/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.io.*;
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-
-public class AlignFrame
- extends Frame implements ActionListener,
- ItemListener, KeyListener, MouseListener
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+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.AlignmentAnnotation;
+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.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.FlowLayout;
+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.Panel;
+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.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import org.jmol.viewer.Viewer;
+
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+ ItemListener, KeyListener, AlignViewControllerGuiI
{
+ public AlignViewControllerI avc;
+
public AlignmentPanel alignPanel;
+
public AlignViewport viewport;
- int DEFAULT_WIDTH = 700;
- int DEFAULT_HEIGHT = 500;
+
+ // width and height may be overridden by applet parameters
+ int frameWidth = 700;
+
+ int frameHeight = 500;
String jalviewServletURL;
- public AlignFrame(AlignmentI al,
- jalview.bin.JalviewLite applet,
- String title,
- boolean embedded)
+ /*
+ * Flag for showing autocalculated consensus above or below other consensus
+ * rows
+ */
+ private boolean showAutoCalculatedAbove;
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ /**
+ * Constructor that creates the frame and adds it to the display.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded)
+ {
+ this(al, applet, title, embedded, true);
+ }
+
+ /**
+ * Constructor that optionally allows the frame to be displayed or only
+ * created.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ * @param addToDisplay
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded, boolean addToDisplay)
+ {
+ this(al, null, null, applet, title, embedded, addToDisplay);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded)
{
+ this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ }
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded, boolean addToDisplay)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
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);
+ frameWidth = width;
+ }
+ param = applet.getParameter("windowHeight");
+ if (param != null)
+ {
+ int height = Integer.parseInt(param);
+ frameHeight = height;
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
viewport = new AlignViewport(al, applet);
- alignPanel = new AlignmentPanel(this, viewport);
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ if (columnSelection != null)
+ {
+ viewport.setColumnSelection(columnSelection);
+ }
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
+
+ alignPanel = new AlignmentPanel(this, viewport);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
- annotationPanelMenuItem.setState(viewport.showAnnotation);
-
- seqLimits.setState(viewport.showJVSuffix);
+ displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
+ followMouseOverFlag.setState(viewport.isFollowHighlight());
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());
+ showGroupConservation.setState(viewport.isShowGroupConservation());
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+ annotationPanelMenuItem.setState(viewport.isShowAnnotation());
+ showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAlignmentAnnotations.setState(true);
+ showSequenceAnnotations.setState(false);
+
+ seqLimits.setState(viewport.getShowJVSuffix());
if (applet != null)
{
{
sortPairwiseMenuItem_actionPerformed();
}
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
}
param = applet.getParameter("wrap");
wrapMenuItem_actionPerformed();
}
}
-
- try
+ param = applet.getParameter("centrecolumnlabels");
+ if (param != null)
{
- 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;
- }
+ centreColumnLabelFlag.setState(true);
+ centreColumnLabelFlag_stateChanged();
}
- catch (Exception ex)
- {}
}
-
- //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
+ if (viewport.getAlignment().isNucleotide())
+ {
+ viewport.updateStrucConsensus(alignPanel);
+ if (viewport.getAlignment().hasRNAStructure())
+ {
+ 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
this.addKeyListener(this);
alignPanel.seqPanel.seqCanvas.addKeyListener(this);
alignPanel.idPanel.idCanvas.addKeyListener(this);
alignPanel.scalePanel.addKeyListener(this);
alignPanel.annotationPanel.addKeyListener(this);
+ alignPanel.annotationPanelHolder.addKeyListener(this);
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+ alignPanel.alabels.addKeyListener(this);
- if (embedded)
- {
- setEmbedded();
- }
- else
+ setAnnotationsVisibility();
+
+ if (addToDisplay)
{
- add(alignPanel, BorderLayout.CENTER);
- jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ addToDisplay(embedded);
}
- alignPanel.validate();
+ }
+
+ /**
+ * @param embedded
+ */
+ public void addToDisplay(boolean embedded)
+ {
+ createAlignFrameWindow(embedded);
+ validate();
+ alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
}
}
/**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
+ * 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
*/
- 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)
{
- 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);
- }
- catch (Exception ex)
+ Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours();
+ boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
+ "relaxedidmatch", false);
+ featuresFile = new FeaturesFile(file, type).parse(
+ viewport.getAlignment(), colours, true, relaxedIdMatching);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
if (featuresFile)
{
- if (featureLinks.size() > 0)
+ if (autoenabledisplay)
{
- alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureLinks = featureLinks;
+ viewport.setShowSequenceFeatures(true);
+ sequenceFeatures.setState(true);
+ }
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
+ if (viewport.featureSettings != null)
+ {
+ viewport.featureSettings.refreshTable();
}
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
alignPanel.paintAlignment(true);
+ statusBar.setText(MessageManager
+ .getString("label.successfully_added_features_alignment"));
}
-
+ return featuresFile;
}
+ @Override
public void keyPressed(KeyEvent evt)
{
- if (viewport.cursorMode &&
- ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
- evt.getKeyCode() <= KeyEvent.VK_9)
- ||
- (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
- evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
- )
- && Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
+ if (viewport.cursorMode
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && Character.isDigit(evt.getKeyChar()))
+ {
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed();
- break;
- case KeyEvent.VK_X:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- cut_actionPerformed();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- if (evt.isControlDown() || evt.isMetaDown())
- {
- copy_actionPerformed();
- }
- break;
- case KeyEvent.VK_V:
- if (evt.isControlDown())
- {
- paste(evt.isShiftDown());
- }
- break;
- case KeyEvent.VK_A:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- {
- moveSelectedSequences(false);
- }
- break;
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed();
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- {
- moveSelectedSequences(true);
- }
- break;
+ alignPanel.alabels.cancelDrag();
+ break;
+ case KeyEvent.VK_X:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ cut_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ copy_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_V:
+ if (evt.isControlDown())
+ {
+ paste(evt.isShiftDown());
+ }
+ break;
+ case KeyEvent.VK_A:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ {
+ moveSelectedSequences(false);
+ }
+ break;
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( -1, 0);
- break;
+ case KeyEvent.VK_UP:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, -1);
+ }
+ else
+ {
+ moveSelectedSequences(true);
+ }
+ break;
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( 1, 0);
- break;
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
+ else
+ {
+ alignPanel.seqPanel.moveCursor(-1, 0);
+ }
+ break;
- case KeyEvent.VK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown()
- );
- }
- break;
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
+ else
+ {
+ alignPanel.seqPanel.moveCursor(1, 0);
+ }
+ break;
- case KeyEvent.VK_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
- }
- else
- {
- cut_actionPerformed();
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- break;
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ else
+ {
+ cut_actionPerformed();
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ break;
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
- }
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
- }
- break;
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
- case KeyEvent.VK_F2:
- viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is " +
- (viewport.cursorMode ? "on" : "off"));
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- break;
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
- case KeyEvent.VK_F:
- if (evt.isControlDown())
- {
- findMenuItem_actionPerformed();
- }
- break;
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ break;
- case KeyEvent.VK_H:
+ case KeyEvent.VK_F:
+ if (evt.isControlDown())
{
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- boolean hide = false;
- SequenceGroup sg = viewport.getSelectionGroup();
+ findMenuItem_actionPerformed();
+ }
+ break;
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
- {
- hide = true;
- viewport.hideAllSelectedSeqs();
- }
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- viewport.showAllHiddenSeqs();
- }
- }
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- viewport.hideSelectedColumns();
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- viewport.showAllHiddenColumns();
- }
- }
- break;
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.getWrapAlignment())
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
}
+ break;
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.getWrapAlignment())
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
+
+ case KeyEvent.VK_Z:
+ if (evt.isControlDown())
+ {
+ undoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_Y:
+ if (evt.isControlDown())
+ {
+ redoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_L:
+ if (evt.isControlDown())
+ {
+ trimAlignment(true);
+ }
+ break;
+
+ case KeyEvent.VK_R:
+ if (evt.isControlDown())
+ {
+ trimAlignment(false);
+ }
+ break;
+
+ case KeyEvent.VK_E:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
{
- alignPanel.scrollUp(true);
+ this.removeAllGapsMenuItem_actionPerformed();
}
else
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ removeGappedColumnMenuItem_actionPerformed();
}
- break;
-
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ }
+ break;
+ case KeyEvent.VK_I:
+ if (evt.isControlDown())
+ {
+ if (evt.isAltDown())
{
- alignPanel.scrollUp(false);
+ invertColSel_actionPerformed();
}
else
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ invertSequenceMenuItem_actionPerformed();
}
- break;
+ }
+ break;
- case KeyEvent.VK_Z:
- if (evt.isControlDown())
+ case KeyEvent.VK_G:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
{
- undoMenuItem_actionPerformed();
+ this.unGroup_actionPerformed();
}
- break;
-
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
+ else
{
- redoMenuItem_actionPerformed();
+ this.createGroup_actionPerformed();
}
- break;
+ }
+ break;
- case KeyEvent.VK_L:
- if (evt.isControlDown())
- {
- trimAlignment(true);
- }
- break;
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
- case KeyEvent.VK_R:
- if (evt.isControlDown())
- {
- trimAlignment(false);
- }
- break;
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
- case KeyEvent.VK_E:
- if (evt.isControlDown())
- {
- if (evt.isShiftDown())
- {
- this.removeAllGapsMenuItem_actionPerformed();
- }
- else
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- }
- break;
- case KeyEvent.VK_I:
- if (evt.isControlDown())
- {
- if (evt.isAltDown())
- {
- viewport.invertColumnSelection();
- }
- else
- {
- this.invertSequenceMenuItem_actionPerformed();
- }
- }
- break;
+ }
+ alignPanel.paintAlignment(true);
+ }
- case KeyEvent.VK_U:
- if (evt.isControlDown())
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // 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.hasSelectedColumns()
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
{
- this.deleteGroups_actionPerformed();
+ invertSequenceMenuItem_actionPerformed();
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
}
- break;
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection and indicate it should be hidden.
