X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=122afa8664df4b4874db5c4e4f3405ae90626b4f;hb=8546ee20c998cd48567d324027d1885a771e688f;hp=ab99e065edd79a2053a65ca1de46f243d9e88ccc;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ab99e06..122afa8 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,35 +1,45 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
@@ -51,18 +61,22 @@ import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Canvas;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
@@ -71,6 +85,7 @@ import java.awt.Label;
import java.awt.Menu;
import java.awt.MenuBar;
import java.awt.MenuItem;
+import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
@@ -84,28 +99,81 @@ import java.awt.event.WindowEvent;
import java.io.IOException;
import java.net.URL;
import java.net.URLEncoder;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.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,
+ /*
+ * Flag for showing autocalculated consensus above or below other consensus
+ * rows
+ */
+ private boolean showAutoCalculatedAbove;
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ /**
+ * Constructor that creates the frame and adds it to the display.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded)
+ {
+ this(al, applet, title, embedded, true);
+ }
+
+ /**
+ * Constructor that optionally allows the frame to be displayed or only
+ * created.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ * @param addToDisplay
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded, boolean addToDisplay)
+ {
+ this(al, null, null, applet, title, embedded, addToDisplay);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
String title, boolean embedded)
{
+ this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded, boolean addToDisplay)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -118,23 +186,61 @@ 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 (columnSelection != null)
+ {
+ viewport.setColumnSelection(columnSelection);
+ }
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
+
+ alignPanel = new AlignmentPanel(this, viewport);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
- annotationPanelMenuItem.setState(viewport.showAnnotation);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
- followMouseOverFlag.setState(viewport.getFollowHighlight());
+ 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.showJVSuffix);
+ seqLimits.setState(viewport.getShowJVSuffix());
if (applet != null)
{
@@ -170,23 +276,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
- try
- {
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
- {
- }
}
if (viewport.getAlignment().isNucleotide())
@@ -217,8 +306,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.annotationPanelHolder.addKeyListener(this);
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
- createAlignFrameWindow(embedded, title);
+ setAnnotationsVisibility();
+
+ if (addToDisplay)
+ {
+ addToDisplay(embedded);
+ }
+ }
+
+ /**
+ * @param embedded
+ */
+ public void addToDisplay(boolean embedded)
+ {
+ createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
@@ -263,18 +365,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public boolean parseFeaturesFile(String file, String type,
boolean autoenabledisplay)
{
- // TODO: test if importing a features file onto an alignment which already
- // has features with links overwrites the original links.
-
- Hashtable featureLinks = new Hashtable();
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file, type)
- .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, featureLinks,
- true, viewport.applet.getDefaultParameter(
- "relaxedidmatch", false));
+ Map colours = alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours();
+ boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
+ "relaxedidmatch", false);
+ featuresFile = new FeaturesFile(file, type).parse(
+ viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
@@ -282,21 +381,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (featuresFile)
{
- if (featureLinks.size() > 0)
- {
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
- }
if (autoenabledisplay)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(true);
sequenceFeatures.setState(true);
}
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true);
- statusBar.setText("Successfully added features to alignment.");
+ statusBar.setText(MessageManager
+ .getString("label.successfully_added_features_alignment"));
}
return featuresFile;
}
@@ -309,7 +410,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
+ {
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
@@ -370,16 +473,24 @@ 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:
@@ -440,8 +551,9 @@ 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"));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
@@ -465,7 +577,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
@@ -477,7 +589,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
@@ -543,6 +655,20 @@ 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())
{
@@ -576,9 +702,7 @@ 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.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns()
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
@@ -606,8 +730,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
viewport.showAllHiddenSeqs();
}
@@ -615,7 +738,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (toggleCols)
{
- if (viewport.getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
@@ -627,6 +750,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
viewport.showAllHiddenColumns();
}
+ viewport.sendSelection();
}
}
@@ -643,114 +767,199 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
@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 (evt.getSource() == sortByTree)
+ else if (source == sortByTree)
{
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 (evt.getSource() == showGroupConsensus)
+ else if (source == showGroupConsensus)
{
showGroupConsensus_actionPerformed();
}
- else if (evt.getSource() == showGroupConservation)
+ else if (source == showGroupConservation)
{
showGroupConservation_actionPerformed();
}
- else if (evt.getSource() == showSequenceLogo)
+ else if (source == showSequenceLogo)
{
showSequenceLogo_actionPerformed();
}
- else if (evt.getSource() == normSequenceLogo)
+ else if (source == normSequenceLogo)
{
normSequenceLogo_actionPerformed();
}
- else if (evt.getSource() == showConsensusHistogram)
+ else if (source == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
}
- else if (evt.getSource() == applyAutoAnnotationSettings)
+ else if (source == applyAutoAnnotationSettings)
{
applyAutoAnnotationSettings_actionPerformed();
}
alignPanel.paintAlignment(true);
}
+ /**
+ * Set the visibility state of sequence-related and/or alignment-related
+ * annotations depending on checkbox selections, and repaint.
