/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+ ItemListener, KeyListener, AlignViewControllerGuiI
{
+ public AlignViewControllerI avc;
public AlignmentPanel alignPanel;
public AlignViewport viewport;
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
String title, boolean embedded)
{
-
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
{
ex.printStackTrace();
}
-
+ // need to get window geometry before we calculate alignment layout
+ if (applet != null)
+ {
+ String param;
+ try
+ {
+ param = applet.getParameter("windowWidth");
+ if (param != null)
+ {
+ int width = Integer.parseInt(param);
+ DEFAULT_WIDTH = width;
+ }
+ param = applet.getParameter("windowHeight");
+ if (param != null)
+ {
+ int height = Integer.parseInt(param);
+ DEFAULT_HEIGHT = height;
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
-
+ avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
annotationPanelMenuItem.setState(viewport.showAnnotation);
- displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+ displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.getFollowHighlight());
- showGroupConsensus.setState(viewport.showGroupConsensus);
- showGroupConservation.setState(viewport.showGroupConservation);
- showConsensusHistogram.setState(viewport.showConsensusHistogram);
- showSequenceLogo.setState(viewport.showSequenceLogo);
-
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());
+ showGroupConservation.setState(viewport.isShowGroupConservation());
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+
seqLimits.setState(viewport.showJVSuffix);
if (applet != null)
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
- try
+
+ }
+ if (viewport.getAlignment().isNucleotide())
+ {
+ viewport.updateStrucConsensus(alignPanel);
+ if (viewport.getAlignment().hasRNAStructure())
{
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
+ RNAHelixColour.setEnabled(true);
+ }
+ else
{
+ RNAHelixColour.setEnabled(false);
}
-
}
-
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ purinePyrimidineColour.setEnabled(false);
+ }
// Some JVMS send keyevents to Top frame or lowest panel,
// Havent worked out why yet. So add to both this frame and seqCanvas for
// now
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
createAlignFrameWindow(embedded, title);
- alignPanel.validate();
+
+ validate();
+ alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
}
}
/**
- * DOCUMENT ME!
+ * Load a features file onto the alignment
*
- * @param String
- * DOCUMENT ME!
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
*/
- public void parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, String type)
+ {
+ return parseFeaturesFile(file, type, true);
+ }
+
+ /**
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
+ * @param autoenabledisplay
+ * when true, display features flag will be automatically enabled if
+ * features are loaded
+ * @return true if data parsed as a features file
+ */
+ public boolean parseFeaturesFile(String file, String type,
+ boolean autoenabledisplay)
{
+ // TODO: test if importing a features file onto an alignment which already
+ // has features with links overwrites the original links.
+
Hashtable featureLinks = new Hashtable();
boolean featuresFile = false;
try
{
featuresFile = new jalview.io.FeaturesFile(file, type)
- .parse(viewport.alignment,
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
+ .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, featureLinks,
+ true, viewport.applet.getDefaultParameter(
+ "relaxedidmatch", false));
} catch (Exception ex)
{
ex.printStackTrace();
{
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
}
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
+ if (autoenabledisplay)
+ {
+ viewport.showSequenceFeatures = true;
+ sequenceFeatures.setState(true);
+ }
if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true);
+ statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
}
-
+ return featuresFile;
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
{
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed();
-
- alignPanel.alabels.cancelDrag();
+
+ alignPanel.alabels.cancelDrag();
break;
case KeyEvent.VK_X:
if (evt.isControlDown() || evt.isMetaDown())
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
+ statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
}
break;
+ case KeyEvent.VK_G:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
+ {
+ this.unGroup_actionPerformed();
+ }
+ else
+ {
+ this.createGroup_actionPerformed();
+ }
+ }
+ break;
+
case KeyEvent.VK_U:
if (evt.isControlDown())
{
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
- .getSelected().size() > 0)
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
if (toggleSeqs)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
{
viewport.showAllHiddenSeqs();
}
if (toggleCols)
{
- if (viewport.colSel.getSelected().size() > 0)
+ if (viewport.getColumnSelection().getSelected().size() > 0)
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
{
- viewport.selectionGroup = sg;
+ viewport.setSelectionGroup(sg);
}
}
else if (!hide)
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == displayNonconservedMenuItem)
}
else if (evt.getSource() == autoCalculate)
{
- viewport.autocalculateConsensus = autoCalculate.getState();
+ viewport.autoCalculateConsensus = autoCalculate.getState();
+ }
+ else if (evt.getSource() == sortByTree)
+ {
+ viewport.sortByTree = sortByTree.getState();
}
else if (evt.getSource() == this.centreColumnLabelFlag)
{
{
showSequenceLogo_actionPerformed();
}
+ else if (evt.getSource() == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
else if (evt.getSource() == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
this.alignPanel.annotationPanel.repaint();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
{
showSequenceLogo_actionPerformed();
}