+ invertColSel_actionPerformed();
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
+ {
+ hide = true;
+ viewport.hideAllSelectedSeqs();
+ }
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
+ {
+ viewport.showAllHiddenSeqs();
+ }
+ }
- case KeyEvent.VK_T:
- if (evt.isControlDown())
+ if (toggleCols)
+ {
+ if (viewport.hasSelectedColumns())
+ {
+ viewport.hideSelectedColumns();
+ if (!toggleSeqs)
{
- newView();
+ viewport.setSelectionGroup(sg);
}
- break;
-
+ }
+ else if (!hide)
+ {
+ viewport.showAllHiddenColumns();
+ }
+ viewport.sendSelection();
}
- alignPanel.paintAlignment(true);
}
+ @Override
public void keyReleased(KeyEvent evt)
- {}
+ {
+ }
+ @Override
public void keyTyped(KeyEvent evt)
- {}
+ {
+ }
+ @Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == colourTextMenuItem)
+ final Object source = evt.getSource();
+ if (source == displayNonconservedMenuItem)
+ {
+ displayNonconservedMenuItem_actionPerformed();
+ }
+ else if (source == colourTextMenuItem)
{
colourTextMenuItem_actionPerformed();
}
- else if (evt.getSource() == wrapMenuItem)
+ else if (source == wrapMenuItem)
{
wrapMenuItem_actionPerformed();
}
- else if (evt.getSource() == scaleAbove)
+ else if (source == scaleAbove)
{
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
- else if (evt.getSource() == scaleLeft)
+ else if (source == scaleLeft)
{
viewport.setScaleLeftWrapped(scaleLeft.getState());
}
- else if (evt.getSource() == scaleRight)
+ else if (source == scaleRight)
{
viewport.setScaleRightWrapped(scaleRight.getState());
}
- else if (evt.getSource() == seqLimits)
+ else if (source == seqLimits)
{
seqLimits_itemStateChanged();
}
- else if (evt.getSource() == viewBoxesMenuItem)
+ else if (source == viewBoxesMenuItem)
{
viewport.setShowBoxes(viewBoxesMenuItem.getState());
}
- else if (evt.getSource() == viewTextMenuItem)
+ else if (source == viewTextMenuItem)
{
viewport.setShowText(viewTextMenuItem.getState());
}
- else if (evt.getSource() == renderGapsMenuItem)
+ else if (source == renderGapsMenuItem)
{
viewport.setRenderGaps(renderGapsMenuItem.getState());
}
- else if (evt.getSource() == annotationPanelMenuItem)
+ else if (source == annotationPanelMenuItem)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ boolean showAnnotations = annotationPanelMenuItem.getState();
+ showAlignmentAnnotations.setEnabled(showAnnotations);
+ showSequenceAnnotations.setEnabled(showAnnotations);
+ viewport.setShowAnnotation(showAnnotations);
+ alignPanel.setAnnotationVisible(showAnnotations);
}
- else if (evt.getSource() == sequenceFeatures)
+ else if (source == sequenceFeatures)
{
- viewport.showSequenceFeatures(sequenceFeatures.getState());
+ viewport.setShowSequenceFeatures(sequenceFeatures.getState());
alignPanel.seqPanel.seqCanvas.repaint();
}
- else if (evt.getSource() == conservationMenuItem)
+ else if (source == showAlignmentAnnotations)
+ {
+ setAnnotationsVisibility();
+ }
+ else if (source == showSequenceAnnotations)
+ {
+ setAnnotationsVisibility();
+ }
+ else if (source == sortAnnBySequence)
+ {
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ setViewportAnnotationOrder();
+ }
+ else if (source == sortAnnByLabel)
+ {
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ setViewportAnnotationOrder();
+ }
+ else if (source == showAutoFirst)
+ {
+ showAutoLast.setState(!showAutoFirst.getState());
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ setViewportAnnotationOrder();
+ }
+ else if (source == showAutoLast)
+ {
+ showAutoFirst.setState(!showAutoLast.getState());
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ setViewportAnnotationOrder();
+ }
+ else if (source == conservationMenuItem)
{
conservationMenuItem_actionPerformed();
}
- else if (evt.getSource() == abovePIDThreshold)
+ else if (source == abovePIDThreshold)
{
abovePIDThreshold_actionPerformed();
}
- else if (evt.getSource() == applyToAllGroups)
+ else if (source == applyToAllGroups)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
}
- else if (evt.getSource() == autoCalculate)
+ else if (source == autoCalculate)
{
- viewport.autocalculateConsensus = autoCalculate.getState();
+ viewport.autoCalculateConsensus = autoCalculate.getState();
+ }
+ else if (source == sortByTree)
+ {
+ viewport.sortByTree = sortByTree.getState();
+ }
+ else if (source == this.centreColumnLabelFlag)
+ {
+ centreColumnLabelFlag_stateChanged();
+ }
+ else if (source == this.followMouseOverFlag)
+ {
+ mouseOverFlag_stateChanged();
+ }
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
}
-
alignPanel.paintAlignment(true);
}
+ /**
+ * Set the visibility state of sequence-related and/or alignment-related
+ * annotations depending on checkbox selections, and repaint.
