabbedPane_mousePressed(MouseEvent e) { if (SwingUtilities.isRightMouseButton(e)) { - String reply = JOptionPane.showInternalInputDialog(this, - MessageManager.getString("label.enter_view_name"), - MessageManager.getString("label.enter_view_name"), + String msg = MessageManager.getString("label.enter_view_name"); + String reply = JOptionPane.showInternalInputDialog(this, msg, msg, JOptionPane.QUESTION_MESSAGE); if (reply != null) { viewport.viewName = reply; + // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } } @@ -5347,7 +5434,7 @@ this, @Override protected void showDbRefs_actionPerformed(ActionEvent e) { - viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); + viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); } /* @@ -5359,7 +5446,7 @@ this, @Override protected void showNpFeats_actionPerformed(ActionEvent e) { - viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); + viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); } /** @@ -5368,7 +5455,7 @@ this, * * @param av */ - public boolean closeView(AlignViewport av) + public boolean closeView(AlignViewportI av) { if (viewport == av) { @@ -5514,7 +5601,10 @@ this, } }); - fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()}))); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from", + new Object[] { src.getDbName() }))); dfetch.add(fetchr); comp++; } @@ -5525,8 +5615,8 @@ this, // fetch all entry DbSourceProxy src = otherdb.get(0); fetchr = new JMenuItem(MessageManager.formatMessage( - "label.fetch_all_param", new String[] - { src.getDbSource() })); + "label.fetch_all_param", + new Object[] { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override @@ -5547,11 +5637,19 @@ this, } }); - fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{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 String[]{src.getDbSource()})); + ifetch = new JMenu(MessageManager.formatMessage( + "label.source_from_db_source", + new Object[] { src.getDbSource() })); icomp = 0; String imname = null; int i = 0; @@ -5564,11 +5662,11 @@ this, 0, 10) + "..." : dbname; if (imname == null) { - imname = MessageManager.formatMessage("label.from_msname", new String[]{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() { @@ -5591,7 +5689,9 @@ this, }); fetchr.setToolTipText("" - + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname})); + + MessageManager.formatMessage( + "label.fetch_retrieve_from", new Object[] + { dbname })); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) @@ -5648,8 +5748,8 @@ this, public void setShowSeqFeatures(boolean b) { - showSeqFeatures.setSelected(true); - viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); } /* @@ -5756,6 +5856,18 @@ this, } } + public void clearAlignmentSeqRep() + { + // TODO refactor alignmentseqrep to controller + if (viewport.getAlignment().hasSeqrep()) + { + viewport.getAlignment().setSeqrep(null); + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + @Override protected void createGroup_actionPerformed(ActionEvent e) { @@ -5784,10 +5896,13 @@ this, 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 - & alignPanels.indexOf(alignmentPanel) != tabbedPane + && tabbedPane.getTabCount() > 0 + && alignPanels.indexOf(alignmentPanel) != tabbedPane .getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); @@ -5810,6 +5925,13 @@ this, for (AlignmentAnnotation aa : alignPanel.getAlignment() .getAlignmentAnnotation()) { + /* + * don't display non-positional annotations on an alignment + */ + if (aa.annotations == null) + { + continue; + } boolean apply = (aa.sequenceRef == null && forAlignment) || (aa.sequenceRef != null && forSequences); if (apply) @@ -5817,7 +5939,7 @@ this, aa.visible = visible; } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); alignPanel.alignmentChanged(); } @@ -5832,6 +5954,79 @@ this, .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); alignPanel.paintAlignment(true); } + + /** + * + * @return alignment panels in this alignment frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + } + + /** + * Open a new alignment window, with the cDNA associated with this (protein) + * alignment, aligned as is the protein. + */ + protected void viewAsCdna_actionPerformed() + { + // TODO no longer a menu action - refactor as required + final AlignmentI alignment = getViewport().getAlignment(); + Set mappings = alignment.getCodonFrames(); + if (mappings == null) + { + return; + } + List cdnaSeqs = new ArrayList(); + for (SequenceI aaSeq : alignment.getSequences()) + { + for (AlignedCodonFrame acf : mappings) + { + SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); + if (dnaSeq != null) + { + /* + * There is a cDNA mapping for this protein sequence - add to new + * alignment. It will share the same dataset sequence as other mapped + * cDNA (no new mappings need to be created). + */ + final Sequence newSeq = new Sequence(dnaSeq); + newSeq.setDatasetSequence(dnaSeq); + cdnaSeqs.add(newSeq); + } + } + } + if (cdnaSeqs.size() == 0) + { + // show a warning dialog no mapped cDNA + return; + } + AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs + .size()])); + AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + cdna.alignAs(alignment); + String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + + this.title; + Desktop.addInternalFrame(alignFrame, newtitle, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + } + + /** + * Set visibility of dna/protein complement view (available when shown in a + * split frame). + * + * @param show + */ + @Override + protected void showComplement_actionPerformed(boolean show) + { + SplitContainerI sf = getSplitViewContainer(); + if (sf != null) + { + sf.setComplementVisible(this, show); + } + } } class PrintThread extends Thread