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
else if (source == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
else if (source == alProperties)
{
StringBuffer contents = new jalview.io.AlignmentProperties(
- viewport.alignment).formatAsString();
+ viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
- + getTitle(), 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
+ 400, 250);
}
else if (source == overviewMenuItem)
{
else if (source == clustalColour)
{
abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(),
- viewport.alignment.getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
}
else if (source == zappoColour)
{
{
changeColour(new NucleotideColourScheme());
}
+ else if (source == purinePyrimidineColour)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ else if (source == RNAHelixColour)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
else if (source == modifyPID)
{
modifyPID_actionPerformed();
{
changeColour(new Blosum62ColourScheme());
}
+ else if (source == tcoffeeColour)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
else if (source == annotationColour)
{
new AnnotationColourChooser(viewport, alignPanel);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
}
protected void outputText_actionPerformed(ActionEvent e)
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.showJVSuffix));
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations file here.");
+ cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
}
public String outputAnnotations(boolean displayTextbox)
{
String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.alignment
- .getAlignmentAnnotation() : null, viewport.alignment
- .getGroups(),
- ((Alignment) viewport.alignment).alignmentProperties);
+ viewport.showAnnotation ? viewport.getAlignment()
+ .getAlignmentAnnotation() : null, viewport
+ .getAlignment().getGroups(), ((Alignment) viewport
+ .getAlignment()).alignmentProperties);
if (displayTextbox)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
private Hashtable getDisplayedFeatureCols()
{
- if (alignPanel.getFeatureRenderer() != null)
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.featuresDisplayed != null)
{
FeatureRenderer fr = alignPanel.getFeatureRenderer();
Hashtable fcols = new Hashtable();
String features;
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(
- viewport.alignment.getSequencesArray(),
+ features = new FeaturesFile().printJalviewFormat(viewport
+ .getAlignment().getSequencesArray(),
getDisplayedFeatureCols());
}
else
{
- features = new FeaturesFile().printGFFFormat(
- viewport.alignment.getSequencesArray(),
- getDisplayedFeatureCols());
+ features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols());
}
if (displayTextbox)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ boolean frimport = false;
+ if (features == null || features.equals("No Features Visible"))
+ {
+ features = "# No features visible - paste some and import them here.";
+ frimport = true;
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
+ if (frimport)
+ {
+ cap.setAnnotationImport();
+ }
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
-
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
+ else
+ {
+ if (features == null)
+ features = "";
+ }
return features;
}
public void closeMenuItem_actionPerformed()
{
PaintRefresher.RemoveComponent(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+ if (alignPanel.seqPanel != null
+ && alignPanel.seqPanel.seqCanvas != null)
+ {
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+ }
+ if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
+ {
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+ }
if (PaintRefresher.components.size() == 0 && viewport.applet == null)
{
System.exit(0);
}
-
+ else
+ {
+ }
+ viewport = null;
+ alignPanel = null;
this.dispose();
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104
*/
void updateEditMenuBar()
{
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel("Undo " + command.getDescription());
+ undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
}
if (viewport.redoList.size() > 0)
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel("Redo " + command.getDescription());
+ redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
}
}
+ /**
+ * TODO: JAL-1104
+ */
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
viewport.historyList.push(command);
viewport.redoList.removeAllElements();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.updateHiddenColumns();
}
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
command.undoCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst undoing");
+ }
+ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
command.doCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst re-doing");
+ }
+ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
AlignViewport getOriginatingSource(CommandI command)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
{
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
{
originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
break;
// the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ up ? null : viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
+ List<SequenceI> sg = new Vector<SequenceI>();
if (viewport.cursorMode)
{
- sg.addElement(viewport.alignment
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.alignment
- .getHeight())
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
return;
}
- Vector invertGroup = new Vector();
+ Vector<SequenceI> invertGroup = new Vector();
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
- if (!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
- SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
+ .size()]);
for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ seqs2[i] = invertGroup.elementAt(i);
SlideSequencesCommand ssc;
if (right)
