X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2a2fc70d870f905f42fdcc47161a36bb314866d8;hb=2db5d47c785c67cdb7a82b609b3a7eb8af4e7e0c;hp=9f7777240c9294dfca8d6559da4f41f8a648499b;hpb=b5053b9113d7bbc0ce87775c9b54d66df73cb3c7;p=jalview.git
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
old mode 100755
new mode 100644
index 9f77772..2a2fc70
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,57 +1,190 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * 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.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import java.applet.Applet;
-import java.awt.*;
-import java.awt.event.*;
-
-import org.jmol.api.JmolViewer;
-
-import jalview.analysis.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
+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.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+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.HiddenColumns;
+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.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+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.RNAHelicesColour;
+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 jalview.viewmodel.ViewportRanges;
+
+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.Rectangle;
+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.io.UnsupportedEncodingException;
+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
+ ItemListener, KeyListener, AlignViewControllerGuiI
{
+ public AlignViewControllerI avc;
+
public AlignmentPanel alignPanel;
public AlignViewport viewport;
- int DEFAULT_WIDTH = 700;
+ // width and height may be overridden by applet parameters
+ int frameWidth = 700;
- int DEFAULT_HEIGHT = 500;
+ 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,
+ HiddenColumns hidden, JalviewLite applet, String title,
+ boolean embedded)
{
+ this(al, hiddenSeqs, hidden, applet, title, embedded, true);
+ }
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ HiddenColumns hidden, JalviewLite applet, String title,
+ boolean embedded, boolean addToDisplay)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -64,17 +197,61 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
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 (hidden != null)
+ {
+ viewport.getAlignment().setHiddenColumns(hidden);
+ }
+ 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);
- displayNonconservedMenuItem.setState(viewport.getShowunconserved());
-
- 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)
{
@@ -110,26 +287,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
- try
+
+ }
+ if (viewport.getAlignment().isNucleotide())
+ {
+ conservationMenuItem.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
+ viewport.updateStrucConsensus(alignPanel);
+ if (viewport.getAlignment().hasRNAStructure())
{
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
+ RNAHelixColour.setEnabled(true);
+ }
+ else
{
+ RNAHelixColour.setEnabled(false);
}
-
}
-
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.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
@@ -138,9 +325,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.idPanel.idCanvas.addKeyListener(this);
alignPanel.scalePanel.addKeyListener(this);
alignPanel.annotationPanel.addKeyListener(this);
- createAlignFrameWindow(embedded, title);
- alignPanel.validate();
- alignPanel.paintAlignment(true);
+ alignPanel.annotationPanelHolder.addKeyListener(this);
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+ alignPanel.alabels.addKeyListener(this);
+
+ setAnnotationsVisibility();
+
+ if (addToDisplay)
+ {
+ addToDisplay(embedded);
+ }
+ }
+
+ /**
+ * @param embedded
+ */
+ public void addToDisplay(boolean embedded)
+ {
+ createAlignFrameWindow(embedded);
+ validate();
+ alignPanel.adjustAnnotationHeight();
+ alignPanel.paintAlignment(true, true);
}
public AlignViewport getAlignViewport()
@@ -154,22 +359,43 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/**
- * DOCUMENT ME!
+ * Load a features file onto the alignment
*
- * @param String
- * DOCUMENT ME!
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
*/
- public void parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, DataSourceType type)
+ {
+ return parseFeaturesFile(file, type, true);
+ }
+
+ /**
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param sourceType
+ * 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, DataSourceType sourceType,
+ 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);
+ Map colours = alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours();
+ boolean relaxedIdMatching = viewport.applet
+ .getDefaultParameter("relaxedidmatch", false);
+ featuresFile = new FeaturesFile(file, sourceType).parse(
+ viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
@@ -177,34 +403,48 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
}
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ setStatus(MessageManager
+ .getString("label.successfully_added_features_alignment"));
}
-
+ return featuresFile;
}
+ @Override
public void keyPressed(KeyEvent evt)
{
+ ViewportRanges ranges = viewport.getRanges();
+
if (viewport.cursorMode
- && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
- .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
- .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && ((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();
+
+ alignPanel.alabels.cancelDrag();
break;
case KeyEvent.VK_X:
if (evt.isControlDown() || evt.isMetaDown())
@@ -258,16 +498,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(-1, 0);
+ }
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_SPACE:
@@ -328,12 +576,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
+ setStatus(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;
+ alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
+ alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
}
break;
@@ -353,27 +602,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
+ ranges.pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
+ ranges.pageDown();
break;
case KeyEvent.VK_Z:
@@ -431,6 +664,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
break;
+ case KeyEvent.VK_G:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
+ {
+ this.unGroup_actionPerformed();
+ }
+ else
+ {
+ this.createGroup_actionPerformed();
+ }
+ }
+ break;
+
case KeyEvent.VK_U:
if (evt.isControlDown())
{
@@ -446,7 +693,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
break;
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if the keystroke warrants it
+ alignPanel.paintAlignment(true, true);
}
/**
@@ -464,10 +712,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
- .getSelected().size() > 0)
- || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
- .getEndRes()))
+ 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.
