X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=447f5e368680bb28c8f4d95609efb8e2384d46c1;hb=c94c1390298db2e80abc04b371d3e7767f5e5968;hp=638a68fc8b4c2a208bc15571017e51033ce68478;hpb=60504d4176b00ae80fb98a738d33429865ff137b;p=jalview.git
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 638a68f..447f5e3 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,31 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureRenderer;
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;
@@ -53,13 +57,15 @@ import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
+import jalview.schemes.RNAInteractionColourScheme;
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 java.awt.BorderLayout;
@@ -87,9 +93,11 @@ import java.awt.event.WindowEvent;
import java.io.IOException;
import java.net.URL;
import java.net.URLEncoder;
-import java.util.Enumeration;
+import java.util.Arrays;
+import java.util.Deque;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
@@ -97,6 +105,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
+
public AlignmentPanel alignPanel;
public AlignViewport viewport;
@@ -107,9 +116,33 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
String jalviewServletURL;
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
+ /**
+ * 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)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -122,14 +155,36 @@ 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);
+ DEFAULT_WIDTH = width;
+ }
+ param = applet.getParameter("windowHeight");
+ if (param != null)
+ {
+ int height = Integer.parseInt(param);
+ DEFAULT_HEIGHT = height;
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
- annotationPanelMenuItem.setState(viewport.showAnnotation);
+ annotationPanelMenuItem.setState(viewport.isShowAnnotation());
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.getFollowHighlight());
showGroupConsensus.setState(viewport.isShowGroupConsensus());
@@ -137,8 +192,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
- seqLimits.setState(viewport.showJVSuffix);
+ seqLimits.setState(viewport.getShowJVSuffix());
if (applet != null)
{
@@ -174,23 +230,6 @@ 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())
@@ -221,8 +260,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.annotationPanelHolder.addKeyListener(this);
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
- createAlignFrameWindow(embedded, title);
+ if (addToDisplay)
+ {
+ addToDisplay(embedded);
+ }
+ }
+
+ /**
+ * @param embedded
+ */
+ public void addToDisplay(boolean embedded)
+ {
+ createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
@@ -276,7 +326,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
featuresFile = new jalview.io.FeaturesFile(file, type)
.parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, featureLinks,
+ .getFeatureRenderer().getFeatureColours(), featureLinks,
true, viewport.applet.getDefaultParameter(
"relaxedidmatch", false));
} catch (Exception ex)
@@ -292,15 +342,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
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(MessageManager.getString("label.successfully_added_features_alignment"));
+ statusBar.setText(MessageManager
+ .getString("label.successfully_added_features_alignment"));
}
return featuresFile;
}
@@ -313,7 +369,9 @@ 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())
{
@@ -374,16 +432,24 @@ 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:
@@ -444,7 +510,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(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;
@@ -468,7 +536,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
@@ -480,7 +548,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
@@ -559,7 +627,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
break;
-
+
case KeyEvent.VK_U:
if (evt.isControlDown())
{
@@ -707,7 +775,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
else if (evt.getSource() == sequenceFeatures)
{
- viewport.showSequenceFeatures(sequenceFeatures.getState());
+ viewport.setShowSequenceFeatures(sequenceFeatures.getState());
alignPanel.seqPanel.seqCanvas.repaint();
}
else if (evt.getSource() == conservationMenuItem)
@@ -988,8 +1056,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
- 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 400, 250);
}
else if (source == overviewMenuItem)
{
@@ -1040,6 +1109,10 @@ 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);
@@ -1072,6 +1145,10 @@ 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();
@@ -1132,7 +1209,8 @@ 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, MessageManager.getString("label.input_cut_paste"), 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.input_cut_paste"), 500, 500);
}
protected void outputText_actionPerformed(ActionEvent e)
@@ -1140,58 +1218,52 @@ 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,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(
e.getActionCommand(), viewport.getAlignment(),
- viewport.showJVSuffix));
+ viewport.getShowJVSuffix()));
}
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_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, MessageManager.getString("action.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, MessageManager.getString("label.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;
}
@@ -1227,13 +1299,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
else
{
if (features == null)
+ {
features = "";
+ }
}
return features;
@@ -1361,11 +1436,13 @@ 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(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ CommandI command = viewport.getHistoryList().peek();
+ undoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.undo_command", new Object[]
+ { command.getDescription() }));
}
else
{
@@ -1373,12 +1450,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ CommandI command = viewport.getRedoList().peek();
+ redoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.redo_command", new Object[]
+ { command.getDescription() }));
}
else
{
@@ -1390,12 +1469,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* 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();
}
@@ -1409,13 +1489,13 @@ 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);
@@ -1441,13 +1521,13 @@ 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);
@@ -1507,6 +1587,12 @@ 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();
@@ -1517,6 +1603,21 @@ 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);
+ // TODO need to trigger a repaint of the complementary panel - how?
+ // would prefer to handle in SplitFrame but it is not overriding key
+ // listener chiz
+ }
}
synchronized void slideSequences(boolean right, int size)
@@ -1545,7 +1646,9 @@ 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()]);
@@ -1553,30 +1656,44 @@ 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)
@@ -1588,16 +1705,19 @@ 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();
}
@@ -1630,12 +1750,8 @@ 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 });
}
@@ -1735,14 +1851,14 @@ 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);
@@ -1777,7 +1893,8 @@ 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()));
@@ -1827,8 +1944,9 @@ 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);
@@ -1905,7 +2023,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void makeGrpsFromSelection_actionPerformed()
{
- if (avc.makeGroupsFromSelection()) {
+ if (avc.makeGroupsFromSelection())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
@@ -1916,6 +2035,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
avc.createGroup();
}
+
protected void unGroup_actionPerformed()
{
if (avc.unGroup())
@@ -1923,6 +2043,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.alignmentChanged();
}
}
+
protected void deleteGroups_actionPerformed()
{
if (avc.deleteGroups())
@@ -2026,7 +2147,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.getSelectionGroup());
}
- statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
@@ -2066,7 +2189,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+ 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
@@ -2190,8 +2315,8 @@ 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;
}
@@ -2205,7 +2330,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- return fr.getGroups();
+ List gps = fr.getFeatureGroups();
+ int p=0;
+ String[] _gps = new String[gps.size()];
+ for (Object gp:gps)
+ {
+ _gps[p++] = gp.toString();
+ }
+ return _gps;
}
return null;
}
@@ -2223,7 +2355,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- return fr.getGroups(visible);
+ List gps = fr.getGroups(visible);
+ int p=0;
+ String[] _gps = new String[gps.size()];
+ for (Object gp:gps)
+ {
+ _gps[p++] = gp.toString();
+ }
+ return _gps;
}
return null;
}
@@ -2240,11 +2379,12 @@ 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)
{
@@ -2268,7 +2408,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void displayNonconservedMenuItem_actionPerformed()
{
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
@@ -2293,8 +2433,9 @@ 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, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
- overview.getPreferredSize().width,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[]
+ { this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
@@ -2323,42 +2464,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
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);
@@ -2471,7 +2590,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
@@ -2573,12 +2693,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.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, MessageManager.getString("label.load_tree_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);
}
@@ -2598,8 +2720,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
.sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[]
+ { title }), oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2695,27 +2818,31 @@ 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(MessageManager.formatMessage("label.jalviewLite_release", new String[]{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(MessageManager.formatMessage("label.jaview_build_date", new String[]{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(
- MessageManager.getString("label.jalview_authors_1"),
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
- g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
g.drawString(
- MessageManager.getString("label.jalview_dev_managers"),
- x, y += fh);
- g.drawString(
- MessageManager.getString("label.jalview_distribution_lists"),
- x, y += fh);
- g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
+ MessageManager.getString("label.jalview_dev_managers"), x,
+ y += fh);
+ g.drawString(MessageManager
+ .getString("label.jalview_distribution_lists"), x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"),
+ x, y += fh + 8);
g.drawString(
MessageManager.getString("label.jalview_cite_1_authors"),
x, y += fh);
g.drawString(
- MessageManager.getString("label.jalview_cite_1_title"),
- x, y += fh);
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
@@ -2724,7 +2851,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
}
@@ -2747,17 +2875,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
- MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
- MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
- MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features").concat("..."));
- MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations").concat("..."));
- MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
@@ -2765,13 +2899,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
- Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
- MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
- MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
- MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
+ MenuItem invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
@@ -2827,6 +2965,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem purinePyrimidineColour = new MenuItem();
+ MenuItem RNAInteractionColour = new MenuItem();
+
MenuItem RNAHelixColour = new MenuItem();
MenuItem userDefinedColour = new MenuItem();
@@ -2847,7 +2987,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
@@ -2978,13 +3119,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.setLabel(MessageManager
+ .getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.setLabel(MessageManager
+ .getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setLabel(MessageManager
+ .getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.setLabel(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
@@ -2992,29 +3137,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
+ 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.setLabel(MessageManager
+ .getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy").concat("..."));
removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem
- .setLabel(MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ outputTextboxMenu.setLabel(MessageManager
+ .getString("label.out_to_textbox"));
clustalColour.setLabel(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(this);
@@ -3022,43 +3174,60 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
zappoColour.addActionListener(this);
taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
+ RNAInteractionColour.setLabel(MessageManager
+ .getString("label.rna_interaction"));
+ RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager
+ .getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
// provided
tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem
- .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
- overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
undoMenuItem.setEnabled(false);
undoMenuItem.setLabel(MessageManager.getString("action.undo"));
@@ -3066,24 +3235,29 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
redoMenuItem.setEnabled(false);
redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.setLabel(MessageManager
+ .getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
- deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
+ 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"));
@@ -3098,7 +3272,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
pasteNew.addActionListener(this);
pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
font.setLabel(MessageManager.getString("action.font"));
@@ -3115,20 +3290,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
scaleRight.setState(true);
scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
- modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_thereshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
sort.setLabel(MessageManager.getString("action.sort"));
calculate.setLabel(MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
sortByTree.addItemListener(this);
- inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
helpMenu.setLabel(MessageManager.getString("action.help"));
documentation.setLabel(MessageManager.getString("label.documentation"));
@@ -3137,34 +3318,56 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
about.setLabel(MessageManager.getString("label.about"));
about.addActionListener(this);
seqLimits.setState(true);
- seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
- featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
+ featureSettings.setLabel(MessageManager
+ .getString("label.feature_settings"));
featureSettings.addActionListener(this);
- sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
- annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
- invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
+
+ annotationColumnSelection.setLabel("Select by Annotation");
+ annotationColumnSelection.addActionListener(this);
+
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
menu1.setLabel(MessageManager.getString("action.show"));
showColumns.setLabel(MessageManager.getString("label.all_columns"));
showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
- menu2.setLabel(MessageManager.getString("aciton.hide"));
- hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
- hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
- hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
- hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
- showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
- showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
- showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
- showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
- showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
- normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
- applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
+ menu2.setLabel(MessageManager.getString("action.hide"));
+ hideColumns
+ .setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager
+ .getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager
+ .getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager
+ .getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager
+ .getString("label.all_sequences_columns"));
+ showGroupConsensus.setLabel(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager
+ .getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager
+ .getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager
+ .getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
+ autoAnnMenu.setLabel(MessageManager
+ .getString("label.autocalculated_annotation"));
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
@@ -3260,6 +3463,7 @@ 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();
@@ -3319,11 +3523,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumnSelection);
}
-
- public void setStatus(String string) {
+ public void setStatus(String string)
+ {
statusBar.setText(string);
};
@@ -3333,6 +3538,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem annotationColour = new MenuItem();
+ MenuItem annotationColumnSelection = new MenuItem();
+
MenuItem invertColSel = new MenuItem();
Menu menu1 = new Menu();
@@ -3368,46 +3575,11 @@ 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
{
@@ -3416,19 +3588,69 @@ 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,
+ jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
+ DEFAULT_WIDTH,
DEFAULT_HEIGHT);
}
}
/**
+ * 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
@@ -3489,7 +3711,7 @@ 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.
@@ -3561,6 +3783,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
}
}
return true;