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
+ int index = viewport.getAlignment().findIndex(seq);
orderedSeqs.put(index + "", seq);
}
int index = 0, startRes, endRes;
char ch;
- if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
+ if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
{
for (int i = 0; i < seqs.length; i++)
{
- viewport.alignment.addSequence(seqs[i]);
+ viewport.getAlignment().addSequence(seqs[i]);
}
// !newAlignment
addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
+ seqs, 0, viewport.getAlignment().getWidth(),
+ viewport.getAlignment()));
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.firePropertyChange("alignment", null,
- viewport.alignment.getSequences());
+ viewport.setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getAlignment().getWidth();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
}
// If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
*/
addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
/*
* (non-Javadoc)
*
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ protected void normSequenceLogo_actionPerformed()
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
protected void applyAutoAnnotationSettings_actionPerformed()
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
protected void makeGrpsFromSelection_actionPerformed()
{
- if (viewport.getSelectionGroup() != null)
- {
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()),
- viewport.alignment.getGroups());
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- // gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.alignment.addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq
- .hasMoreElements(); viewport.setSequenceColour(
- (SequenceI) sq.nextElement(), col))
- ;
- }
+ if (avc.makeGroupsFromSelection()) {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
+ protected void createGroup_actionPerformed()
+ {
+ avc.createGroup();
+ }
+ protected void unGroup_actionPerformed()
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
protected void deleteGroups_actionPerformed()
{
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
-
- alignPanel.paintAlignment(true);
+ if (avc.deleteGroups())
+ {
+ alignPanel.alignmentChanged();
+ }
}
public void selectAllSequenceMenuItem_actionPerformed()
{
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth() - 1);
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
{
trimRegion = new TrimRegionCommand("Remove Left",
TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
viewport.setStartRes(0);
}
else
{
trimRegion = new TrimRegionCommand("Remove Right",
TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
}
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
-
+ statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
addHistoryItem(trimRegion);
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
public void removeGappedColumnMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
- "Remove Gapped Columns", seqs, start, end, viewport.alignment);
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
// This is to maintain viewport position on first residue
// of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
public void removeAllGapsMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
// This is to maintain viewport position on first residue
// of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.alignment));
+ viewport.getAlignment()));
viewport.setStartRes(seq.findIndex(startRes) - 1);
public AlignFrame newView(String viewtitle)
{
AlignmentI newal;
- if (viewport.hasHiddenRows)
+ if (viewport.hasHiddenRows())
{
newal = new Alignment(viewport.getAlignment().getHiddenSequences()
.getFullAlignment().getSequencesArray());
}
else
{
- newal = new Alignment(viewport.alignment.getSequencesArray());
+ newal = new Alignment(viewport.getAlignment().getSequencesArray());
}
- if (viewport.alignment.getAlignmentAnnotation() != null)
+ if (viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
{
- if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
{
- newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+ newal.addAnnotation(viewport.getAlignment()
+ .getAlignmentAnnotation()[i]);
}
}
}
AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
- newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+ newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel,
newaf.alignPanel.av.getSequenceSetId());
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
+ final AlignmentPanel ap = alignPanel;
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
- alignPanel.setOverviewPanel(null);
+ if (ap != null)
+ {
+ ap.setOverviewPanel(null);
+ }
};
});
{
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
+ viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background"));
+ }
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs.setConservationApplied(true);
+ viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
-
}
else
{
- cs.setConservation(null);
+ cs.setConservationApplied(false);
}
-
- cs.setConsensus(viewport.hconsensus);
-
}
viewport.setGlobalColourScheme(cs);
- if (viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(viewport.hiddenRepSequences),
- sg.getWidth());
- }
- else
- {
- try
- {
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.hiddenRepSequences), 0,
- sg.getWidth()));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(viewport.hiddenRepSequences), 0,
- viewport.alignment.getWidth() - 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- }
- }
-
if (alignPanel.getOverviewPanel() != null)
{
alignPanel.getOverviewPanel().updateOverviewImage();
}
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sequenceColoursChanged(
- alignPanel);
+ .getStructureSelectionManager(viewport.applet)
+ .sequenceColoursChanged(alignPanel);
alignPanel.paintAlignment(true);
}
protected void modifyPID_actionPerformed()