@@ -488,12 +734,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (toggleSeqs)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
viewport.showAllHiddenSeqs();
}
@@ -501,112 +747,231 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (toggleCols)
{
- if (viewport.colSel.getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
{
- viewport.selectionGroup = sg;
+ viewport.setSelectionGroup(sg);
}
}
else if (!hide)
{
viewport.showAllHiddenColumns();
}
+ viewport.sendSelection();
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == displayNonconservedMenuItem)
+ final Object source = evt.getSource();
+ if (source == displayNonconservedMenuItem)
{
displayNonconservedMenuItem_actionPerformed();
}
- else if (evt.getSource() == colourTextMenuItem)
+ 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();
+ }
+ else if (source == sortByTree)
{
- viewport.autocalculateConsensus = autoCalculate.getState();
+ viewport.sortByTree = sortByTree.getState();
}
- else if (evt.getSource() == this.centreColumnLabelFlag)
+ else if (source == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
}
- else if (evt.getSource() == this.followMouseOverFlag)
+ 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();
+ }
+ // TODO: repaint flags set only if warranted
+ alignPanel.paintAlignment(true, 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);
+ }
- alignPanel.paintAlignment(true);
+ private void setShowAutoCalculatedAbove(boolean showAbove)
+ {
+ this.showAutoCalculatedAbove = showAbove;
}
private void mouseOverFlag_stateChanged()
{
- viewport.followHighlight = followMouseOverFlag.getState();
+ viewport.setFollowHighlight(followMouseOverFlag.getState());
// TODO: could kick the scrollTo mechanism to reset view for current
// searchresults.
}
@@ -617,8 +982,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
this.alignPanel.annotationPanel.repaint();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
+ viewport.applet.currentAlignFrame = this;
+
Object source = evt.getSource();
if (source == inputText)
@@ -697,6 +1065,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
delete_actionPerformed();
}
+ else if (source == createGroup)
+ {
+ createGroup_actionPerformed();
+ }
+ else if (source == unGroup)
+ {
+ unGroup_actionPerformed();
+ }
else if (source == grpsFromSelection)
{
makeGrpsFromSelection_actionPerformed();
@@ -716,11 +1092,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
+ alignPanel.paintAlignment(false, false);
+ viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
{
@@ -753,28 +1132,35 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
else if (source == showColumns)
{
viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ // uncomment if we want to slave sequence selections in split frame
+ // viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ // uncomment if we want to slave sequence selections in split frame
+ // viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ viewport.sendSelection();
}
else if (source == hideAllSelection)
{
@@ -782,58 +1168,55 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
+ viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, 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);
+ showFeatureSettingsUI();
}
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));
- }
- }
-
+ 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, "Alignment Properties: "
- + getTitle(), 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.alignment_properties", new String[]
+ { getTitle() }), 400, 250);
}
else if (source == overviewMenuItem)
{
@@ -846,9 +1229,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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)
{
@@ -882,6 +1263,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
changeColour(new NucleotideColourScheme());
}
+ else if (source == purinePyrimidineColour)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ // else if (source == RNAInteractionColour)
+ // {
+ // changeColour(new RNAInteractionColourScheme());
+ // }
+ else if (source == RNAHelixColour)
+ {
+ changeColour(new RNAHelicesColour(viewport.getAlignment()));
+ // new RNAHelicesColourChooser(viewport, alignPanel);
+ }
else if (source == modifyPID)
{
modifyPID_actionPerformed();
@@ -902,10 +1296,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
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();
@@ -966,7 +1368,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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)
@@ -974,57 +1377,66 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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));
+ JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
+
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
+ 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)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
return annotation;
}
- private Hashtable getDisplayedFeatureCols()
+ private Map getDisplayedFeatureCols()
{
- if (alignPanel.getFeatureRenderer() != null)
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
{
- FeatureRenderer fr = alignPanel.getFeatureRenderer();
- Hashtable fcols = new Hashtable();
- Enumeration en = viewport.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- Object col = en.nextElement();
- fcols.put(col, fr.featureColours.get(col));
- }
- return fcols;
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
+
+ }
+ return null;
+ }
+
+ private List getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
}
return null;
}
@@ -1032,28 +1444,47 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
+ FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(
- viewport.alignment.getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(
+ viewport.getAlignment().getSequencesArray(),
+ alignPanel.getFeatureRenderer(), true, false);
}
else
{
- features = new FeaturesFile().printGFFFormat(
- viewport.alignment.getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printGffFormat(
+ viewport.getAlignment().getSequencesArray(),
+ alignPanel.getFeatureRenderer(), true, false);
}
if (displayTextbox)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ boolean frimport = false;
+ if (features == null || features.equals("No Features Visible"))
+ {
+ features = "# No features visible - paste some and import them here.";
+ frimport = true;
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
+ if (frimport)
+ {
+ cap.setAnnotationImport();
+ }
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
-
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
+ else
+ {
+ if (features == null)
+ {
+ features = "";
+ }
+ }
return features;
}
@@ -1062,8 +1493,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
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)
{
@@ -1074,27 +1510,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.applet.getParameter("annotations") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));
+ url.append(
+ appendProtocol(viewport.applet.getParameter("annotations")));
}
- if (viewport.applet.getParameter("jnetfile") != null)
+ if (viewport.applet.getParameter("jnetfile") != null
+ || viewport.applet.getParameter("jpredfile") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+ url.append(appendProtocol(
+ viewport.applet.getParameter("jnetfile") != null
+ ? viewport.applet.getParameter("jnetfile")
+ : viewport.applet.getParameter("jpredfile")));
}
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)
{
@@ -1133,7 +1572,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
try
{
new URL(url);
- url = URLEncoder.encode(url);
+ url = URLEncoder.encode(url, "UTF-8");
}
/*
* When we finally deprecate 1.1 compatibility, we can start to use
@@ -1145,6 +1584,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
catch (java.net.MalformedURLException ex)
{
url = viewport.applet.getCodeBase() + url;
+ } catch (UnsupportedEncodingException ex)
+ {
+ System.err.println(
+ "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+ + url);
+ ex.printStackTrace();
}
return url;
}
@@ -1152,113 +1597,149 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
}
+ viewport = null;
+ if (alignPanel != null && alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.dispose();
+ }
+ 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!