+ *
+ * @param visible
+ */
+ private void setAnnotationsVisibility()
+ {
+ boolean showForAlignment = showAlignmentAnnotations.getState();
+ boolean showForSequences = showSequenceAnnotations.getState();
+ if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean visible = (aa.sequenceRef == null ? showForAlignment
+ : showForSequences);
+ aa.visible = visible;
+ }
+ }
+ alignPanel.validateAnnotationDimensions(true);
+ validate();
+ repaint();
+ }
+
+ private void setAnnotationSortOrder(SequenceAnnotationOrder order)
+ {
+ this.annotationSortOrder = order;
+ }
+
+ /**
+ * Set flags on the viewport that control annotation ordering
+ */
+ private void setViewportAnnotationOrder()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
+ }
+
+ private void setShowAutoCalculatedAbove(boolean showAbove)
+ {
+ this.showAutoCalculatedAbove = showAbove;
+ }
+
private void mouseOverFlag_stateChanged()
{
- viewport.followHighlight = followMouseOverFlag.getState();
+ viewport.setFollowHighlight(followMouseOverFlag.getState());
// TODO: could kick the scrollTo mechanism to reset view for current
// searchresults.
}
@@ -764,6 +973,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
@Override
public void actionPerformed(ActionEvent evt)
{
+ viewport.applet.currentAlignFrame = this;
+
Object source = evt.getSource();
if (source == inputText)
@@ -861,11 +1072,14 @@ 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);
+ viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
{
@@ -899,27 +1113,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
viewport.showAllHiddenColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
+ // uncomment if we want to slave sequence selections in split frame
+ // viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
alignPanel.paintAlignment(true);
+ // uncomment if we want to slave sequence selections in split frame
+ // viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == hideAllSelection)
{
@@ -928,12 +1149,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
else if (source == showGroupConsensus)
{
@@ -971,8 +1194,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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)
{
@@ -1023,6 +1247,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
changeColour(new PurinePyrimidineColourScheme());
}
+ // else if (source == RNAInteractionColour)
+ // {
+ // changeColour(new RNAInteractionColourScheme());
+ // }
else if (source == RNAHelixColour)
{
new RNAHelicesColourChooser(viewport, alignPanel);
@@ -1055,6 +1283,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
new AnnotationColourChooser(viewport, alignPanel);
}
+ else if (source == annotationColumnSelection)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
else if (source == sortPairwiseMenuItem)
{
sortPairwiseMenuItem_actionPerformed();
@@ -1115,7 +1347,8 @@ 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)
@@ -1123,58 +1356,54 @@ 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(
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
+
+ FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
e.getActionCommand(), viewport.getAlignment(),
- viewport.showJVSuffix));
+ viewport.getShowJVSuffix()));
}
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations / T-coffee score 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.getAlignment()
- .getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), ((Alignment) viewport
- .getAlignment()).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
- && viewport.featuresDisplayed != 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;
}
@@ -1182,15 +1411,15 @@ 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
- .getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols());
}
else
{
- features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+ features = formatter.printGffFormat(viewport.getAlignment()
.getSequencesArray(), getDisplayedFeatureCols());
}
@@ -1210,13 +1439,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
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;
@@ -1226,7 +1458,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
StringBuffer url = new StringBuffer(jalviewServletURL);
- url.append("?open="
+ // 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)
@@ -1344,41 +1581,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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.updateHiddenColumns();
}
@@ -1392,16 +1634,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
*/
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);
+ AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
@@ -1424,16 +1666,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
*/
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);
+ AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
@@ -1449,9 +1691,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
.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
@@ -1490,6 +1732,12 @@ 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();
@@ -1500,6 +1748,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
+
+ /*
+ * Also move cDNA/protein complement sequences
+ */
+ AlignViewportI complement = viewport.getCodingComplement();
+ if (complement != null)
+ {
+ SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
+ viewport, complement);
+ complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
+ up ? null : complement.getHiddenRepSequences(), up);
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
