/*
- * 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.
*
*/
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;
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;
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;
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.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.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;
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<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
/**
* Last format used to load or save alignments in this window
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();
}
*/
void init()
{
+ if (!Jalview.isHeadlessMode())
+ {
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ }
+
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
-
- if (viewport.wrapAlignment)
+
+ if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
}
addKeyListener();
+ final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
+ final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+ 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<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
+ 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);
+ }
+
}
/**
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()
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;
}
else
{
- alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ alignPanel.getSeqPanel().deleteGapAtCursor(
+ evt.isControlDown() || evt.isShiftDown()
+ || evt.isAltDown());
}
break;
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;
break;
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
}
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
- alignPanels.addElement(ap);
+ alignPanels.add(ap);
PaintRefresher.Register(ap, ap.av.getSequenceSetId());
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);
}
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);
}).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);
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.
*/
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
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());
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);
updateEditMenuBar();
}
- // methods for implementing IProgressIndicator
- // need to refactor to a reusable stub class
- Hashtable progressBars, progressBarHandlers;
+ private IProgressIndicator progressBar;
/*
* (non-Javadoc)
@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);
}
/**
@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
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
+ .getAlignPanel());
}
@Override
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);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
currentFileFormat = chooser.getSelectedFormat();
- if (currentFileFormat == null)
+ while (currentFileFormat == null)
{
JOptionPane
.showInternalMessageDialog(
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();
.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
{
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)
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;
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);
}
@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);
}
+ 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<int[]> 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<int[]> hiddenCols = new ArrayList<int[]>();
+ 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!
*
@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);
{
alignPanel.makeSVG(f);
}
+
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
@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
// 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();
}
}
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)
}
/**
- * 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();
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
{
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
{
{
if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.clear();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
updateEditMenuBar();
viewport.updateHiddenColumns();
// viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
{
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;
}
@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)
@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)
}
}
- 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
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ List<Component> 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;
}
}
synchronized void slideSequences(boolean right, int size)
{
- List<SequenceI> sg = new Vector();
+ List<SequenceI> sg = new ArrayList<SequenceI>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
return;
}
- Vector invertGroup = new Vector();
+ List<SequenceI> invertGroup = new ArrayList<SequenceI>();
- 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);
}
}
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;
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<CommandI> 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());
}
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
return;
}
- Vector hiddenColumns = null;
+ ArrayList<int[]> hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
- hiddenColumns = new Vector();
+ hiddenColumns = new ArrayList<int[]>();
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() }));
}
/**
//
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++)
alignment.getSequences());
if (alignPanels != null)
{
- for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+ for (AlignmentPanel ap : alignPanels)
{
ap.validateAnnotationDimensions(false);
}
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+ for (int[] region : hc)
{
- int[] region = (int[]) hc.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
// 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.
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+ for (int region[] : hc)
{
- int[] region = (int[]) hc.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
// 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.
return;
}
- List<SequenceI> seqs = new ArrayList<SequenceI>(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,
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,
}
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);
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
.getSequences());
}
- // else
- {
- // if (justifySeqs>0)
- {
- // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
- }
- }
-
- // }
-
/**
* DOCUMENT ME!
*
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)
{
index = 1;// we count from 1 if given a specific name
}
String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+
+ List<Component> 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<String> 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<String> getExistingViewNames(List<Component> comps)
+ {
+ List<String> existingNames = new ArrayList<String>();
+ 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)
{
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
- .calculateIdWidth());
+ alignPanel.getIdPanel().getIdCanvas()
+ .setPreferredSize(alignPanel.calculateIdWidth());
alignPanel.paintAlignment(true);
}
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
- viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
alignPanel.paintAlignment(true);
}
@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);
scaleLeft.setVisible(wrapMenuItem.isSelected());
scaleRight.setVisible(wrapMenuItem.isSelected());
viewport.setWrapAlignment(wrapMenuItem.isSelected());
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.updateLayout();
}
@Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+ // alignPanel.paintAlignment(true);
}
/**
public FeatureSettings featureSettings;
@Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
.isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
+ if (viewport.isShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
viewport.setShowSequenceFeatures(true);
{
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
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);
}
/**
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()
}
@Override
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
+
+ @Override
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
*/
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);
}
{
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"))
@Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel("AV", "PID", "Average distance tree using PID");
}
/**
@Override
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
}
/**
@Override
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
}
/**
@Override
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
/**
* @param title
* DOCUMENT ME!
*/
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
TreePanel tp;
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()
{
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);
@Override
public void actionPerformed(ActionEvent e)
{
- NewTreePanel(type, (String) pwtype, title);
+ newTreePanel(type, pwtype, title);
}
});
calculateTree.add(tm);
}
sortByTreeMenu.removeAll();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ List<Component> comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- Vector treePanels = new Vector();
- int i, iSize = comps.size();
- for (i = 0; i < iSize; i++)
+ List<TreePanel> treePanels = new ArrayList<TreePanel>();
+ 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;
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));
}
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;
// 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!
* DOCUMENT ME!
*/
@Override
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
} catch (Exception e)
{
}
- ;
}
final AlignFrame me = this;
buildingMenu = true;
final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
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
.debug("Exception during web service menu building process.",
e);
}
- ;
}
});
} catch (Exception e)
{
}
- ;
-
buildingMenu = false;
}
}).start();
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);
}
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()
{
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()];
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<AlignedCodonFrame> 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)
{
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);
}
};
}
}
- @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
{
if (type.equalsIgnoreCase("PDB"))
{
- filesmatched.add(new Object[]
- { file, protocol, mtch });
+ filesmatched.add(new Object[] { file, protocol, mtch });
continue;
}
}
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"),
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- "<html>"+MessageManager
- .formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new String[]
- { Integer.valueOf(
- filesnotmatched
- .size())
- .toString() })+"</html>",
+ "<html>"
+ + MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[] { Integer
+ .valueOf(
+ filesnotmatched
+ .size())
+ .toString() })
+ + "</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
// 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)
{
{
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
}
}
+ /**
+ * 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);
}
}
@Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
- viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+ viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
}
/*
@Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
- viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+ viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
}
/**
*
* @param av
*/
- public boolean closeView(AlignViewport av)
+ public boolean closeView(AlignViewportI av)
{
if (viewport == av)
{
}
});
- 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++;
}
// 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
}
});
- 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;
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()
{
});
fetchr.setToolTipText("<html>"
- + 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()))
public void setShowSeqFeatures(boolean b)
{
- showSeqFeatures.setSelected(true);
- viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(b);
+ viewport.setShowSequenceFeatures(b);
}
/*
}
}
+ 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)
{
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));
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)
aa.visible = visible;
}
}
- alignPanel.validateAnnotationDimensions(false);
+ alignPanel.validateAnnotationDimensions(true);
alignPanel.alignmentChanged();
}
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
alignPanel.paintAlignment(true);
}
+
+ /**
+ *
+ * @return alignment panels in this alignment frame
+ */
+ public List<? extends AlignmentViewPanel> 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<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ if (mappings == null)
+ {
+ return;
+ }
+ List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+ 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);
+ }
+ }
}
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