+ * 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.getAlignment().getSequences());
}
/**
- * 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.getAlignment().getSequences());
}
- AlignViewport getOriginatingSource(CommandI command)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
+ AlignmentViewport originalSource = null;
// For sequence removal and addition, we need to fire
// the property change event FROM the viewport where the
// original alignment was altered
@@ -1267,13 +1748,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ Vector comps = 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;
break;
@@ -1288,7 +1769,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
@@ -1297,6 +1778,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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();
@@ -1304,65 +1791,39 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
return;
}
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ up ? null : viewport.getHiddenRepSequences(), up);
+ alignPanel.paintAlignment(true, false);
- if (up)
+ /*
+ * Also move cDNA/protein complement sequences
+ */
+ AlignViewportI complement = viewport.getCodingComplement();
+ if (complement != null)
{
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
+ SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
+ viewport, complement);
+ complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
+ up ? null : complement.getHiddenRepSequences(), up);
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
+ false);
}
-
- alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
+ List sg = new Vector<>();
if (viewport.cursorMode)
{
- sg.addElement(viewport.alignment
+ sg.add(viewport.getAlignment()
.getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.alignment
- .getHeight())
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
+ sg = viewport.getSelectionGroup()
+ .getSequences(viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
@@ -1370,44 +1831,59 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
return;
}
- Vector invertGroup = new Vector();
+ Vector 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);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
@@ -1419,23 +1895,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque 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)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
static StringBuffer copiedSequences;
- static Vector copiedHiddenColumns;
+ static HiddenColumns copiedHiddenColumns;
protected void copy_actionPerformed()
{
@@ -1446,30 +1924,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
+ Map orderedSeqs = new HashMap<>();
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++)
- {
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ copiedHiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
else
{
@@ -1482,11 +1957,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
while (seq == null)
{
- if (orderedSeqs.containsKey(index + ""))
+ if (orderedSeqs.containsKey(index))
{
- seq = (SequenceI) orderedSeqs.get(index + "");
+ seq = orderedSeqs.get(index);
index++;
-
break;
}
else
@@ -1517,14 +1991,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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");
}
}
@@ -1543,13 +2013,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
try
{
-
if (copiedSequences == null)
{
return;
}
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+ "\t");
Vector seqs = new Vector();
while (st.hasMoreElements())
{
@@ -1566,28 +2036,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ af.viewport.setHiddenColumns(copiedHiddenColumns);
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ frameHeight);
}
else
{
@@ -1604,17 +2071,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
for (int i = 0; i < seqs.length; i++)
{
- viewport.alignment.addSequence(seqs[i]);
+ viewport.getAlignment().addSequence(seqs[i]);
}
// !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
-
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
+ seqs, 0, viewport.getAlignment().getWidth(),
+ viewport.getAlignment()));
+
+ viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+ // 2019.04.18
+ viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null,
- viewport.alignment.getSequences());
+ viewport.getAlignment().getSequences());
}
@@ -1641,9 +2111,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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())
{
+ 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);
}
@@ -1657,61 +2150,112 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/*
* //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();
+ }
+
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /**
+ * 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 (viewport.getSelectionGroup() != null)
+ if (avc.makeGroupsFromSelection())
{
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()),
- viewport.alignment.getGroups());
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- // gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.alignment.addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq
- .hasMoreElements(); viewport.setSequenceColour(
- (SequenceI) sq.nextElement(), col))
- ;
- }
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- // alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true, true);
}
}
- protected void deleteGroups_actionPerformed()
+ protected void createGroup_actionPerformed()
{
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
+ avc.createGroup();
+ }
- alignPanel.paintAlignment(true);
+ protected void unGroup_actionPerformed()
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ protected void deleteGroups_actionPerformed()
+ {
+ if (avc.deleteGroups())
+ {
+ alignPanel.alignmentChanged();
+ }
}
public void selectAllSequenceMenuItem_actionPerformed()
@@ -1721,10 +2265,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
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, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void deselectAllSequenceMenuItem_actionPerformed()
@@ -1739,8 +2287,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertSequenceMenuItem_actionPerformed()
@@ -1752,21 +2304,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
void trimAlignment(boolean trimLeft)
{
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
ColumnSelection colSel = viewport.getColumnSelection();
int column;
- if (colSel.size() > 0)
+ if (!colSel.isEmpty())
{
if (trimLeft)
{
@@ -1780,122 +2336,120 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = al.getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
- viewport.setStartRes(0);
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, al);
+ ranges.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, al);
}
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
-
+ setStatus(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 : al.getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ al.deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, al.getSequences());
