X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b484118337b696f7f0093b0c6dfd4eaa7f210954;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=c7792a5398d2eb011b94ee08adf58058ba9fd364;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index c7792a5..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 ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ 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. * @@ -20,73 +20,23 @@ */ package jalview.gui; -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; -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.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; - -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.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; @@ -98,10 +48,12 @@ 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.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; @@ -111,7 +63,6 @@ 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; @@ -140,6 +91,7 @@ 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; @@ -147,6 +99,52 @@ import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; 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.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; + /** * DOCUMENT ME! * @@ -287,7 +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(); } @@ -314,6 +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) @@ -348,7 +371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); - + if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); @@ -363,7 +386,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final List selviews = new ArrayList(); final List origview = new ArrayList(); - ViewSelectionMenu vsel = new ViewSelectionMenu("Transfer colours from", + final String menuLabel = MessageManager + .getString("label.copy_format_from"); + ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, new ViewSetProvider() { @@ -372,7 +397,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { origview.clear(); origview.add(alignPanel); - return Desktop.getAlignmentPanels(null); + // 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() { @@ -382,37 +411,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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(); - origview.get(0).getAlignViewport().setViewStyle(vs); - AlignViewportI complement = origview.get(0) - .getAlignViewport().getCodingComplement(); - if (complement != null) + 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); - if (complement.isNucleotide()) - { - complement.setViewStyle(vs); - vs.setCharWidth(vs.getCharWidth() / 3); - } - else - { - int rw = vs.getCharWidth(); - vs.setCharWidth(rw * 3); - complement.setViewStyle(vs); - vs.setCharWidth(rw); - } - af.alignPanel.updateLayout(); + ((SplitFrame) af.getSplitViewContainer()) + .adjustLayout(); af.setMenusForViewport(); } - origview.get(0).updateLayout(); - origview.get(0).setSelected(true); - origview.get(0).alignFrame.setMenusForViewport(); + + ap.updateLayout(); + ap.setSelected(true); + ap.alignFrame.setMenusForViewport(); } } }); - formatMenu.add(vsel); + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("devel") > -1 + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("test") > -1) + { + formatMenu.add(vsel); + } } @@ -509,8 +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; @@ -533,8 +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; @@ -582,8 +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; @@ -751,7 +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); @@ -855,9 +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) @@ -867,78 +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 Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); - } - }); - progressPanel.add(cancel, BorderLayout.EAST); - } + progressBar.registerHandler(id, handler); } /** @@ -948,18 +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 @@ -1056,7 +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 @@ -1097,7 +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); @@ -1152,16 +1132,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - /* - * First save any linked Chimera session. - */ - Desktop.instance.saveChimeraSessions(file); - 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 @@ -1170,35 +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) @@ -1217,8 +1184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new Object[] - { fileName, format })); + new Object[] { fileName, format })); } catch (Exception ex) { success = false; @@ -1230,8 +1196,8 @@ 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); } @@ -1263,37 +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 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); @@ -1302,6 +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! * @@ -1311,18 +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) { - new BioJsHTMLOutput(alignPanel, - alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); + bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1356,6 +1405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { alignPanel.makeSVG(f); } + @Override public void pageSetup_actionPerformed(ActionEvent e) { @@ -1451,6 +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) @@ -1495,8 +1549,8 @@ 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 { @@ -1510,8 +1564,8 @@ 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 { @@ -1553,8 +1607,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport != null) { - return new AlignmentI[] - { viewport.getAlignment() }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } @@ -1781,10 +1834,14 @@ 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 @@ -1825,7 +1882,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + omitHidden, null); StringSelection ss = new StringSelection(output); @@ -1855,17 +1912,17 @@ 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() })); } /** @@ -2074,8 +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++) @@ -2193,7 +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. @@ -2252,7 +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. @@ -2522,8 +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); @@ -2572,8 +2631,9 @@ 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 @@ -2698,12 +2758,17 @@ 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); @@ -2818,8 +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); } @@ -2849,7 +2914,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Set the 'follow' flag on the Viewport (and scroll to position if now * true). */ - if (viewport.followHighlight = this.followHighlightMenuItem.getState()) + final boolean state = this.followHighlightMenuItem.getState(); + viewport.setFollowHighlight(state); + if (state) { alignPanel.scrollToPosition( alignPanel.getSeqPanel().seqCanvas.searchResults, false); @@ -2902,7 +2969,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); -// alignPanel.paintAlignment(true); + // alignPanel.paintAlignment(true); } /** @@ -3115,6 +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) @@ -3201,14 +3274,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); editPane.setText(MessageManager.formatMessage("label.html_content", - new 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); } /** @@ -3229,8 +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 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() @@ -3423,115 +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.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 - { - 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.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); } @@ -4038,7 +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 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() { @@ -4157,8 +4142,7 @@ 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()); @@ -4307,8 +4291,7 @@ 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! @@ -4466,8 +4449,8 @@ 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 @@ -4755,8 +4738,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final long sttime = System.currentTimeMillis(); AlignFrame.this.setProgressBar(MessageManager.formatMessage( - "status.searching_for_sequences_from", new Object[] - { source }), sttime); + "status.searching_for_sequences_from", + new Object[] { source }), sttime); try { // update our local dataset reference @@ -4779,8 +4762,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); - Set cf = prods.getCodonFrames(); al.setDataset(ds); + + /* + * 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); @@ -4792,12 +4782,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + getTitle(); naf.setTitle(newtitle); - // remove this flag once confirmed we want a split view - boolean asSplitFrame = true; + // temporary flag until SplitFrame is released + boolean asSplitFrame = Cache.getDefault( + Preferences.ENABLE_SPLIT_FRAME, true); if (asSplitFrame) { - final Alignment copyAlignment = new Alignment(new Alignment( - AlignFrame.this.viewport.getSequenceSelection())); + /* + * 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()); @@ -4835,9 +4846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignFrame.this.setProgressBar(MessageManager.formatMessage( "status.finished_searching_for_sequences_from", - new Object[] - { source }), - sttime); + new Object[] { source }), sttime); } }; @@ -4881,10 +4890,10 @@ 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; } @@ -4892,9 +4901,9 @@ 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 @@ -4902,12 +4911,19 @@ 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); - final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); - viewport.openSplitFrame(af, new Alignment(seqs), al.getCodonFrames()); - // Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); + 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); + } } } @@ -4928,39 +4944,27 @@ 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 @@ -5093,8 +5097,7 @@ 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; } } @@ -5113,10 +5116,10 @@ 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"), @@ -5153,14 +5156,16 @@ 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)) @@ -5203,8 +5208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse as annotation. boolean isAnnotation = (format == null || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, protocol) - : false; + .annotateAlignmentView(viewport, file, protocol) : false; if (!isAnnotation) { @@ -5597,7 +5601,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - 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++; } @@ -5608,8 +5615,8 @@ 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 @@ -5630,11 +5637,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - 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; @@ -5647,11 +5662,11 @@ 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() { @@ -5674,7 +5689,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText("" - + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname})); + + MessageManager.formatMessage( + "label.fetch_retrieve_from", new Object[] + { dbname })); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) @@ -5731,8 +5748,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void setShowSeqFeatures(boolean b) { - showSeqFeatures.setSelected(true); - viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); } /* @@ -5838,10 +5855,12 @@ 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(); @@ -5877,7 +5896,9 @@ 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 @@ -5904,6 +5925,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -5911,7 +5939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, aa.visible = visible; } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); alignPanel.alignmentChanged(); } @@ -5933,8 +5961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) - : alignPanels; + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; } /** @@ -5951,8 +5978,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } List cdnaSeqs = new ArrayList(); - for (SequenceI aaSeq : alignment.getSequences()) { - for (AlignedCodonFrame acf : mappings) { + for (SequenceI aaSeq : alignment.getSequences()) + { + for (AlignedCodonFrame acf : mappings) + { SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); if (dnaSeq != null) { @@ -5980,8 +6009,7 @@ 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); } /** @@ -5994,7 +6022,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showComplement_actionPerformed(boolean show) { SplitContainerI sf = getSplitViewContainer(); - if (sf != null) { + if (sf != null) + { sf.setComplementVisible(this, show); } }