+ }
}
synchronized void slideSequences(boolean right, int size)
@@ -1528,7 +1789,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
@@ -1536,30 +1799,44 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
.size()]);
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = invertGroup.elementAt(i);
+ }
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
+ {
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)
@@ -1571,16 +1848,19 @@ 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
+ .appendSlideCommand((SlideSequencesCommand) historyList
.peek());
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
@@ -1598,12 +1878,12 @@ 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.getAlignment().findIndex(seq);
- orderedSeqs.put(index + "", seq);
+ orderedSeqs.put(index, seq);
}
int index = 0, startRes, endRes;
@@ -1613,14 +1893,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
-
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ copiedHiddenColumns.addElement(new int[] {
+ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
else
@@ -1634,11 +1910,10 @@ 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
@@ -1718,14 +1993,17 @@ 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);
@@ -1738,8 +2016,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ frameHeight);
}
else
{
@@ -1760,7 +2038,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
// !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
@@ -1794,9 +2073,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
seqs.addElement(seq);
}
- // If the cut affects all sequences, remove highlighted columns
+ /*
+ * 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);
}
@@ -1810,8 +2112,9 @@ 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,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
@@ -1888,41 +2191,33 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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.getAlignment()
- .getGroups());
- viewport.getAlignment().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.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
- viewport.setSequenceColour(sq, col);
- }
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
- protected void deleteGroups_actionPerformed()
+ protected void createGroup_actionPerformed()
{
- viewport.getAlignment().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()
@@ -1934,7 +2229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
@@ -1951,7 +2249,10 @@ 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);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
@@ -1981,7 +2282,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
ColumnSelection colSel = viewport.getColumnSelection();
int column;
- if (colSel.size() > 0)
+ if (!colSel.isEmpty())
{
if (trimLeft)
{
@@ -2006,22 +2307,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
-
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns",
+ new String[] { Integer.valueOf(trimRegion.getSize())
+ .toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
@@ -2061,8 +2360,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns",
+ new String[] { Integer.valueOf(removeGapCols.getSize())
+ .toString() }));
// This is to maintain viewport position on first residue
// of first sequence
@@ -2186,8 +2487,8 @@ 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;
}
@@ -2201,7 +2502,9 @@ 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;
}
@@ -2219,7 +2522,9 @@ 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;
}
@@ -2236,11 +2541,12 @@ 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)
{
@@ -2264,7 +2570,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void displayNonconservedMenuItem_actionPerformed()
{
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
@@ -2289,7 +2595,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[] { this.getTitle() }),
overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
@@ -2311,62 +2618,31 @@ 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());
+ viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
+ cs, "Background"));
}
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs.setConservationApplied(true);
+ viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
-
}
else
{
- cs.setConservation(null);
+ cs.setConservationApplied(false);
}
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
-
}
viewport.setGlobalColourScheme(cs);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(viewport.applet)
- .sequenceColoursChanged(alignPanel);
-
alignPanel.paintAlignment(true);
}
@@ -2467,7 +2743,8 @@ 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);
}
}
@@ -2565,16 +2842,18 @@ 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(alignPanel, treeFile, "From File - ", tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile,
+ MessageManager.getString("label.load_tree_from_file"), tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
@@ -2594,7 +2873,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
.sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[] { title }), oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2691,28 +2971,32 @@ 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, Jan Engelhardt, Lauren Lui,",
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
- g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
g.drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- 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);