}
}
public void removeGappedColumnMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
+ int start = 0;
+ int end = ranges.getAbsoluteAlignmentWidth() - 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);
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ setStatus(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);
- int startRes = seq.findPosition(viewport.startRes);
+ SequenceI seq = al.getSequenceAt(0);
+ int startRes = seq.findPosition(ranges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, al.getSequences());
}
public void removeAllGapsMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
+ int start = 0;
+ int end = ranges.getAbsoluteAlignmentWidth() - 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);
- int startRes = seq.findPosition(viewport.startRes);
+ SequenceI seq = al.getSequenceAt(0);
+ int startRes = seq.findPosition(ranges.getStartRes());
- addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.alignment));
+ addHistoryItem(
+ new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null, al.getSequences());
}
@@ -1913,30 +2467,33 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public AlignFrame newView(String viewtitle)
{
AlignmentI newal;
- if (viewport.hasHiddenRows)
+ if (viewport.hasHiddenRows())
{
newal = new Alignment(viewport.getAlignment().getHiddenSequences()
.getFullAlignment().getSequencesArray());
}
else
{
- newal = new Alignment(viewport.alignment.getSequencesArray());
+ newal = new Alignment(viewport.getAlignment().getSequencesArray());
}
- if (viewport.alignment.getAlignmentAnnotation() != null)
+ if (viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < viewport.getAlignment()
+ .getAlignmentAnnotation().length; i++)
{
- if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ if (!viewport.getAlignment()
+ .getAlignmentAnnotation()[i].autoCalculated)
{
- newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+ newal.addAnnotation(
+ viewport.getAlignment().getAlignmentAnnotation()[i]);
}
}
}
AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
- newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+ newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel,
newaf.alignPanel.av.getSequenceSetId());
@@ -1946,8 +2503,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
newaf.alignPanel.av.getSequenceSetId());
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ Vector comps = PaintRefresher.components
+ .get(viewport.getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)
{
@@ -1973,8 +2530,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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;
}
@@ -1988,7 +2545,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- return fr.getGroups();
+ List gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
}
return null;
}
@@ -2006,7 +2565,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- return fr.getGroups(visible);
+ List gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
}
return null;
}
@@ -2023,11 +2584,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
FeatureRenderer fr = null;
this.sequenceFeatures.setState(true);
- viewport.showSequenceFeatures(true);
+ viewport.setShowSequenceFeatures(true);
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- fr.setGroupState(groups, state);
+
+ fr.setGroupVisibility(Arrays.asList(groups), state);
alignPanel.seqPanel.seqCanvas.repaint();
if (alignPanel.overviewPanel != null)
{
@@ -2040,19 +2602,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
viewport.setShowJVSuffix(seqLimits.getState());
alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void displayNonconservedMenuItem_actionPerformed()
{
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(false, false);
}
protected void wrapMenuItem_actionPerformed()
@@ -2062,7 +2624,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void overviewMenuItem_actionPerformed()
@@ -2073,19 +2635,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
Frame frame = new Frame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
+ final 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,
+ 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);
+ overview.dispose();
+ if (ap != null)
+ {
+ ap.setOverviewPanel(null);
+ }
};
});
@@ -2093,135 +2662,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
- 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());
- }
-
- 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"));
-
- }
- else
- {
- cs.setConservation(null);
- }
-
- 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);
+ alignPanel.paintAlignment(true, true);
}
protected void modifyPID_actionPerformed()
{
if (viewport.getAbovePIDThreshold()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
}
@@ -2229,55 +2684,74 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void modifyConservation_actionPerformed()
{
if (viewport.getConservationSelected()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme, "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showConservationSlider();
}
}
protected void conservationMenuItem_actionPerformed()
{
- viewport.setConservationSelected(conservationMenuItem.getState());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setState(false);
+ boolean selected = conservationMenuItem.getState();
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
+ viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
- modifyConservation_actionPerformed();
+ if (selected)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
}
public void abovePIDThreshold_actionPerformed()
{
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
- conservationMenuItem.setState(false);
- viewport.setConservationSelected(false);
+ boolean selected = abovePIDThreshold.getState();
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
changeColour(viewport.getGlobalColourScheme());
- modifyPID_actionPerformed();
+ if (selected)
+ {
+ modifyPID_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
}
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
+ AlignmentSorter.sortByPID(viewport.getAlignment(),
+ viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
- alignPanel.paintAlignment(true);
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
}
public void sortIDMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
- alignPanel.paintAlignment(true);
+ addHistoryItem(
+ new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
}
public void sortLengthMenuItem_actionPerformed()
@@ -2285,8 +2759,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.alignment));
- alignPanel.paintAlignment(true);
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
}
public void sortGroupMenuItem_actionPerformed()
@@ -2294,8 +2768,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.alignment));
- alignPanel.paintAlignment(true);
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
}
@@ -2311,7 +2785,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
@@ -2319,12 +2794,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void PCAMenuItem_actionPerformed()