{
if (viewport.getAbovePIDThreshold()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
viewport.getGlobalColourScheme(), "Background");
protected void modifyConservation_actionPerformed()
{
if (viewport.getConservationSelected()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme, "Background");
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
public void PCAMenuItem_actionPerformed()
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
void NewTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
if ((viewport.getSelectionGroup() != null && viewport
.getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null && viewport.alignment
- .getHeight() > 1))
+ || (viewport.getAlignment().getHeight() > 1))
{
final TreePanel tp = new TreePanel(alignPanel, type, pwType);
void loadTree_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your Newick tree file here.");
+ cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
}
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
.sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
- viewport.alignment));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
sortByTreeMenu.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
sortByTree(treePanel, title); // treePanel.getTitle());
treePanel.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowOpened(WindowEvent e)
{
if (viewport.sortByTree)
super.windowOpened(e);
}
+ @Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
};
});
}
+
public boolean sortBy(AlignmentOrder alorder, String undoname)
{
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
if (viewport.applet.debug)
{
- System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
+ System.err.println("Sorting " + alorder.getOrder().size()
+ + " in alignment '" + getTitle() + "'");
}
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
- if (undoname!=null)
+ if (undoname != null)
{
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
}
alignPanel.paintAlignment(true);
return true;
}
+
protected void documentation_actionPerformed()
{
- showURL("http://www.jalview.org/help.html", "HELP");
+ alignPanel.av.applet.openJalviewHelpUrl();
}
protected void about_actionPerformed()
this.builddate = builddate;
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.white);
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("JalviewLite - Release " + version, x, y += fh);
+ g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: " + builddate, x, y += fh);
+ g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
g.drawString(
- "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
+ MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
- g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
g.drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ MessageManager.getString("label.jalview_dev_managers"),
x, y += fh);
g.drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ MessageManager.getString("label.jalview_distribution_lists"),
x, y += fh);
- g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
g.drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ MessageManager.getString("label.jalview_cite_1_authors"),
x, y += fh);
g.drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ MessageManager.getString("label.jalview_cite_1_title"),
x, y += fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
}
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
}
}
else
{
- try
- {
- if (url.indexOf(":") == -1)
- {
- // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
- // form valid URL
- if (url.indexOf("/") == 0)
- {
- String codebase = viewport.applet.getCodeBase().toString();
- url = codebase.substring(0, codebase.length()
- - viewport.applet.getCodeBase().getFile().length())
- + url;
- }
- else
- {
- url = viewport.applet.getCodeBase() + url;
- }
- System.out.println("Show url (prepended codebase): " + url);
- }
- else
- {
- System.out.println("Show url: " + url);
- }
- if (url.indexOf("javascript:") == 0)
- {
- // no target for the javascript context
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url));
- }
- else
- {
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url), target);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ viewport.applet.showURL(url, target);
}
}
MenuBar alignFrameMenuBar = new MenuBar();
- Menu fileMenu = new Menu("File");
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem loadApplication = new MenuItem("View in Full Application");
+ MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+ MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+ MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
- MenuItem outputFeatures = new MenuItem("Export Features ...");
+ MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+ MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
- MenuItem closeMenuItem = new MenuItem("Close");
+ MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
- Menu editMenu = new Menu("Edit");
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- Menu viewMenu = new Menu("View");
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
- Menu colourMenu = new Menu("Colour");
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
- Menu calculateMenu = new Menu("Calculate");
+ Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+ MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+ MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
MenuItem buriedColour = new MenuItem();
+ MenuItem purinePyrimidineColour = new MenuItem();
+
+ MenuItem RNAHelixColour = new MenuItem();
+
MenuItem userDefinedColour = new MenuItem();
MenuItem PIDColour = new MenuItem();
MenuItem BLOSUM62Colour = new MenuItem();
+ MenuItem tcoffeeColour = new MenuItem();
+
MenuItem njTreeBlosumMenuItem = new MenuItem();
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem("Alignment Properties...");
+ MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
MenuItem grpsFromSelection = new MenuItem();
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
MenuItem delete = new MenuItem();
MenuItem copy = new MenuItem();
CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
"Autocalculate Consensus", true);
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+ "Sort Alignment With New Tree", true);
+
Menu sortByTreeMenu = new Menu();
Menu sort = new Menu();
CheckboxMenuItem seqLimits = new CheckboxMenuItem();
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
+
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
- Menu autoAnnMenu=new Menu();
- CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
+
+ Menu autoAnnMenu = new Menu();
+
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
+
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+
CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+
CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+
CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+
private void jbInit() throws Exception
{
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
+ remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
+ remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+ removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
+ removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
+ viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
+ viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
+ sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
+ sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
+ sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
+ removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
+ PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
averageDistanceTreeMenuItem
- .setLabel("Average Distance Using % Identity");
+ .setLabel(MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ clustalColour.setLabel(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
+ helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
+ strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
+ purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
+ RNAHelixColour.addActionListener(this);
+ userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
+ PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
+ BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(this);
+ tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
+ // provided
+ tcoffeeColour.addActionListener(this);
avDistanceTreeBlosumMenuItem
- .setLabel("Average Distance Using BLOSUM62");
+ .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
+ njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
+ annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
+ colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show nonconserved");
+ displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
+ overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
undoMenuItem.addActionListener(this);
redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
+ conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
+ wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
+ renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
+ findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel("Above Identity Threshold");
+ abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
+ nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
+ deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
+ grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
+ createGroup.setLabel(MessageManager.getString("action.create_group"));
+ unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ copy.setLabel(MessageManager.getString("action.copy"));
copy.addActionListener(this);
- cut.setLabel("Cut");
+ cut.setLabel(MessageManager.getString("action.cut"));
cut.addActionListener(this);
- delete.setLabel("Delete");
+ delete.setLabel(MessageManager.getString("action.delete"));
delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
+ applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
+ font.setLabel(MessageManager.getString("action.font"));
font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
scaleAbove.setState(true);
scaleAbove.setEnabled(false);
scaleAbove.addItemListener(this);
scaleLeft.setEnabled(false);
scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
scaleLeft.addItemListener(this);
scaleRight.setEnabled(false);
scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
+ modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
+ sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
+ sort.setLabel(MessageManager.getString("action.sort"));
+ calculate.setLabel(MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
- inputText.setLabel("Input from textbox");
+ sortByTree.addItemListener(this);
+ inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel("Centre column labels");
+ centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel("Automatic Scrolling");
+ followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
+ helpMenu.setLabel(MessageManager.getString("action.help"));
+ documentation.setLabel(MessageManager.getString("label.documentation"));
documentation.addActionListener(this);
- about.setLabel("About...");
+ about.setLabel(MessageManager.getString("label.about"));
about.addActionListener(this);
seqLimits.setState(true);
- seqLimits.setLabel("Show Sequence Limits");
+ seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
- featureSettings.setLabel("Feature Settings...");
+ featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
featureSettings.addActionListener(this);
- sequenceFeatures.setLabel("Sequence Features");
+ sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
- annotationColour.setLabel("by Annotation...");
+ annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel("Invert Sequence Selection");