+ *
+ * @param visible
+ */
+ private void setAnnotationsVisibility()
+ {
+ boolean showForAlignment = showAlignmentAnnotations.getState();
+ boolean showForSequences = showSequenceAnnotations.getState();
+ if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean visible = (aa.sequenceRef == null ? showForAlignment
+ : showForSequences);
+ aa.visible = visible;
+ }
+ }
+ alignPanel.validateAnnotationDimensions(true);
+ validate();
+ repaint();
+ }
+
+ private void setAnnotationSortOrder(SequenceAnnotationOrder order)
+ {
+ this.annotationSortOrder = order;
+ }
+
+ /**
+ * Set flags on the viewport that control annotation ordering
+ */
+ private void setViewportAnnotationOrder()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
+ }
+
+ private void setShowAutoCalculatedAbove(boolean showAbove)
+ {
+ this.showAutoCalculatedAbove = showAbove;
+ }
+
+ private void mouseOverFlag_stateChanged()
+ {
+ viewport.setFollowHighlight(followMouseOverFlag.getState());
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
+ }
+
+ private void centreColumnLabelFlag_stateChanged()
+ {
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();
+ this.alignPanel.annotationPanel.repaint();
+ }
+
+ @Override
public void actionPerformed(ActionEvent evt)
{
+ viewport.applet.currentAlignFrame = this;
+
Object source = evt.getSource();
if (source == inputText)
{
delete_actionPerformed();
}
+ else if (source == grpsFromSelection)
+ {
+ makeGrpsFromSelection_actionPerformed();
+ }
else if (source == deleteGroups)
{
deleteGroups_actionPerformed();
else if (source == invertSequenceMenuItem)
{
invertSequenceMenuItem_actionPerformed();
+ // uncomment to slave sequence selections in split frame
+ // viewport.sendSelection();
}
else if (source == invertColSel)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
{
}
else if (source == newView)
{
- newView();
+ newView(null);
}
else if (source == showColumns)
{
viewport.showAllHiddenColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ // uncomment if we want to slave sequence selections in split frame
+ // viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
+ }
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
+ {
+ viewport.hideAllSelectedSeqs();
+ alignPanel.paintAlignment(true);
+ // uncomment if we want to slave sequence selections in split frame
+ // viewport.sendSelection();
+ }
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
+ alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
- else if (source == hideSequences && viewport.getSelectionGroup() != null)
+ else if (source == hideAllSelection)
{
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ viewport.sendSelection();
+ }
+ else if (source == showAllHidden)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ viewport.sendSelection();
+ }
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
}
else if (source == featureSettings)
{
new FeatureSettings(alignPanel);
}
- else if(source== alProperties)
+ else if (source == alProperties)
{
- StringBuffer contents = new StringBuffer();
-
- float avg = 0;
- int min=Integer.MAX_VALUE, max=0;
- for(int i=0; i<viewport.alignment.getHeight(); i++)
- {
- int size = viewport.alignment.getSequenceAt(i).getEnd()
- -viewport.alignment.getSequenceAt(i).getStart();
- avg += size;
- if(size>max)
- max = size;
- if(size<min)
- min = size;
- }
- avg = avg/(float)viewport.alignment.getHeight();
-
- contents.append("\nSequences: "+ viewport.alignment.getHeight());
- contents.append("\nMinimum Sequence Length: "+min);
- contents.append("\nMaximum Sequence Length: "+max);
- contents.append("\nAverage Length: "+(int)avg);
-
- if (((Alignment)viewport.alignment).alignmentProperties != null)
- {
- Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
- Enumeration en = props.keys();
- while(en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- contents.append("\n"+key+"\t"+props.get(key));
- }
- }
-
- 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);
+ StringBuffer contents = new jalview.io.AlignmentProperties(
+ 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, 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 == RNAInteractionColour)
+ // {
+ // changeColour(new RNAInteractionColourScheme());
+ // }
+ 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);
}
+ else if (source == annotationColumnSelection)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
else if (source == sortPairwiseMenuItem)
{
sortPairwiseMenuItem_actionPerformed();
{
sortIDMenuItem_actionPerformed();
}
+ else if (source == sortLengthMenuItem)
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
else if (source == sortGroupMenuItem)
{
sortGroupMenuItem_actionPerformed();
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)
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- "Alignment output - " + e.getActionCommand(),
- 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
- viewport.getAlignment(),
- viewport.showJVSuffix));
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
+
+ FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
+ e.getActionCommand(), viewport.getAlignment(),
+ viewport.getShowJVSuffix()));
}
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);
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(viewport);
if (displayTextbox)
{
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
- "Annotations",
- 600, 500);
+ MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
return annotation;
}
+ private Map<String, FeatureColourI> getDisplayedFeatureCols()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
+ FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(
- viewport.alignment.getSequencesArray(),
- viewport.featuresDisplayed);
+ features = formatter.printJalviewFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols());
}
else
{
- features = new FeaturesFile().printGFFFormat(
- viewport.alignment.getSequencesArray(),
- viewport.featuresDisplayed);
+ features = formatter.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);
-
+ MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
+ else
+ {
+ if (features == null)
+ {
+ features = "";
+ }
+ }
return features;
}
{
StringBuffer url = new StringBuffer(jalviewServletURL);
- url.append("?open=" +
- appendProtocol(viewport.applet.getParameter("file")));
+ // allow servlet parameters to be passed in applet parameter
+ String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
+ : "?";
+ url.append(firstSep);
+
+ url.append("open="
+ + appendProtocol(viewport.applet.getParameter("file")));
if (viewport.applet.getParameter("features") != null)
{
if (viewport.applet.getParameter("defaultColour") != null)
{
- url.append("&colour=" +
- removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
- );
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("defaultColour")));
}
if (viewport.applet.getParameter("userDefinedColour") != null)
{
- url.append("&colour=" +
- removeWhiteSpace(viewport.applet.getParameter(
- "userDefinedColour"))
- );
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("userDefinedColour")));
}
- if (viewport.applet.getParameter("tree")!=null)
+ if (viewport.applet.getParameter("tree") != null)
{
- url.append("&tree="+appendProtocol(viewport.applet.getParameter("tree")));
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("tree")));
}
- if (viewport.applet.getParameter("treeFile")!=null)
+ if (viewport.applet.getParameter("treeFile") != null)
{
- url.append("&tree="+appendProtocol(viewport.applet.getParameter("treeFile")));
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("treeFile")));
}
showURL(url.toString(), "FULL_APP");
try
{
new URL(url);
+ url = URLEncoder.encode(url);
}
+ /*
+ * When we finally deprecate 1.1 compatibility, we can start to use
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
+ * ex.printStackTrace(); }
+ */
catch (java.net.MalformedURLException ex)
{
url = viewport.applet.getCodeBase() + url;
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()
{
- if (viewport.historyList.size() > 0)
+ if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel("Undo " + command.getDescription());
+ CommandI command = viewport.getHistoryList().peek();
+ undoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.undo_command",
+ new Object[] { command.getDescription() }));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
}
- if (viewport.redoList.size() > 0)
+ if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel("Redo " + command.getDescription());
+ CommandI command = viewport.getRedoList().peek();
+ redoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.redo_command",
+ new Object[] { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
}
}
+ /**
+ * TODO: JAL-1104
+ */
+ @Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.removeAllElements();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.updateHiddenColumns();
}
}
+
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed()
{
- if (viewport.historyList.size() < 1)
+ if (viewport.getHistoryList().isEmpty())
{
return;
}
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
+ CommandI command = viewport.getHistoryList().pop();
+ viewport.addToRedoList(command);
command.undoCommand(null);
- AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ AlignmentViewport originalSource = getOriginatingSource(command);
+ // 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!