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- 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);
@@ -2333,12 +2809,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
if ((viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() < 4 && viewport
- .getSelectionGroup().getSize() > 0)
+ && viewport.getSelectionGroup().getSize() < 4
+ && viewport.getSelectionGroup().getSize() > 0)
|| viewport.getAlignment().getHeight() < 4)
{
return;
@@ -2355,33 +2831,40 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
+ "Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
+ "Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
+ ScoreModels.getInstance().getBlosum62().getName(),
+ "Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
+ ScoreModels.getInstance().getBlosum62().getName(),
+ "Average distance tree using BLOSUM62");
}
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- 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);
@@ -2390,16 +2873,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
- 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);
@@ -2410,16 +2892,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
}
@@ -2435,13 +2919,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void sortByTree(TreePanel treePanel, String title)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter
- .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ AlignmentSorter.sortByTree(viewport.getAlignment(),
+ treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
- viewport.alignment));
- alignPanel.paintAlignment(true);
+ addHistoryItem(new OrderCommand(MessageManager
+ .formatMessage("label.order_by_params", new String[]
+ { title }), oldOrder, viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
}
/**
@@ -2458,6 +2943,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
sortByTreeMenu.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
sortByTree(treePanel, title); // treePanel.getTitle());
@@ -2466,6 +2952,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
treePanel.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowOpened(WindowEvent e)
{
if (viewport.sortByTree)
@@ -2475,6 +2962,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
super.windowOpened(e);
}
+ @Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
@@ -2482,9 +2970,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
});
}
+ 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, false);
+ return true;
+ }
+
protected void documentation_actionPerformed()
{
- showURL("http://www.jalview.org/help.html", "HELP");
+ alignPanel.av.applet.openJalviewHelpUrl();
}
protected void about_actionPerformed()
@@ -2502,6 +3008,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
this.builddate = builddate;
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.white);
@@ -2514,36 +3021,39 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("JalviewLite - Release " + version, x, y += fh);
+ g.drawString(MessageManager
+ .formatMessage("label.jalviewLite_release", new String[]
+ { version }), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: " + builddate, x, y += fh);
+ g.drawString(MessageManager.formatMessage("label.jaview_build_date",
+ new String[]
+ { builddate }), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString(
- "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
- x, y += fh * 1.5);
- g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
- g.drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- x, y += fh);
- g.drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
- x, y += fh);
- g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g.drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ 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(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(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ MessageManager.getString("label.jalview_cite_1_authors"), x,
+ y += fh);
+ g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
x, y += fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
}
Frame frame = new Frame();
- frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
- .getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
+ frame.add(new AboutPanel(JalviewLite.getVersion(),
+ JalviewLite.getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
}
@@ -2555,44 +3065,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
else
{
- try
- {
- if (url.indexOf(":") == -1)
- {
- // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
- // form valid URL
- if (url.indexOf("/") == 0)
- {
- String codebase = viewport.applet.getCodeBase().toString();
- url = codebase.substring(0, codebase.length()
- - viewport.applet.getCodeBase().getFile().length())
- + url;
- }
- else
- {
- url = viewport.applet.getCodeBase() + url;
- }
- System.out.println("Show url (prepended codebase): " + url);
- }
- else
- {
- System.out.println("Show url: " + url);
- }
- if (url.indexOf("javascript:") == 0)
- {
- // no target for the javascript context
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url));
- }
- else
- {
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url), target);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ viewport.applet.showURL(url, target);
}
}
@@ -2601,33 +3074,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuBar alignFrameMenuBar = new MenuBar();
- Menu fileMenu = new Menu("File");
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem loadApplication = new MenuItem("View in Full Application");
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
- MenuItem outputFeatures = new MenuItem("Export Features ...");
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features"));
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations"));
- MenuItem closeMenuItem = new MenuItem("Close");
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
- Menu editMenu = new Menu("Edit");
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
- Menu viewMenu = new Menu("View");
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
- 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 invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
@@ -2663,8 +3137,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public Label statusBar = new Label();
- Menu outputTextboxMenu = new Menu();
-
MenuItem clustalColour = new MenuItem();
MenuItem zappoColour = new MenuItem();
@@ -2681,12 +3153,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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();
@@ -2697,7 +3177,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem("Alignment Properties...");
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
@@ -2723,6 +3204,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem grpsFromSelection = new MenuItem();
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
MenuItem delete = new MenuItem();
MenuItem copy = new MenuItem();
@@ -2749,19 +3234,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem modifyConservation = new MenuItem();