+ 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(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ MessageManager.getString("label.jalview_cite_1_authors"),
x, y += fh);
g.drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
- x, y += fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
}
@@ -2720,7 +3004,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
}
@@ -2741,33 +3026,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuBar alignFrameMenuBar = new MenuBar();
- Menu fileMenu = new Menu("File");
-
- MenuItem loadApplication = new MenuItem("View in Full Application");
-
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem outputFeatures = new MenuItem("Export Features ...");
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
- MenuItem closeMenuItem = new MenuItem("Close");
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
- Menu editMenu = new Menu("Edit");
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features"));
- Menu viewMenu = new Menu("View");
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations"));
- Menu colourMenu = new Menu("Colour");
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
- Menu calculateMenu = new Menu("Calculate");
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_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();
@@ -2803,8 +3089,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public Label statusBar = new Label();
- Menu outputTextboxMenu = new Menu();
-
MenuItem clustalColour = new MenuItem();
MenuItem zappoColour = new MenuItem();
@@ -2823,6 +3107,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem purinePyrimidineColour = new MenuItem();
+ // MenuItem RNAInteractionColour = new MenuItem();
+
MenuItem RNAHelixColour = new MenuItem();
MenuItem userDefinedColour = new MenuItem();
@@ -2843,7 +3129,8 @@ 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();
@@ -2869,6 +3156,10 @@ 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();
@@ -2895,22 +3186,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem modifyConservation = new MenuItem();
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
- "Autocalculate Consensus", true);
+ CheckboxMenuItem autoCalculate = null;
CheckboxMenuItem sortByTree = new CheckboxMenuItem(
"Sort Alignment With New Tree", true);
Menu sortByTreeMenu = new Menu();
- Menu sort = new Menu();
-
- Menu calculate = new Menu();
-
MenuItem inputText = new MenuItem();
- Menu helpMenu = new Menu();
-
MenuItem documentation = new MenuItem();
MenuItem about = new MenuItem();
@@ -2921,8 +3205,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
- Menu autoAnnMenu = new Menu();
-
CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
@@ -2935,18 +3217,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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
+ /*
+ * Configure File menu items and actions
+ */
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText.addActionListener(this);
+ Menu outputTextboxMenu = new Menu(
+ MessageManager.getString("label.out_to_textbox"));
for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- item = new MenuItem(
+ MenuItem item = new MenuItem(
jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
@@ -2962,249 +3253,372 @@ 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");
+
+ /*
+ * Configure Edit menu items and actions
+ */
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
+ undoMenuItem.addActionListener(this);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
+ redoMenuItem.addActionListener(this);
+ copy.setLabel(MessageManager.getString("action.copy"));
+ copy.addActionListener(this);
+ cut.setLabel(MessageManager.getString("action.cut"));
+ cut.addActionListener(this);
+ delete.setLabel(MessageManager.getString("action.delete"));
+ delete.addActionListener(this);
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
+ pasteNew.addActionListener(this);
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
+ pasteThis.addActionListener(this);
+ remove2LeftMenuItem.setLabel(MessageManager
+ .getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
+ remove2RightMenuItem.setLabel(MessageManager
+ .getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+ removeGappedColumnMenuItem.setLabel(MessageManager
+ .getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
+ removeAllGapsMenuItem.setLabel(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.addActionListener(this);
+
+ /*
+ * Configure Select menu items and actions
+ */
+ findMenuItem.setLabel(MessageManager.getString("action.find"));
+ findMenuItem.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.addActionListener(this);
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
+ invertColSel.addActionListener(this);
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
+ deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel(MessageManager
+ .getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(this);
+ createGroup.setLabel(MessageManager.getString("action.create_group"));
+ unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ annotationColumnSelection.setLabel(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumnSelection.addActionListener(this);
+
+ /*
+ * Configure View menu items and actions
+ */
+ newView.setLabel(MessageManager.getString("action.new_view"));
+ newView.addActionListener(this);
+ Menu showMenu = new Menu(MessageManager.getString("action.show"));
+ showColumns.setLabel(MessageManager.getString("label.all_columns"));
+ showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
+ Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
+ hideColumns
+ .setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager
+ .getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager
+ .getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager
+ .getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager
+ .getString("label.all_sequences_columns"));
+ showColumns.addActionListener(this);
+ showSeqs.addActionListener(this);
+ hideColumns.addActionListener(this);
+ hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.addActionListener(this);
+ featureSettings.setLabel(MessageManager
+ .getString("action.feature_settings"));
+ featureSettings.addActionListener(this);
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.show_sequence_features"));
+ sequenceFeatures.addItemListener(this);
+ sequenceFeatures.setState(false);
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
+ followMouseOverFlag.addItemListener(this);
+ alProperties.addActionListener(this);
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
+ overviewMenuItem.addActionListener(this);
+
+ /*
+ * Configure Annotations menu items and actions
+ */
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.addItemListener(this);
+ showGroupConsensus.setLabel(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager
+ .getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager
+ .getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager
+ .getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager
+ .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setState(true);
+ Menu autoAnnMenu = new Menu(
+ MessageManager.getString("label.autocalculated_annotation"));
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+ applyAutoAnnotationSettings.addItemListener(this);
+ showAlignmentAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_al_annotations"));
+ showSequenceAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_seq_annotations"));
+ sortAnnBySequence = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_sequence"));
+ sortAnnByLabel = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_label"));
+ showAutoFirst = new CheckboxMenuItem(
+ MessageManager.getString("label.show_first"));
+ showAutoFirst.setState(false); // pending applet parameter
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ showAutoLast = new CheckboxMenuItem(
+ MessageManager.getString("label.show_last"));
+ showAutoLast.setState(!showAutoFirst.getState());
+ showAlignmentAnnotations.addItemListener(this);
+ showSequenceAnnotations.addItemListener(this);
+ sortAnnBySequence.addItemListener(this);
+ sortAnnByLabel.addItemListener(this);
+ showAutoFirst.addItemListener(this);
+ showAutoLast.addItemListener(this);
+
+ /*
+ * Configure Format menu items and actions
+ */
+ font.setLabel(MessageManager.getString("action.font"));
+ font.addActionListener(this);
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
+ scaleAbove.setState(true);
+ scaleAbove.setEnabled(false);
+ scaleAbove.addItemListener(this);
+ scaleLeft.setEnabled(false);
+ scaleLeft.setState(true);
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
+ scaleLeft.addItemListener(this);
+ scaleRight.setEnabled(false);
+ scaleRight.setState(true);
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
+ scaleRight.addItemListener(this);
+ viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
+ viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- 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");
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
+ colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.addItemListener(this);
+ wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
+ wrapMenuItem.addItemListener(this);
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addItemListener(this);
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelFlag.addItemListener(this);
+ seqLimits.setState(true);
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
+ seqLimits.addItemListener(this);
+ /*
+ * Configure Colour menu items and actions
+ */
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addItemListener(this);
+ clustalColour.setLabel(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel("Purine/Pyrimidine");
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel("by RNA Helices");
+ // RNAInteractionColour.setLabel(MessageManager
+ // .getString("label.rna_interaction"));
+ // RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager
+ .getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel("T-Coffee Scores");
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
- // provided
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ // it will be enabled only if a score file is provided
+ tcoffeeColour.setEnabled(false);
tcoffeeColour.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);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
+ conservationMenuItem.setLabel(MessageManager
+ .getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
- findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel("Above Identity Threshold");
+ abovePIDThreshold.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
+ nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
- grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
+ annotationColour.addActionListener(this);
+
+ /*
+ * Configure Calculate menu items and actions
+ */
+ sortPairwiseMenuItem.setLabel(MessageManager