- *
- * @param e DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed()
{
- if (viewport.redoList.size() < 1)
+ if (viewport.getRedoList().isEmpty())
{
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
+ CommandI command = viewport.getRedoList().pop();
+ viewport.addToHistoryList(command);
command.doCommand(null);
- AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ AlignmentViewport originalSource = getOriginatingSource(command);
+ // 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)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
- //For sequence removal and addition, we need to fire
- //the property change event FROM the viewport where the
- //original alignment was altered
+ 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
AlignmentI al = null;
if (command instanceof EditCommand)
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components
- .get(viewport.getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
for (int i = 0; i < comps.size(); i++)
{
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;
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
break;
}
}
if (originalSource == null)
{
- //The original view is closed, we must validate
- //the current view against the closed view first
+ // The original view is closed, we must validate
+ // the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
return originalSource;
}
+ /**
+ * Move the currently selected sequences up or down one position in the
+ * alignment
+ *
+ * @param up
+ */
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
{
return;
}
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ up ? null : viewport.getHiddenRepSequences(), up);
+ alignPanel.paintAlignment(true);
- 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
+ /*
+ * Also move cDNA/protein complement sequences
+ */
+ AlignViewportI complement = viewport.getCodingComplement();
+ if (complement != null)
{
- 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);
- }
+ SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
+ viewport, complement);
+ complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
+ up ? null : complement.getHiddenRepSequences(), up);
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
}
-
- alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
- if(viewport.cursorMode)
+ List<SequenceI> sg = new Vector<SequenceI>();
+ if (viewport.cursorMode)
+ {
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
- sg.addElement(viewport.alignment.getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.getHiddenRepSequences());
}
- else if(viewport.getSelectionGroup()!=null
- && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
- }
- if(sg.size()<1)
+ 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)
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs2, seqs1, size,
- viewport.getGapCharacter()
- );
+ {
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
+ }
else
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs1, seqs2, size,
- viewport.getGapCharacter()
- );
+ {
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor( -size, 0);
+ {
+ alignPanel.seqPanel.moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
-
boolean appendHistoryItem = false;
- if(viewport.historyList!=null
- && viewport.historyList.size()>0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque<CommandI> historyList = viewport.getHistoryList();
+ if (historyList != null && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc.appendSlideCommand(
- (SlideSequencesCommand)viewport.historyList.peek())
- ;
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) historyList
+ .peek());
}
- if(!appendHistoryItem)
+ if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
static StringBuffer copiedSequences;
+
static Vector copiedHiddenColumns;
+
protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
- orderedSeqs.put(index + "", 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 < viewport.getColumnSelection().getHiddenColumns().size();
- i++)
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[])
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);
-
- copiedHiddenColumns.addElement(new int[]
- {region[0] - hiddenOffset,
- region[1] - hiddenOffset});
+ copiedHiddenColumns.addElement(new int[] {
+ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
else
while (seq == null)
{
- if (orderedSeqs.containsKey(index + ""))
+ if (orderedSeqs.containsKey(index))
{
- seq = (SequenceI) orderedSeqs.get(index + "");
+ seq = orderedSeqs.get(index);
index++;
-
break;
}
else
}
}
- //FIND START RES
- //Returns residue following index if gap
+ // FIND START RES
+ // Returns residue following index if gap
startRes = seq.findPosition(sg.getStartRes());
- //FIND END RES
- //Need to find the residue preceeding index if gap
+ // FIND END RES
+ // Need to find the residue preceeding index if gap
endRes = 0;
for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
{
ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
+ if (!jalview.util.Comparison.isGap((ch)))
{
endRes++;
}
endRes += seq.getStart() - 1;
}
- copiedSequences.append(seq.getName() + "\t" +
- startRes + "\t" +
- endRes + "\t" +
- seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
+ copiedSequences.append(seq.getName()
+ + "\t"
+ + startRes
+ + "\t"
+ + endRes
+ + "\t"
+ + seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1) + "\n");
}
}
if (newAlignment)
{
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
+ String newtitle = MessageManager
+ .getString("label.copied_sequences");
+ if (getTitle().startsWith(
+ MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
- newtitle = newtitle.concat("- from " + getTitle());
+ newtitle = newtitle.concat(MessageManager.formatMessage(
+ "label.from_msname", new String[] { getTitle() }));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
- viewport.applet,
- newtitle,
- false);
+ viewport.applet, newtitle, false);
if (copiedHiddenColumns != null)
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
}
}
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ frameHeight);
}
else
{
addSequences(newSeqs);
}
- }
- catch (Exception ex)
- {} // could be anything being pasted in here
+ } catch (Exception ex)
+ {
+ } // could be anything being pasted in here
}
{
for (int i = 0; i < seqs.length; i++)
{
- viewport.alignment.addSequence(seqs[i]);
+ viewport.getAlignment().addSequence(seqs[i]);
}
- //!newAlignment
+ // !newAlignment
addHistoryItem(new EditCommand(
- "Add sequences",
- EditCommand.PASTE,
- seqs,
- 0,
- viewport.alignment.getWidth(),
- viewport.alignment)
- );
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
+ 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());
}
seqs.addElement(seq);
}
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
+ /*
+ * If the cut affects all sequences, warn, remove highlighted columns
+ */
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
+ {
+ String title = MessageManager.getString("label.delete_all");
+ Panel infoPanel = new Panel();
+ infoPanel.setLayout(new FlowLayout());
+ infoPanel
+ .add(new Label(MessageManager.getString("warn.delete_all")));
+
+ final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+ dialog.setMainPanel(infoPanel);
+ dialog.ok.setLabel(MessageManager.getString("action.ok"));
+ dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+ dialog.setVisible(true);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+ }
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
}
/*
- //ADD HISTORY ITEM
+ * //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences",
- EditCommand.CUT,
- cut,
- sg.getStartRes(),
- sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
this.setVisible(false);
}
+ viewport.sendSelection();
}
- protected void deleteGroups_actionPerformed()
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
{
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * group conservation toggled.
+ */
+ protected void showGroupConservation_actionPerformed()
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed()
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed()
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ 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 (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()
+ {
+ 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);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void deselectAllSequenceMenuItem_actionPerformed()
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertSequenceMenuItem_actionPerformed()
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ public void invertColSel_actionPerformed()
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
void trimAlignment(boolean trimLeft)
ColumnSelection colSel = viewport.getColumnSelection();
int column;
- if (colSel.size() > 0)
+ if (!colSel.isEmpty())
{
if (trimLeft)
{
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
- 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)))
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
}
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);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ 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);
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "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);
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
- // viewport.getColumnSelection().compensateForEdits(shifts);
+ // viewport.getColumnSelection().compensateForEdits(shifts);
viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
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);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ 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);
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- addHistoryItem(new RemoveGapsCommand("Remove Gaps",
- seqs,
- start, end,
- viewport.alignment));
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.getAlignment()));
viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
new Finder(alignPanel);
}
- public void newView()
+ /**
+ * create a new view derived from the current view
+ *
+ * @param viewtitle
+ * @return frame for the new view
+ */
+ public AlignFrame newView(String viewtitle)
{
AlignmentI newal;
- if (viewport.hasHiddenRows)
+ if (viewport.hasHiddenRows())
{
- newal = new Alignment(viewport.getAlignment().
- getHiddenSequences()
- .getFullAlignment().
- getSequencesArray());
+ 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);
+ 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());
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
- Vector comps = (Vector) PaintRefresher.components.get(viewport.
- getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)
{
}
String title = new String(this.getTitle());
- if (title.indexOf("(View") > -1)
+ if (viewtitle != null)
{
- title = title.substring(0, title.indexOf("(View"));
+ title = viewtitle + " ( " + title + ")";
+ }
+ else
+ {
+ if (title.indexOf("(View") > -1)
+ {
+ title = title.substring(0, title.indexOf("(View"));
+ }
+ title += "(View " + viewSize + ")";
}
-
- title += "(View " + viewSize + ")";
newaf.setTitle(title.toString());
- newaf.viewport.historyList = viewport.historyList;
- newaf.viewport.redoList = viewport.redoList;
+ newaf.viewport.setHistoryList(viewport.getHistoryList());
+ newaf.viewport.setRedoList(viewport.getRedoList());
+ return newaf;
+ }
+
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+ public String[] getFeatureGroups()
+ {
+ FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ /**
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ /**
+ * Change the display state for the given feature groups
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ FeatureRenderer fr = null;
+ this.sequenceFeatures.setState(true);
+ viewport.setShowSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ fr.setGroupVisibility(Arrays.asList(groups), state);
+ alignPanel.seqPanel.seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
}
public void seqLimits_itemStateChanged()
alignPanel.paintAlignment(true);
}
+ protected void displayNonconservedMenuItem_actionPerformed()
+ {
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
protected void wrapMenuItem_actionPerformed()
{
viewport.setWrapAlignment(wrapMenuItem.getState());
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
- overview.getPreferredSize().width,
- overview.getPreferredSize().height + 50);
+ 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);
+ }
};
});
}
- void changeColour(ColourSchemeI cs)
+ @Override
+ public void changeColour(ColourSchemeI cs)
{
- int threshold = 0;
if (cs != 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,
- "Background"));
-
+ 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);
-
alignPanel.paintAlignment(true);
}
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
+ if (viewport.getAbovePIDThreshold()
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
+ if (viewport.getConservationSelected()
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
- "Background");
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0));
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
+
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
public void sortIDMenuItem_actionPerformed()
{
- // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
- // HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
public void sortGroupMenuItem_actionPerformed()
{
- // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
- // HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
public void pairwiseAlignmentMenuItem_actionPerformed()
{
if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() > 1)
+ && viewport.getSelectionGroup().getSize() > 1)
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
public void PCAMenuItem_actionPerformed()
{
- //are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
alignPanel.paintAlignment(true);
}
- if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() < 4 &&
- viewport.getSelectionGroup().getSize() > 0)
- || viewport.getAlignment().getHeight() < 4)
+ if ((viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() < 4 && viewport
+ .getSelectionGroup().getSize() > 0)
+ || viewport.getAlignment().getHeight() < 4)
{
return;
}
try
{
new PCAPanel(viewport);
- }
- catch (java.lang.OutOfMemoryError ex)
+ } catch (java.lang.OutOfMemoryError ex)
{
}
void NewTreePanel(String type, String pwType, String title)
{
- //are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
}
- if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null
- && viewport.alignment.getHeight() > 1))
+ if ((viewport.getSelectionGroup() != null && viewport
+ .getSelectionGroup().getSize() > 1)
+ || (viewport.getAlignment().getHeight() > 1))
{
- final TreePanel tp = new TreePanel(viewport,
- type,
- pwType);
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
addTreeMenuItem(tp, title);
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(viewport,
- 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);
}
- void addTreeMenuItem(final TreePanel treePanel, String title)
+ /**
+ * sort the alignment using the given treePanel
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
+ */
+ public void sortByTree(TreePanel treePanel, String title)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[] { title }), oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
+ * @param treePanel
+ * @param title
+ */
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
{
final MenuItem item = new MenuItem(title);
sortByTreeMenu.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- // HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
- alignPanel.paintAlignment(true);
+ sortByTree(treePanel, title); // treePanel.getTitle());
}
});
treePanel.addWindowListener(new WindowAdapter()
{
+ @Override
+ public void windowOpened(WindowEvent e)
+ {
+ if (viewport.sortByTree)
+ {
+ sortByTree(treePanel, title);
+ }
+ super.windowOpened(e);
+ }
+
+ @Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
});
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting " + alorder.getOrder().size()
+ + " in alignment '" + getTitle() + "'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ 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()
{
- class AboutPanel
- extends Canvas
+ class AboutPanel extends Canvas
{
String version;
- public AboutPanel(String version)
+
+ String builddate;
+
+ public AboutPanel(String version, String builddate)
{
this.version = version;
+ this.builddate = builddate;
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.white);
int fh = fm.getHeight();
int y = 5, x = 7;
g.setColor(Color.black);
+ // 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("Jalview - Release " + version, 200, 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(MessageManager.formatMessage(
+ "label.jaview_build_date", new String[] { builddate }), x,
+ y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
- x, y += fh * 2);
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
- x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
+ x, y += fh * 1.5);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
g.drawString(
- "For any issues relating to Jalview, email help@jalview.org", x,
- y += fh);
- g.drawString("If you use JalView, please cite:", x, y += fh + 8);
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
- x, y += fh);
- g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
- }
- }
-
- String version = "test";
- java.net.URL url = getClass().getResource("/.build_properties");
- if (url != null)
- {
- try
- {
- BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
- String line;
- while ( (line = reader.readLine()) != null)
- {
- if (line.indexOf("VERSION") > -1)
- {
- version = line.substring(line.indexOf("=") + 1);
- }
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
+ MessageManager.getString("label.jalview_dev_managers"), x,
+ y += fh);
+ g.drawString(MessageManager
+ .getString("label.jalview_distribution_lists"), x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"),
+ x, y += fh + 8);
+ g.drawString(
+ MessageManager.getString("label.jalview_cite_1_authors"),
+ x, y += fh);
+ g.drawString(
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
+ x, y += fh);
}
}
Frame frame = new Frame();
- frame.add(new AboutPanel(version));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
}
}
else
{
- try
- {
- System.out.println("Show url: " + url);
- viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
- //////////////////////////////////////////////////////////////////////////////////
- //JBuilder Graphics here
-
- MenuBar alignFrameMenuBar = new MenuBar();
- Menu fileMenu = new Menu("File");
- MenuItem loadApplication = new MenuItem("View in Full Application");
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
- MenuItem loadAnnotations = new MenuItem(
- "Load Features/Annotations ...");
- MenuItem outputFeatures = new MenuItem("Export Features ...");
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
- MenuItem closeMenuItem = new MenuItem("Close");
- Menu editMenu = new Menu("Edit");
- Menu viewMenu = new Menu("View");
- Menu colourMenu = new Menu("Colour");
- Menu calculateMenu = new Menu("Calculate");
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
- MenuItem remove2LeftMenuItem = new MenuItem();
- MenuItem remove2RightMenuItem = new MenuItem();
- MenuItem removeGappedColumnMenuItem = new MenuItem();
- MenuItem removeAllGapsMenuItem = new MenuItem();
- CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
- MenuItem sortPairwiseMenuItem = new MenuItem();
- MenuItem sortIDMenuItem = new MenuItem();
- MenuItem sortGroupMenuItem = new MenuItem();
- MenuItem removeRedundancyMenuItem = new MenuItem();
- MenuItem pairwiseAlignmentMenuItem = new MenuItem();
- MenuItem PCAMenuItem = new MenuItem();
- MenuItem averageDistanceTreeMenuItem = new MenuItem();
- MenuItem neighbourTreeMenuItem = new MenuItem();
+ viewport.applet.showURL(url, target);
+ }
+ }
+
+ // ////////////////////////////////////////////////////////////////////////////////
+ // JBuilder Graphics here
+
+ MenuBar alignFrameMenuBar = new MenuBar();
+
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
+
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
+
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features"));
+
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations"));
+
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
+
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
+
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
+
+ MenuItem invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
+
+ MenuItem remove2LeftMenuItem = new MenuItem();
+
+ MenuItem remove2RightMenuItem = new MenuItem();
+
+ MenuItem removeGappedColumnMenuItem = new MenuItem();
+
+ MenuItem removeAllGapsMenuItem = new MenuItem();
+
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+
+ MenuItem sortPairwiseMenuItem = new MenuItem();
+
+ MenuItem sortIDMenuItem = new MenuItem();
+
+ MenuItem sortLengthMenuItem = new MenuItem();
+
+ MenuItem sortGroupMenuItem = new MenuItem();
+
+ MenuItem removeRedundancyMenuItem = new MenuItem();
+
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+
+ MenuItem PCAMenuItem = new MenuItem();
+
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();
+
+ MenuItem neighbourTreeMenuItem = new MenuItem();
+
BorderLayout borderLayout1 = new BorderLayout();
+
public Label statusBar = new Label();
- Menu outputTextboxMenu = new Menu();
- MenuItem clustalColour = new MenuItem();
- MenuItem zappoColour = new MenuItem();
- MenuItem taylorColour = new MenuItem();
- MenuItem hydrophobicityColour = new MenuItem();
- MenuItem helixColour = new MenuItem();
- MenuItem strandColour = new MenuItem();
- MenuItem turnColour = new MenuItem();
- MenuItem buriedColour = new MenuItem();
- MenuItem userDefinedColour = new MenuItem();
- MenuItem PIDColour = new MenuItem();
- MenuItem BLOSUM62Colour = new MenuItem();
- MenuItem njTreeBlosumMenuItem = new MenuItem();
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
- CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem("Alignment Properties...");
- MenuItem overviewMenuItem = new MenuItem();
- MenuItem undoMenuItem = new MenuItem();
- MenuItem redoMenuItem = new MenuItem();
- CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
- MenuItem noColourmenuItem = new MenuItem();
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
- MenuItem findMenuItem = new MenuItem();
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
- MenuItem nucleotideColour = new MenuItem();
- MenuItem deleteGroups = new MenuItem();
- MenuItem delete = new MenuItem();
- MenuItem copy = new MenuItem();
- MenuItem cut = new MenuItem();
- Menu pasteMenu = new Menu();
- MenuItem pasteNew = new MenuItem();
- MenuItem pasteThis = new MenuItem();
- CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
- MenuItem font = new MenuItem();
- CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
- CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
- CheckboxMenuItem scaleRight = new CheckboxMenuItem();
- MenuItem modifyPID = new MenuItem();
- MenuItem modifyConservation = new MenuItem();
- CheckboxMenuItem autoCalculate
- = new CheckboxMenuItem("Autocalculate Consensus", true);
- Menu sortByTreeMenu = new Menu();
- Menu sort = new Menu();
- Menu calculate = new Menu();
- MenuItem inputText = new MenuItem();
- Menu helpMenu = new Menu();
- MenuItem documentation = new MenuItem();
- MenuItem about = new MenuItem();
- CheckboxMenuItem seqLimits = new CheckboxMenuItem();
- Panel embeddedMenu;
- Label embeddedEdit;
- Label embeddedSelect;
- Label embeddedView;
- Label embeddedFormat;
- Label embeddedColour;
- Label embeddedFile;
- Label embeddedHelp;
- Label embeddedCalculate;
- FlowLayout flowLayout1;
-
- private void jbInit()
- throws Exception
- {
- setMenuBar(alignFrameMenuBar);
+ MenuItem clustalColour = new MenuItem();
- MenuItem item;
+ MenuItem zappoColour = new MenuItem();
- // dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
- i++)
- {
+ MenuItem taylorColour = new MenuItem();
- item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ MenuItem hydrophobicityColour = new MenuItem();
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- outputText_actionPerformed(e);
- }
- });
+ MenuItem helixColour = new MenuItem();
- outputTextboxMenu.add(item);
+ MenuItem strandColour = new MenuItem();
+
+ MenuItem turnColour = new MenuItem();
+
+ MenuItem buriedColour = new MenuItem();
+
+ MenuItem purinePyrimidineColour = new MenuItem();
+
+ // MenuItem RNAInteractionColour = 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 annotationPanelMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
+
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
+
+ MenuItem overviewMenuItem = new MenuItem();
+
+ MenuItem undoMenuItem = new MenuItem();
+
+ MenuItem redoMenuItem = new MenuItem();
+
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+ MenuItem findMenuItem = new MenuItem();
+
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+
+ MenuItem nucleotideColour = new MenuItem();
+
+ MenuItem deleteGroups = new MenuItem();
+
+ MenuItem grpsFromSelection = new MenuItem();
+
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
+ MenuItem delete = new MenuItem();
+
+ MenuItem copy = new MenuItem();
+
+ MenuItem cut = new MenuItem();
+
+ Menu pasteMenu = new Menu();
+
+ MenuItem pasteNew = new MenuItem();
+
+ MenuItem pasteThis = new MenuItem();
+
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+
+ MenuItem font = new MenuItem();
+
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
+ MenuItem modifyPID = new MenuItem();
+
+ MenuItem modifyConservation = new MenuItem();
+
+ CheckboxMenuItem autoCalculate = null;
+
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+ "Sort Alignment With New Tree", true);
+
+ Menu sortByTreeMenu = new Menu();
+
+ MenuItem inputText = new MenuItem();
+
+ MenuItem documentation = new MenuItem();
+
+ MenuItem about = new MenuItem();
+
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
+
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
+
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
+
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+
+ /**
+ * Initialise menus and other items
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ setMenuBar(alignFrameMenuBar);
+
+ /*
+ * Configure File menu items and actions
+ */
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText.addActionListener(this);
+ Menu outputTextboxMenu = new Menu(
+ MessageManager.getString("label.out_to_textbox"));
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+
+ MenuItem item = new MenuItem(
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputTextboxMenu.add(item);
}
closeMenuItem.addActionListener(this);
loadApplication.addActionListener(this);
-
loadTree.addActionListener(this);
loadAnnotations.addActionListener(this);
outputFeatures.addActionListener(this);
outputAnnotations.addActionListener(this);
- selectAllSequenceMenuItem.addActionListener(this);
- deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
+
+ /*
+ * Configure Edit menu items and actions
+ */
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
+ undoMenuItem.addActionListener(this);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
+ redoMenuItem.addActionListener(this);
+ copy.setLabel(MessageManager.getString("action.copy"));
+ copy.addActionListener(this);
+ cut.setLabel(MessageManager.getString("action.cut"));
+ cut.addActionListener(this);
+ delete.setLabel(MessageManager.getString("action.delete"));
+ delete.addActionListener(this);
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
+ pasteNew.addActionListener(this);
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
+ pasteThis.addActionListener(this);
+ 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");
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.addActionListener(this);
+
+ /*
+ * Configure Select menu items and actions
+ */
+ findMenuItem.setLabel(MessageManager.getString("action.find"));
+ findMenuItem.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.addActionListener(this);
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
+ invertColSel.addActionListener(this);
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
+ deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel(MessageManager
+ .getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(this);
+ createGroup.setLabel(MessageManager.getString("action.create_group"));
+ unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ annotationColumnSelection.setLabel(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumnSelection.addActionListener(this);
+
+ /*
+ * Configure View menu items and actions
+ */
+ newView.setLabel(MessageManager.getString("action.new_view"));
+ newView.addActionListener(this);
+ Menu showMenu = new Menu(MessageManager.getString("action.show"));
+ showColumns.setLabel(MessageManager.getString("label.all_columns"));
+ showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
+ Menu hideMenu = new Menu(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"));
+ showColumns.addActionListener(this);
+ showSeqs.addActionListener(this);
+ hideColumns.addActionListener(this);
+ hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.addActionListener(this);
+ featureSettings.setLabel(MessageManager
+ .getString("action.feature_settings"));
+ featureSettings.addActionListener(this);
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.show_sequence_features"));
+ sequenceFeatures.addItemListener(this);
+ sequenceFeatures.setState(false);
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
+ followMouseOverFlag.addItemListener(this);
+ alProperties.addActionListener(this);
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
+ overviewMenuItem.addActionListener(this);
+
+ /*
+ * Configure Annotations menu items and actions
+ */
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.addItemListener(this);
+ 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);
+ Menu autoAnnMenu = new Menu(
+ MessageManager.getString("label.autocalculated_annotation"));
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+ applyAutoAnnotationSettings.addItemListener(this);
+ showAlignmentAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_al_annotations"));
+ showSequenceAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_seq_annotations"));
+ sortAnnBySequence = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_sequence"));
+ sortAnnByLabel = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_label"));
+ showAutoFirst = new CheckboxMenuItem(
+ MessageManager.getString("label.show_first"));
+ showAutoFirst.setState(false); // pending applet parameter
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ showAutoLast = new CheckboxMenuItem(
+ MessageManager.getString("label.show_last"));
+ showAutoLast.setState(!showAutoFirst.getState());
+ showAlignmentAnnotations.addItemListener(this);
+ showSequenceAnnotations.addItemListener(this);
+ sortAnnBySequence.addItemListener(this);
+ sortAnnByLabel.addItemListener(this);
+ showAutoFirst.addItemListener(this);
+ showAutoLast.addItemListener(this);
+
+ /*
+ * Configure Format menu items and actions
+ */
+ font.setLabel(MessageManager.getString("action.font"));
+ font.addActionListener(this);
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
+ scaleAbove.setState(true);
+ scaleAbove.setEnabled(false);
+ scaleAbove.addItemListener(this);
+ scaleLeft.setEnabled(false);
+ scaleLeft.setState(true);
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
+ scaleLeft.addItemListener(this);
+ scaleRight.setEnabled(false);
+ scaleRight.setState(true);
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
+ scaleRight.addItemListener(this);
+ 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.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(
- "Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % 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");
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
+ colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.addItemListener(this);
+ wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
+ wrapMenuItem.addItemListener(this);
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addItemListener(this);
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelFlag.addItemListener(this);
+ seqLimits.setState(true);
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
+ seqLimits.addItemListener(this);
+ /*
+ * Configure Colour menu items and actions
+ */
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addItemListener(this);
+ 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);
+ // RNAInteractionColour.setLabel(MessageManager
+ // .getString("label.rna_interaction"));
+ // RNAInteractionColour.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);
- avDistanceTreeBlosumMenuItem.setLabel(
- "Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
- colourTextMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ // it will be enabled only if a score file is provided
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(this);
+ 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.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("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.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
+ annotationColour.addActionListener(this);
+
+ /*
+ * Configure Calculate menu items and actions
+ */
+ sortPairwiseMenuItem.setLabel(MessageManager
+ .getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(this);
+ sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel(MessageManager
+ .getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(this);
+ sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(this);
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(this);
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(this);
+ autoCalculate = new CheckboxMenuItem(
+ MessageManager.getString("label.autocalculate_consensus"), true);
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(this);
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(this);
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(this);
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(this);
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
+ Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
+ Menu calculateTreeMenu = new Menu(
+ MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
- inputText.setLabel("Input from textbox");
- inputText.addActionListener(this);
+ sortByTree.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
+ /*
+ * Configure Help menu items and actions
+ */
+ Menu helpMenu = new Menu(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.addItemListener(this);
- featureSettings.setLabel("Feature Settings...");
- featureSettings.addActionListener(this);
- sequenceFeatures.setLabel("Sequence Features");
- sequenceFeatures.addItemListener(this);
- sequenceFeatures.setState(false);
- annotationColour.setLabel("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");
- invertColSel.addActionListener(this);
- showColumns.addActionListener(this);
- showSeqs.addActionListener(this);
- hideColumns.addActionListener(this);
- hideSequences.addActionListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
- newView.addActionListener(this);
+
+ /*
+ * Add top level menus to frame
+ */
alignFrameMenuBar.add(fileMenu);
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
alignFrameMenuBar.add(editMenu);
+ Menu selectMenu = new Menu(MessageManager.getString("action.select"));
alignFrameMenuBar.add(selectMenu);
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
alignFrameMenuBar.add(viewMenu);
+ Menu annotationsMenu = new Menu(
+ MessageManager.getString("action.annotations"));
+ alignFrameMenuBar.add(annotationsMenu);
+ Menu formatMenu = new Menu(MessageManager.getString("action.format"));
alignFrameMenuBar.add(formatMenu);
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
alignFrameMenuBar.add(colourMenu);
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(helpMenu);
+ /*
+ * File menu
+ */
fileMenu.add(inputText);
fileMenu.add(loadTree);
fileMenu.add(loadAnnotations);
-
fileMenu.addSeparator();
fileMenu.add(outputTextboxMenu);
fileMenu.add(outputFeatures);
fileMenu.add(outputAnnotations);
-
if (jalviewServletURL != null)
{
fileMenu.add(loadApplication);
}
-
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+ /*
+ * Edit menu
+ */
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
+
+ /*
+ * Select menu
+ */
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumnSelection);
+
+ /*
+ * View menu
+ */
viewMenu.add(newView);
viewMenu.addSeparator();
- viewMenu.add(menu1);
- viewMenu.add(menu2);
+ showMenu.add(showColumns);
+ showMenu.add(showSeqs);
+ showMenu.add(showAllHidden);
+ viewMenu.add(showMenu);
+ hideMenu.add(hideColumns);
+ hideMenu.add(hideSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+ viewMenu.add(hideMenu);
viewMenu.addSeparator();
- viewMenu.add(annotationPanelMenuItem);
+ viewMenu.add(followMouseOverFlag);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
viewMenu.add(alProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
+
+ /*
+ * Annotations menu
+ */
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAlignmentAnnotations);
+ annotationsMenu.add(showSequenceAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ annotationsMenu.add(autoAnnMenu);
+
+ /*
+ * Format menu
+ */
+ formatMenu.add(font);
+ formatMenu.add(seqLimits);
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(displayNonconservedMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelFlag);
+
+ /*
+ * Colour menu
+ */
colourMenu.add(applyToAllGroups);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
+ colourMenu.add(RNAHelixColour);
+
+ /*
+ * Calculate menu
+ */
+ sortMenu.add(sortIDMenuItem);
+ sortMenu.add(sortLengthMenuItem);
+ sortMenu.add(sortByTreeMenu);
+ sortMenu.add(sortGroupMenuItem);
+ sortMenu.add(sortPairwiseMenuItem);
+ calculateMenu.add(sortMenu);
+ calculateTreeMenu.add(averageDistanceTreeMenuItem);
+ calculateTreeMenu.add(neighbourTreeMenuItem);
+ calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
+ calculateTreeMenu.add(njTreeBlosumMenuItem);
+ calculateMenu.add(calculateTreeMenu);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.add(autoCalculate);
- this.add(statusBar, BorderLayout.SOUTH);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortByTreeMenu);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
+ calculateMenu.add(sortByTree);
+
+ /*
+ * Help menu
+ */
helpMenu.add(documentation);
helpMenu.add(about);
- menu1.add(showColumns);
- menu1.add(showSeqs);
- menu2.add(hideColumns);
- menu2.add(hideSequences);
- formatMenu.add(font);
- formatMenu.add(seqLimits);
- formatMenu.add(wrapMenuItem);
- formatMenu.add(scaleAbove);
- formatMenu.add(scaleLeft);
- formatMenu.add(scaleRight);
- formatMenu.add(viewBoxesMenuItem);
- formatMenu.add(viewTextMenuItem);
- formatMenu.add(colourTextMenuItem);
- formatMenu.add(renderGapsMenuItem);
- selectMenu.add(findMenuItem);
- selectMenu.addSeparator();
- selectMenu.add(selectAllSequenceMenuItem);
- selectMenu.add(deselectAllSequenceMenuItem);
- selectMenu.add(invertSequenceMenuItem);
- selectMenu.add(invertColSel);
- selectMenu.add(deleteGroups);
- }
- public void setEmbedded()
- {
-
- embeddedMenu = new Panel();
- embeddedEdit = new Label("Edit");
- embeddedSelect = new Label("Select");
- embeddedView = new Label("View");
- embeddedFormat = new Label("Format");
- embeddedColour = new Label("Colour");
- embeddedFile = new Label("File");
- embeddedHelp = new Label("Help");
- embeddedCalculate = new Label("Calculate");
- flowLayout1 = new FlowLayout();
- embeddedMenu.setBackground(Color.lightGray);
- embeddedMenu.setLayout(flowLayout1);
- embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedMenu.add(embeddedFile);
- embeddedMenu.add(embeddedEdit);
- embeddedMenu.add(embeddedSelect);
- embeddedMenu.add(embeddedView);
- embeddedMenu.add(embeddedFormat);
- embeddedMenu.add(embeddedColour);
- embeddedMenu.add(embeddedCalculate);
- embeddedMenu.add(embeddedHelp);
- flowLayout1.setAlignment(FlowLayout.LEFT);
- flowLayout1.setHgap(2);
- flowLayout1.setVgap(0);
- embeddedFile.addMouseListener(this);
- embeddedEdit.addMouseListener(this);
- embeddedSelect.addMouseListener(this);
- embeddedView.addMouseListener(this);
- embeddedFormat.addMouseListener(this);
- embeddedColour.addMouseListener(this);
- embeddedCalculate.addMouseListener(this);
- embeddedHelp.addMouseListener(this);
+ /*
+ * Status bar
+ */
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ this.add(statusBar, BorderLayout.SOUTH);
+ }
- fileMenu.remove(closeMenuItem);
- fileMenu.remove(3); // Seperator
+ @Override
+ public void setStatus(String string)
+ {
+ statusBar.setText(string);
+ };
- viewport.applet.setLayout(new BorderLayout());
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
- viewport.applet.add(statusBar, BorderLayout.SOUTH);
+ MenuItem featureSettings = new MenuItem();
- alignPanel.setSize(viewport.applet.getSize().width,
- viewport.applet.getSize().height
- - embeddedMenu.HEIGHT - statusBar.HEIGHT);
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
- viewport.applet.add(alignPanel, BorderLayout.CENTER);
- viewport.applet.validate();
+ MenuItem annotationColour = new MenuItem();
- }
+ MenuItem annotationColumnSelection = new MenuItem();
- PopupMenu filePopup, editPopup, searchPopup,
- viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
- MenuItem featureSettings = new MenuItem();
- CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
- MenuItem annotationColour = new MenuItem();
MenuItem invertColSel = new MenuItem();
- Menu menu1 = new Menu();
+
MenuItem showColumns = new MenuItem();
+
MenuItem showSeqs = new MenuItem();
- Menu menu2 = new Menu();
+
MenuItem hideColumns = new MenuItem();
+
MenuItem hideSequences = new MenuItem();
- Menu formatMenu = new Menu();
- Menu selectMenu = new Menu();
+
+ MenuItem hideAllButSelection = new MenuItem();
+
+ MenuItem hideAllSelection = new MenuItem();
+
+ MenuItem showAllHidden = new MenuItem();
+
MenuItem newView = new MenuItem();
- public void mousePressed(MouseEvent evt)
+ private CheckboxMenuItem showAlignmentAnnotations;
+
+ private CheckboxMenuItem showSequenceAnnotations;
+
+ private CheckboxMenuItem sortAnnBySequence;
+
+ private CheckboxMenuItem sortAnnByLabel;
+
+ private CheckboxMenuItem showAutoFirst;
+
+ private CheckboxMenuItem showAutoLast;
+
+ private SplitFrame splitFrame;
+
+ /**
+ * Attach the alignFrame panels after embedding menus, if necessary. This used
+ * to be called setEmbedded, but is now creates the dropdown menus in a
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.
+ *
+ * @param reallyEmbedded
+ * true to attach the view to the applet area on the page rather than
+ * in a new window
+ */
+ public void createAlignFrameWindow(boolean reallyEmbedded)
+ {
+ if (reallyEmbedded)
+ {
+ embedAlignFrameInApplet(viewport.applet);
+ }
+ else
+ {
+ // //////
+ // test and embed menu bar if necessary.
+ //
+ if (embedMenuIfNeeded(alignPanel))
+ {
+ /*
+ * adjust for status bar height too. ? pointless as overridden by layout
+ * manager
+ */
+ alignPanel.setSize(getSize().width,
+ getSize().height - statusBar.getHeight());
+ }
+ add(statusBar, BorderLayout.SOUTH);
+ add(alignPanel, BorderLayout.CENTER);
+ // and register with the applet so it can pass external API calls to us
+ jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
+ frameHeight);
+ }
+ }
+
+ /**
+ * Add the components of this AlignFrame to the applet container.
+ *
+ * @param theApplet
+ */
+ public void embedAlignFrameInApplet(final JalviewLite theApplet)
+ {
+ // ////
+ // Explicitly build the embedded menu panel for the on-page applet
+ //
+ // view cannot be closed if its actually on the page
+ fileMenu.remove(closeMenuItem);
+ fileMenu.remove(3); // Remove Separator
+ // construct embedded menu, using default font
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
+ // and actually add the components to the applet area
+ theApplet.setLayout(new BorderLayout());
+ theApplet.add(embeddedMenu, BorderLayout.NORTH);
+ theApplet.add(statusBar, BorderLayout.SOUTH);
+ // TODO should size be left to the layout manager?
+ alignPanel.setSize(theApplet.getSize().width,
+ theApplet.getSize().height - embeddedMenu.getHeight()
+ - statusBar.getHeight());
+ theApplet.add(alignPanel, BorderLayout.CENTER);
+ final AlignFrame me = this;
+ theApplet.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ if (theApplet.currentAlignFrame == me)
+ {
+ theApplet.currentAlignFrame = null;
+ }
+ }
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ theApplet.currentAlignFrame = me;
+ }
+ });
+ theApplet.validate();
+ }
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note This method doesn't work
+ * without an additional javascript library to exchange messages between the
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ */
+ public SequenceStructureBinding addStructureViewInstance(
+ Object jmolviewer, String[] sequenceIds)
+ {
+ Viewer viewer = null;
+ try
+ {
+ viewer = (Viewer) jmolviewer;
+ } catch (ClassCastException ex)
+ {
+ System.err.println("Unsupported viewer object :"
+ + jmolviewer.getClass());
+ }
+ if (viewer == null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs = null;
+ if (sequenceIds == null || sequenceIds.length == 0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ Vector sqi = new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid = 0; sid < sequenceIds.length; sid++)
+ {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq != null)
+ {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size() > 0)
+ {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ }
+ else
+ {
+ return null;
+ }
+ }
+ AAStructureBindingModel jmv = null;
+ // 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 });
+ }
+ 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)
{
- PopupMenu popup = null;
- Label source = (Label) evt.getSource();
- if (source == embeddedFile)
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
{
- popup = filePopup = genPopupMenu(filePopup, fileMenu);
+ Vector pdbe = toaddpdb.getAllPDBEntries();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ pdbentry.setProperty("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
+ }
}
- else if (source == embeddedEdit)
+ return true;
+ }
+
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
{
- popup = editPopup = genPopupMenu(editPopup, editMenu);
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[] { seqs[i],
+ (chains != null) ? chains[i] : null });
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
}
- else if (source == embeddedSelect)
+ return new Object[] { seqs, chains };
+
+ }
+
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
{
- popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
- else if (source == embeddedView)
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
{
- popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
+ protocol = (String) pdb.getProperty("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
}
- else if (source == embeddedFormat)
+ if (applet.useXtrnalSviewer)
{
- popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
+ // register the association(s) and quit, don't create any windows.
+ if (StructureSelectionManager.getStructureSelectionManager(applet)
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ {
+ System.err.println("Failed to map " + pdb.getFile() + " ("
+ + protocol + ") to any sequences");
+ }
+ return;
}
- else if (source == embeddedColour)
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
{
- popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm != null)
+ {
+ System.err
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ // try and add the pdb structure
+ // ajm.addS
+ ajm = null;
+ }
}
- else if (source == embeddedCalculate)
+ // otherwise, create a new window
+ if (applet.jmolAvailable)
{
- popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
}
- else if (source == embeddedHelp)
+ else
{
- popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
- embeddedMenu.add(popup);
- popup.show(embeddedMenu,
- source.getBounds().x,
- source.getBounds().y + source.getBounds().getSize().height);
}
- PopupMenu genPopupMenu(PopupMenu popup, Menu original)
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
+ }
+
+ /**
+ * 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)
{
- if (popup != null)
+ 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())
{
- return popup;
+ // TODO: raise dialog for gui
+ System.err.println("Problems parsing T-Coffee scores: "
+ + file.getWarningMessage());
+ System.err.println("Origin was:\n" + source);
+ return false;
}
- popup = new PopupMenu();
- int m, mSize = original.getItemCount();
- for (m = 0; m < mSize; m++)
+
+ /*
+ * 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))
{
- popup.add(original.getItem(m));
- mSize--;
- m--;
+ 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;
+ }
+
+ public SplitFrame getSplitFrame()
+ {
+ return this.splitFrame;
+ }
- return popup;
+ public void setSplitFrame(SplitFrame sf)
+ {
+ this.splitFrame = sf;
}
- public void mouseClicked(MouseEvent evt)
- {}
+ // may not need this
+ @Override
+ public void setShowSeqFeatures(boolean b)
+ {
+ // showSeqFeatures.setSelected(b);
+ viewport.setShowSequenceFeatures(b);
+
+ }
- public void mouseReleased(MouseEvent evt)
- {}
+ @Override
+ public void setMenusForViewport()
+ {
+ // setMenusFromViewport(viewport);
- public void mouseEntered(MouseEvent evt)
- {}
+ }
- public void mouseExited(MouseEvent evt)
- {}
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ if (enableIfNecessary)
+ {
+ sequenceFeatures.setState(true);
+ alignPanel.av.setShowSequenceFeatures(true);
+ }
+ }
+
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return alignPanel.av.featureSettings;
+ }
}
git://source.jalview.org / jalview.git / blobdiff