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
- "Autocalculate Consensus", true);
-
- Menu sortByTreeMenu = new Menu();
+ CheckboxMenuItem autoCalculate = null;
- Menu sort = new Menu();
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+ "Sort Alignment With New Tree", true);
- Menu calculate = new Menu();
+ Menu sortByTreeMenu = new Menu();
MenuItem inputText = new MenuItem();
- Menu helpMenu = new Menu();
-
MenuItem documentation = new MenuItem();
MenuItem about = new MenuItem();
@@ -2772,22 +3253,42 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
- MenuItem item;
-
- // dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ /*
+ * 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 (String ff : FileFormats.getInstance().getWritableFormats(true))
{
-
- item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(ff);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
@@ -2798,224 +3299,384 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
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");
- remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
- remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
- removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel("by Length");
- sortLengthMenuItem.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");
- clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
- helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
- strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
- turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("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);
- displayNonconservedMenuItem.setLabel("Show nonconserved");
- displayNonconservedMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
+ /*
+ * Configure Edit menu items and actions
+ */
undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
undoMenuItem.addActionListener(this);
redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("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.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
- nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
- grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
+ copy.setLabel(MessageManager.getString("action.copy"));
copy.addActionListener(this);
- cut.setLabel("Cut");
+ cut.setLabel(MessageManager.getString("action.cut"));
cut.addActionListener(this);
- delete.setLabel("Delete");
+ delete.setLabel(MessageManager.getString("action.delete"));
delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
+ remove2LeftMenuItem
+ .setLabel(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.addActionListener(this);
+ remove2RightMenuItem
+ .setLabel(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.addActionListener(this);
+ removeGappedColumnMenuItem.setLabel(
+ MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.addActionListener(this);
+ removeAllGapsMenuItem
+ .setLabel(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.addActionListener(this);
+ 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"));
+ createGroup.addActionListener(this);
+ unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ unGroup.addActionListener(this);
+
+ 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("Scale Above");
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
scaleAbove.setState(true);
scaleAbove.setEnabled(false);
scaleAbove.addItemListener(this);
scaleLeft.setEnabled(false);
scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
scaleLeft.addItemListener(this);
scaleRight.setEnabled(false);
scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
+ viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addItemListener(this);
+ viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addItemListener(this);
+ colourTextMenuItem
+ .setLabel(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem
+ .setLabel(MessageManager.getString("label.show_non_conserved"));
+ 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.colourScheme_clustal"));
+ clustalColour.addActionListener(this);
+ zappoColour
+ .setLabel(MessageManager.getString("label.colourScheme_zappo"));
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel(
+ MessageManager.getString("label.colourScheme_taylor"));
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour.addActionListener(this);
+ helixColour.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
+ helixColour.addActionListener(this);
+ strandColour.setLabel(MessageManager
+ .getString("label.colourScheme_strandpropensity"));
+ strandColour.addActionListener(this);
+ turnColour.setLabel(
+ MessageManager.getString("label.colourScheme_turnpropensity"));
+ turnColour.addActionListener(this);
+ buriedColour.setLabel(
+ MessageManager.getString("label.colourScheme_buriedindex"));
+ buriedColour.addActionListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.colourScheme_purine/pyrimidine"));
+ purinePyrimidineColour.addActionListener(this);
+ // RNAInteractionColour.setLabel(MessageManager
+ // .getString("label.rna_interaction"));
+ // RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(
+ MessageManager.getString("label.colourScheme_rnahelices"));
+ RNAHelixColour.addActionListener(this);
+ userDefinedColour
+ .setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel(
+ MessageManager.getString("label.colourScheme_%identity"));
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel(
+ MessageManager.getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.addActionListener(this);
+ tcoffeeColour.setLabel(
+ MessageManager.getString("label.colourScheme_t-coffeescores"));
+ // 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(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(this);
+ abovePIDThreshold.setLabel(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addItemListener(this);
+ nucleotideColour.setLabel(
+ MessageManager.getString("label.colourScheme_nucleotide"));
+ nucleotideColour.addActionListener(this);
+ modifyPID.setLabel(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.setEnabled(abovePIDThreshold.getState());
modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.setEnabled(conservationMenuItem.getState());
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_blosum62"));
+ 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);
- centreColumnLabelFlag.setLabel("Centre column labels");
- centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel("Automatic Scrolling");
- followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
- documentation.addActionListener(this);
+ sortByTree.addItemListener(this);
- about.setLabel("About...");
+ /*
+ * 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(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");
- hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
- hideAllSelection.setLabel("Selected Region");
- showAllHidden.setLabel("All Sequences and Columns");
- invertColSel.addActionListener(this);
- showColumns.addActionListener(this);
- showSeqs.addActionListener(this);
- hideColumns.addActionListener(this);
- hideSequences.addActionListener(this);
- hideAllButSelection.addActionListener(this);
- hideAllSelection.addActionListener(this);
- showAllHidden.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();
@@ -3024,13 +3685,38 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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(followMouseOverFlag);
- viewMenu.add(annotationPanelMenuItem);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
@@ -3038,6 +3724,48 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
@@ -3052,6 +3780,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
@@ -3059,72 +3790,63 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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(sortLengthMenuItem);
- 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);
- menu1.add(showAllHidden);
- menu2.add(hideColumns);
- menu2.add(hideSequences);
- menu2.add(hideAllSelection);
- menu2.add(hideAllButSelection);
- 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);
- selectMenu.add(findMenuItem);
- selectMenu.addSeparator();
- selectMenu.add(selectAllSequenceMenuItem);
- selectMenu.add(deselectAllSequenceMenuItem);
- selectMenu.add(invertSequenceMenuItem);
- selectMenu.add(invertColSel);
- selectMenu.add(grpsFromSelection);
- selectMenu.add(deleteGroups);
+ /*
+ * Status bar
+ */
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ setStatus(MessageManager.getString("label.status_bar"));
+ this.add(statusBar, BorderLayout.SOUTH);
}
+ @Override
+ public void setStatus(String string)
+ {
+ statusBar.setText(string);
+ };
+
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
MenuItem annotationColour = new MenuItem();
- MenuItem invertColSel = new MenuItem();
+ MenuItem annotationColumnSelection = new MenuItem();
- Menu menu1 = new Menu();
+ MenuItem invertColSel = new MenuItem();
MenuItem showColumns = new MenuItem();
MenuItem showSeqs = new MenuItem();
- Menu menu2 = new Menu();
-
MenuItem hideColumns = new MenuItem();
MenuItem hideSequences = new MenuItem();
@@ -3135,11 +3857,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem showAllHidden = new MenuItem();
- Menu formatMenu = new Menu();
+ MenuItem newView = new MenuItem();
- Menu selectMenu = new Menu();
+ private CheckboxMenuItem showAlignmentAnnotations;
- MenuItem newView = new MenuItem();
+ 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
@@ -3150,27 +3882,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
* true to attach the view to the applet area on the page rather than
* in a new window
*/
- public void createAlignFrameWindow(boolean reallyEmbedded, String title)
+ public void createAlignFrameWindow(boolean reallyEmbedded)
{
if (reallyEmbedded)
{
- // ////
- // Explicly 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 Seperator
- embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
- Font.PLAIN, 10, false); // use our own fonts.
- // and actually add the components to the applet area
- viewport.applet.setLayout(new BorderLayout());
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
- viewport.applet.add(statusBar, BorderLayout.SOUTH);
- alignPanel.setSize(viewport.applet.getSize().width,
- viewport.applet.getSize().height - embeddedMenu.HEIGHT
- - statusBar.HEIGHT);
- viewport.applet.add(alignPanel, BorderLayout.CENTER);
- viewport.applet.validate();
+ embedAlignFrameInApplet(viewport.applet);
}
else
{
@@ -3179,52 +3895,150 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
//
if (embedMenuIfNeeded(alignPanel))
{
- // adjust for status bar height too
- alignPanel.setSize(getSize().width, getSize().height
- - statusBar.HEIGHT);
+ /*
+ * 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, title, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ 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
+ * 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
+ * @param jmolViewer
* JmolViewer instance
* @param sequenceIds
- * - sequence Ids to search for associations This method doesn't
- * work. See http://issues.jalview.org/browse/JAL-621
- *
- * public SequenceStructureBinding addStructureViewInstance(Object
- * jmolviewer, String[] sequenceIds) { org.jmol.api.JmolViewer
- * viewer=null; try { viewer = (org.jmol.api.JmolViewer) 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;sid0) { seqs = new SequenceI[sqi.size()]; for (int
- * sid=0,sSize=sqi.size();sid 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)
{
@@ -3232,7 +4046,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
boolean needtoadd = false;
if (toaddpdb != null)
{
- Vector pdbe = toaddpdb.getPDBId();
+ Vector pdbe = toaddpdb.getAllPDBEntries();
PDBEntry pdbentry = null;
if (pdbe != null && pdbe.size() > 0)
{
@@ -3259,20 +4073,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
// resolve data source
// TODO: this code should be a refactored to an io package
- String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
+ FileFormat.PDB);
if (protocol == null)
{
return false;
}
if (needtoadd)
{
- // make a note of the access mode and add
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- }
- pdbentry.getProperty().put("protocol", protocol);
+ pdbentry.setProperty("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
}
}
return true;
@@ -3287,8 +4099,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
if (seqs[i] != null)
{
- sequences.addElement(new Object[]
- { seqs[i], (chains != null) ? chains[i] : null });
+ sequences
+ .addElement(new Object[]
+ { seqs[i], (chains != null) ? chains[i] : null });
}
}
seqs = new SequenceI[sequences.size()];
@@ -3301,13 +4114,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
chains[i] = (String) oj[1];
}
}
- return new Object[]
- { seqs, chains };
+ return new Object[] { seqs, chains };
}
public void newStructureView(JalviewLite applet, PDBEntry pdb,
- SequenceI[] seqs, String[] chains, String protocol)
+ SequenceI[] seqs, String[] chains, DataSourceType protocol)
{
// Scrub any null sequences from the array
Object[] sqch = cleanSeqChainArrays(seqs, chains);
@@ -3315,13 +4127,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
chains = (String[]) sqch[1];
if (seqs == null || seqs.length == 0)
{
- System.err
- .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ System.err.println(
+ "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
- if (protocol == null || protocol.trim().length() == 0
- || protocol.equals("null"))
+ if (protocol == null)
{
- protocol = (String) pdb.getProperty().get("protocol");
+ String sourceType = (String) pdb.getProperty("protocol");
+ try
+ {
+ protocol = DataSourceType.valueOf(sourceType);
+ } catch (IllegalArgumentException e)
+ {
+ // ignore
+ }
if (protocol == null)
{
System.err.println("Couldn't work out protocol to open structure: "
@@ -3329,16 +4147,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
return;
}
}
+ if (applet.useXtrnalSviewer)
+ {
+ // register the association(s) and quit, don't create any windows.
+ if (StructureSelectionManager.getStructureSelectionManager(applet)
+ .setMapping(seqs, chains, pdb.getFile(), protocol,
+ null) == null)
+ {
+ System.err.println("Failed to map " + pdb.getFile() + " ("
+ + protocol + ") to any sequences");
+ }
+ return;
+ }
if (applet.isAlignPdbStructures() && applet.jmolAvailable)
{
// 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);
+ AppletJmol ajm = null, tajm;
+ Vector jmols = applet.getAppletWindow(AppletJmol.class);
for (int i = 0, iSize = jmols.size(); i < iSize; i++)
{
- tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ tajm = (AppletJmol) jmols.elementAt(i);
if (tajm.ap.alignFrame == this)
{
ajm = tajm;
@@ -3347,8 +4176,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
if (ajm != null)
{
- System.err
- .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ 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;
@@ -3357,14 +4186,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
- protocol);
+ new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
applet.lastFrameX += 40;
applet.lastFrameY += 40;
}
else
{
- new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
}
@@ -3375,4 +4203,161 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// 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,
+ HiddenColumns hidden)
+ {
+ alignPanel.seqPanel.selection(sel, csel, hidden, null);
+ }
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.seqPanel.scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.seqPanel.scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.seqPanel.scrollToColumn(column);
+ }
+
+ /**
+ * @return the alignments unique ID.
+ */
+ public String getSequenceSetId()
+ {
+ return viewport.getSequenceSetId();
+ }
+
+ /**
+ * Load the (T-Coffee) score file from the specified url
+ *
+ * @param source
+ * File/URL/T-COFFEE score file contents
+ * @throws IOException
+ * @return true if alignment was annotated with data from source
+ */
+ public boolean loadScoreFile(String source) throws IOException
+ {
+
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,
+ AppletFormatAdapter.checkProtocol(source));
+ if (!file.isValid())
+ {
+ // TODO: raise dialog for gui
+ System.err.println("Problems parsing T-Coffee scores: "
+ + file.getWarningMessage());
+ System.err.println("Origin was:\n" + source);
+ return false;
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if ((aln = viewport.getAlignment()) != null
+ && (aln.getHeight() != file.getHeight()
+ || aln.getWidth() != file.getWidth()))
+ {
+ // TODO: raise a dialog box here rather than bomb out.
+ System.err.println(
+ "The scores matrix does not match the alignment dimensions");
+
+ }
+
+ // TODO add parameter to indicate if matching should be done
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))
+ {
+ alignPanel.fontChanged();
+ tcoffeeColour.setEnabled(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ return true;
+ }
+ else
+ {
+ System.err.println("Problems resolving T-Coffee scores:");
+ if (file.getWarningMessage() != null)
+ {
+ System.err.println(file.getWarningMessage());
+ }
+ }
+ return false;
+ }
+
+ public SplitFrame getSplitFrame()
+ {
+ return this.splitFrame;
+ }
+
+ public void setSplitFrame(SplitFrame sf)
+ {
+ this.splitFrame = sf;
+ }
+
+ // may not need this
+ @Override
+ public void setShowSeqFeatures(boolean b)
+ {
+ // showSeqFeatures.setSelected(b);
+ viewport.setShowSequenceFeatures(b);
+
+ }
+
+ @Override
+ public void setMenusForViewport()
+ {
+ // setMenusFromViewport(viewport);
+
+ }
+
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ if (enableIfNecessary)
+ {
+ sequenceFeatures.setState(true);
+ alignPanel.av.setShowSequenceFeatures(true);
+ }
+ }
+
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return alignPanel.av.featureSettings;
+ }
+
+ @Override
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
+ return new FeatureSettings(alignPanel);
+ }
+
+ private Rectangle fs_bounds = null;
+
+ @Override
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ fs_bounds = bounds;
+ }
+
+ @Override
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return fs_bounds;
+ }
+
}