+ .getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(this);
+ sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel(MessageManager
+ .getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(this);
+ sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(this);
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(this);
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(this);
+ autoCalculate = new CheckboxMenuItem(
+ MessageManager.getString("label.autocalculate_consensus"), true);
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(this);
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(this);
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(this);
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(this);
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
+ Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
+ Menu calculateTreeMenu = new Menu(
+ MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
sortByTree.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);
- 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");
- showGroupConsensus.setLabel("Group Consensus");
- showGroupConservation.setLabel("Group Conservation");
- showConsensusHistogram.setLabel("Show Consensus Histogram");
- showSequenceLogo.setLabel("Show Consensus Logo");
- normSequenceLogo.setLabel("Normalise Consensus Logo");
- applyAutoAnnotationSettings.setLabel("Apply to all groups");
- applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel("Autocalculated Annotation");
-
- invertColSel.addActionListener(this);
- showColumns.addActionListener(this);
- showSeqs.addActionListener(this);
- hideColumns.addActionListener(this);
- hideSequences.addActionListener(this);
- hideAllButSelection.addActionListener(this);
- hideAllSelection.addActionListener(this);
- showAllHidden.addActionListener(this);
- showGroupConsensus.addItemListener(this);
- showGroupConservation.addItemListener(this);
- showConsensusHistogram.addItemListener(this);
- showSequenceLogo.addItemListener(this);
- normSequenceLogo.addItemListener(this);
- applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
- 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();
@@ -3213,21 +3627,38 @@ 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);
- autoAnnMenu.add(applyAutoAnnotationSettings);
- autoAnnMenu.add(showConsensusHistogram);
- autoAnnMenu.add(showSequenceLogo);
- autoAnnMenu.add(normSequenceLogo);
- autoAnnMenu.addSeparator();
- autoAnnMenu.add(showGroupConservation);
- autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
@@ -3235,6 +3666,48 @@ 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);
@@ -3250,6 +3723,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
@@ -3259,73 +3733,62 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
colourMenu.add(RNAHelixColour);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
+
+ /*
+ * 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);
calculateMenu.add(sortByTree);
- 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);
+
+ /*
+ * 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));
+ statusBar.setText(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();
@@ -3336,11 +3799,21 @@ 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
@@ -3351,46 +3824,11 @@ 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);
- final AlignFrame me = this;
- viewport.applet.addFocusListener(new FocusListener()
- {
-
- @Override
- public void focusLost(FocusEvent e)
- {
- if (me.viewport.applet.currentAlignFrame == me)
- {
- me.viewport.applet.currentAlignFrame = null;
- }
- }
-
- @Override
- public void focusGained(FocusEvent e)
- {
- me.viewport.applet.currentAlignFrame = me;
- }
- });
- viewport.applet.validate();
+ embedAlignFrameInApplet(viewport.applet);
}
else
{
@@ -3399,19 +3837,68 @@ 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
@@ -3427,10 +3914,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public SequenceStructureBinding addStructureViewInstance(
Object jmolviewer, String[] sequenceIds)
{
- org.jmol.api.JmolViewer viewer = null;
+ Viewer viewer = null;
try
{
- viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ viewer = (Viewer) jmolviewer;
} catch (ClassCastException ex)
{
System.err.println("Unsupported viewer object :"
@@ -3472,12 +3959,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
return null;
}
}
- ExtJmol jmv = 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 });
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
}
return jmv;
@@ -3503,7 +3989,7 @@ 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)
{
@@ -3537,13 +4023,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
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;
@@ -3558,8 +4041,8 @@ 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()];
@@ -3572,8 +4055,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
chains[i] = (String) oj[1];
}
}
- return new Object[]
- { seqs, chains };
+ return new Object[] { seqs, chains };
}
@@ -3592,7 +4074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (protocol == null || protocol.trim().length() == 0
|| protocol.equals("null"))
{
- protocol = (String) pdb.getProperty().get("protocol");
+ protocol = (String) pdb.getProperty("protocol");
if (protocol == null)
{
System.err.println("Couldn't work out protocol to open structure: "
@@ -3751,4 +4233,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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;
+ }
+
}