- invertColSel.setLabel("Invert Column Selection");
- menu1.setLabel("Show");
- showColumns.setLabel("All Columns ");
- showSeqs.setLabel("All Sequences");
- menu2.setLabel("Hide");
- hideColumns.setLabel("Selected Columns");
- hideSequences.setLabel("Selected Sequences");
- hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
- hideAllSelection.setLabel("Selected Region");
- showAllHidden.setLabel("All Sequences and Columns");
- showGroupConsensus.setLabel("Group Consensus");
- showGroupConservation.setLabel("Group Conservation");
- showConsensusHistogram.setLabel("Show Consensus Histogram");
- showSequenceLogo.setLabel("Show Consensus Logo");
- applyAutoAnnotationSettings.setLabel("Apply to all groups");
+ invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
+ invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
+ menu1.setLabel(MessageManager.getString("action.show"));
+ showColumns.setLabel(MessageManager.getString("label.all_columns"));
+ showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
+ menu2.setLabel(MessageManager.getString("action.hide"));
+ hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
+ showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel("Autocalculated Annotation");
-
+ autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
+
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
showGroupConservation.addItemListener(this);
showConsensusHistogram.addItemListener(this);
showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+
applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
+ formatMenu.setLabel(MessageManager.getString("action.format"));
+ selectMenu.setLabel(MessageManager.getString("action.select"));
+ newView.setLabel(MessageManager.getString("action.new_view"));
newView.addActionListener(this);
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(RNAHelixColour);
calculateMenu.add(sort);
calculateMenu.add(calculate);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
this.add(statusBar, BorderLayout.SOUTH);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
}
+
+ public void setStatus(String string) {
+ statusBar.setText(string);
+ };
+
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
final AlignFrame me = this;
viewport.applet.addFocusListener(new FocusListener()
{
-
+
@Override
public void focusLost(FocusEvent e)
{
- if (me.viewport.applet.currentAlignFrame==me) {
- me.viewport.applet.currentAlignFrame = null;
- }}
-
+ if (me.viewport.applet.currentAlignFrame == me)
+ {
+ me.viewport.applet.currentAlignFrame = null;
+ }
+ }
+
@Override
public void focusGained(FocusEvent e)
{
// TODO: search for a jmv that involves viewer
if (jmv == null)
{ // create a new viewer/jalview binding.
- jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
+ { seqs });
}
return jmv;
}
+ /**
+ * bind a pdb file to a sequence in the current view
+ *
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or sequenceId location
+ * fails.
+ */
public boolean addPdbFile(String sequenceId, String pdbEntryString,
String pdbFile)
{
if (applet.useXtrnalSviewer)
{
// register the association(s) and quit, don't create any windows.
- StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
+ if (StructureSelectionManager.getStructureSelectionManager(applet)
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ {
+ System.err.println("Failed to map " + pdb.getFile() + " ("
+ + protocol + ") to any sequences");
+ }
return;
}
if (applet.isAlignPdbStructures() && applet.jmolAvailable)
}
/**
- * modify the current selection, providing the user has not made a selection already.
- * @param sel - sequences from this alignment
- * @param csel - columns to be selected on the alignment
+ * modify the current selection, providing the user has not made a selection
+ * already.
+ *
+ * @param sel
+ * - sequences from this alignment
+ * @param csel
+ * - columns to be selected on the alignment
*/
public void select(SequenceGroup sel, ColumnSelection csel)
{
alignPanel.seqPanel.selection(sel, csel, null);
}
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.seqPanel.scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.seqPanel.scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.seqPanel.scrollToColumn(column);
+ }
+
+ /**
+ * @return the alignments unique ID.
+ */
+ public String getSequenceSetId()
+ {
+ return viewport.getSequenceSetId();
+ }
+
+ /**
+ * Load the (T-Coffee) score file from the specified url
+ *
+ * @param source
+ * File/URL/T-COFFEE score file contents
+ * @throws IOException
+ * @return true if alignment was annotated with data from source
+ */
+ public boolean loadScoreFile(String source) throws IOException
+ {
+
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,
+ AppletFormatAdapter.checkProtocol(source));
+ if (!file.isValid())
+ {
+ // TODO: raise dialog for gui
+ System.err.println("Problems parsing T-Coffee scores: "
+ + file.getWarningMessage());
+ System.err.println("Origin was:\n" + source);
+ return false;
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if ((aln = viewport.getAlignment()) != null
+ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
+ .getWidth()))
+ {
+ // TODO: raise a dialog box here rather than bomb out.
+ System.err
+ .println("The scores matrix does not match the alignment dimensions");
+
+ }
+
+ // TODO add parameter to indicate if matching should be done
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))
+ {
+ alignPanel.fontChanged();
+ tcoffeeColour.setEnabled(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ return true;
+ }
+ else
+ {
+ System.err.println("Problems resolving T-Coffee scores:");
+ if (file.getWarningMessage() != null)
+ {
+ System.err.println(file.getWarningMessage());
+ }
+ }
+ return false;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff