/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
-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 jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Canvas;
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.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import org.jmol.viewer.Viewer;
+
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
public 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");
if (param != null)
{
int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
+ frameWidth = width;
}
param = applet.getParameter("windowHeight");
if (param != null)
{
int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
+ frameHeight = height;
}
} catch (Exception ex)
{
}
}
viewport = new AlignViewport(al, applet);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ if (columnSelection != null)
+ {
+ viewport.setColumnSelection(columnSelection);
+ }
+
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.setState(viewport.isShowAnnotation());
+ showSequenceAnnotations.setState(viewport.isShowAnnotation());
- seqLimits.setState(viewport.showJVSuffix);
+ seqLimits.setState(viewport.getShowJVSuffix());
if (applet != null)
{
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);
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));
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
+ .getAlignment(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours(), featureLinks,
+ true, viewport.applet.getDefaultParameter("relaxedidmatch",
+ false));
} catch (Exception ex)
{
ex.printStackTrace();
}
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();
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
statusBar.setText(MessageManager.formatMessage(
- "label.keyboard_editing_mode", new String[]
- { (viewport.cursorMode ? "on" : "off") }));
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
@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());
}
- 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. Repaint after calling.
+ *
+ * @param visible
+ */
+ private void setAnnotationsVisibility()
+ {
+ boolean showForAlignment = showAlignmentAnnotations.getState();
+ boolean showForSequences = showSequenceAnnotations.getState();
+ 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.
}
@Override
public void actionPerformed(ActionEvent evt)
{
+ viewport.applet.currentAlignFrame = this;
+
Object source = evt.getSource();
if (source == inputText)
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new String[]
- { getTitle() }), 400, 250);
+ "label.alignment_properties", new String[] { getTitle() }),
+ 400, 250);
}
else if (source == overviewMenuItem)
{
{
changeColour(new PurinePyrimidineColourScheme());
}
- else if (source == RNAInteractionColour)
- {
- changeColour(new RNAInteractionColourScheme());
- }
+ // else if (source == RNAInteractionColour)
+ // {
+ // changeColour(new RNAInteractionColourScheme());
+ // }
else if (source == RNAHelixColour)
{
new RNAHelicesColourChooser(viewport, alignPanel);
{
new AnnotationColourChooser(viewport, alignPanel);
}
+ else if (source == annotationColumnSelection)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
else if (source == sortPairwiseMenuItem)
{
sortPairwiseMenuItem_actionPerformed();
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_output_command", new String[]
- { e.getActionCommand() }), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(
+ "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()
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)
{
return annotation;
}
- private Hashtable getDisplayedFeatureCols()
+ private Map<String, Object> 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;
}
{
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)
void updateEditMenuBar()
{
- if (viewport.historyList.size() > 0)
+ if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
+ CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setLabel(MessageManager.formatMessage(
- "label.undo_command", new String[]
- { command.getDescription() }));
+ "label.undo_command",
+ new Object[] { command.getDescription() }));
}
else
{
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();
+ CommandI command = viewport.getRedoList().peek();
redoMenuItem.setLabel(MessageManager.formatMessage(
- "label.redo_command", new String[]
- { command.getDescription() }));
+ "label.redo_command",
+ new Object[] { command.getDescription() }));
}
else
{
/**
* 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();
}
*/
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)
{
*/
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)
{
.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
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();
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)
}
boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque<CommandI> historyList = viewport.getHistoryList();
+ if (historyList != null && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .appendSlideCommand((SlideSequencesCommand) historyList
.peek());
}
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
int index = viewport.getAlignment().findIndex(seq);
- orderedSeqs.put(index + "", seq);
+ orderedSeqs.put(index, seq);
}
int index = 0, startRes, endRes;
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
-
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ copiedHiddenColumns.addElement(new int[] {
+ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
else
while (seq == null)
{
- if (orderedSeqs.containsKey(index + ""))
+ if (orderedSeqs.containsKey(index))
{
- seq = (SequenceI) orderedSeqs.get(index + "");
+ seq = orderedSeqs.get(index);
index++;
-
break;
}
else
if (newAlignment)
{
- String newtitle = MessageManager.getString("label.copied_sequences");
- if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
+ String newtitle = MessageManager
+ .getString("label.copied_sequences");
+ if (getTitle().startsWith(
+ MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
- newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
+ newtitle = newtitle.concat(MessageManager.formatMessage(
+ "label.from_msname", new String[] { getTitle() }));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
}
}
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ frameHeight);
}
else
{
}
statusBar.setText(MessageManager.formatMessage(
- "label.removed_columns", new String[]
- { Integer.valueOf(trimRegion.getSize()).toString() }));
+ "label.removed_columns",
+ new String[] { Integer.valueOf(trimRegion.getSize())
+ .toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
addHistoryItem(removeGapCols);
statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns", new String[]
- { Integer.valueOf(removeGapCols.getSize()).toString() }));
+ "label.removed_empty_columns",
+ new String[] { Integer.valueOf(removeGapCols.getSize())
+ .toString() }));
// This is to maintain viewport position on first residue
// of first sequence
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;
}
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- return fr.getGroups();
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
}
return null;
}
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- return fr.getGroups(visible);
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
}
return null;
}
{
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)
{
protected void displayNonconservedMenuItem_actionPerformed()
{
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
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,
+ "label.overview_params", new String[] { this.getTitle() }),
+ overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
}
- void changeColour(ColourSchemeI cs)
+ public void changeColour(ColourSchemeI cs)
{
- int threshold = 0;
if (cs != null)
{
}
viewport.setGlobalColourScheme(cs);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(viewport.applet)
- .sequenceColoursChanged(alignPanel);
-
alignPanel.paintAlignment(true);
}
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
addHistoryItem(new OrderCommand(MessageManager.formatMessage(
- "label.order_by_params", new String[]
- { title }), oldOrder, viewport.getAlignment()));
+ "label.order_by_params", new String[] { title }), oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
g.drawString(MessageManager.formatMessage(
- "label.jalviewLite_release", new String[]
- { version }), x, y += fh);
+ "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);
+ "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"),
x, y += fh * 1.5);
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
- MessageManager.getString("label.export_features").concat("..."));
+ MessageManager.getString("label.export_features"));
MenuItem outputAnnotations = new MenuItem(
- MessageManager.getString("label.export_annotations").concat("..."));
+ MessageManager.getString("label.export_annotations"));
MenuItem closeMenuItem = new MenuItem(
MessageManager.getString("action.close"));
- Menu editMenu = new Menu(MessageManager.getString("action.edit"));
-
- Menu viewMenu = new Menu(MessageManager.getString("action.view"));
-
- Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
-
- Menu calculateMenu = new Menu(
- MessageManager.getString("action.calculate"));
-
MenuItem selectAllSequenceMenuItem = new MenuItem(
MessageManager.getString("action.select_all"));
public Label statusBar = new Label();
- Menu outputTextboxMenu = new Menu();
-
MenuItem clustalColour = new MenuItem();
MenuItem zappoColour = new MenuItem();
MenuItem purinePyrimidineColour = new MenuItem();
- MenuItem RNAInteractionColour = new MenuItem();
+ // MenuItem RNAInteractionColour = new MenuItem();
MenuItem RNAHelixColour = new MenuItem();
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();
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
- Menu autoAnnMenu = new Menu();
-
CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+ /**
+ * Initialise menus and other items
+ *
+ * @throws Exception
+ */
private void jbInit() throws Exception
{
-
setMenuBar(alignFrameMenuBar);
- MenuItem item;
-
- // dynamically fill save as menu with available formats
+ /*
+ * 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()
}
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);
+
+ /*
+ * 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);
removeAllGapsMenuItem.setLabel(MessageManager
.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.addActionListener(this);
+
+ /*
+ * Configure Select menu items and actions
+ */
+ findMenuItem.setLabel(MessageManager.getString("action.find"));
+ findMenuItem.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.addActionListener(this);
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
+ invertColSel.addActionListener(this);
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
+ deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel(MessageManager
+ .getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(this);
+ createGroup.setLabel(MessageManager.getString("action.create_group"));
+ 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"));
+ showAutoLast = new CheckboxMenuItem(
+ MessageManager.getString("label.show_last"));
+ 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(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- 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);
- removeRedundancyMenuItem.setLabel(MessageManager
- .getString("action.remove_redundancy").concat("..."));
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel(MessageManager
- .getString("action.pairwise_alignment"));
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel(MessageManager
- .getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(MessageManager
- .getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem.addActionListener(this);
- 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"));
- clustalColour.setLabel(MessageManager.getString("label.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(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
.getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAInteractionColour.setLabel(MessageManager
- .getString("label.rna_interaction"));
- RNAInteractionColour.addActionListener(this);
+ // RNAInteractionColour.setLabel(MessageManager
+ // .getString("label.rna_interaction"));
+ // RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(MessageManager
.getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
BLOSUM62Colour.addActionListener(this);
tcoffeeColour
.setLabel(MessageManager.getString("label.tcoffee_scores"));
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
- // provided
+ // it will be enabled only if a score file is provided
+ tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.average_distance_bloslum62"));
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel(MessageManager
- .getString("label.colour_text"));
- colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel(MessageManager
- .getString("label.show_non_conversed"));
- displayNonconservedMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel(MessageManager
- .getString("label.overview_window"));
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel(MessageManager.getString("action.undo"));
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel(MessageManager.getString("action.redo"));
- redoMenuItem.addActionListener(this);
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.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel(MessageManager.getString("action.find"));
- findMenuItem.addActionListener(this);
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.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"));
- 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);
- applyToAllGroups.setLabel(MessageManager
- .getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- 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);
modifyPID.setLabel(MessageManager
.getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
.getString("label.modify_conservation_thereshold"));
modifyConservation.addActionListener(this);
+ 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"));
- sort.setLabel(MessageManager.getString("action.sort"));
- calculate.setLabel(MessageManager.getString("action.calculate_tree"));
+ 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(MessageManager.getString("label.input_from_textbox"));
- inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel(MessageManager
- .getString("label.centre_column_labels"));
- centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel(MessageManager
- .getString("label.automatic_scrolling"));
- followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel(MessageManager.getString("action.help"));
+
+ /*
+ * 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(MessageManager
- .getString("label.show_sequence_limits"));
- seqLimits.addItemListener(this);
- featureSettings.setLabel(MessageManager
- .getString("label.feature_settings"));
- featureSettings.addActionListener(this);
- sequenceFeatures.setLabel(MessageManager
- .getString("label.sequence_features"));
- sequenceFeatures.addItemListener(this);
- sequenceFeatures.setState(false);
- 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"));
- menu1.setLabel(MessageManager.getString("action.show"));
- showColumns.setLabel(MessageManager.getString("label.all_columns"));
- showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
- menu2.setLabel(MessageManager.getString("action.hide"));
- hideColumns
- .setLabel(MessageManager.getString("label.selected_columns"));
- hideSequences.setLabel(MessageManager
- .getString("label.selected_sequences"));
- hideAllButSelection.setLabel(MessageManager
- .getString("label.all_but_selected_region"));
- hideAllSelection.setLabel(MessageManager
- .getString("label.selected_region"));
- showAllHidden.setLabel(MessageManager
- .getString("label.all_sequences_columns"));
- showGroupConsensus.setLabel(MessageManager
- .getString("label.group_consensus"));
- showGroupConservation.setLabel(MessageManager
- .getString("label.group_conservation"));
- showConsensusHistogram.setLabel(MessageManager
- .getString("label.show_consensus_histogram"));
- showSequenceLogo.setLabel(MessageManager
- .getString("label.show_consensus_logo"));
- normSequenceLogo.setLabel(MessageManager
- .getString("label.norm_consensus_logo"));
- applyAutoAnnotationSettings.setLabel(MessageManager
- .getString("label.apply_all_groups"));
- applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel(MessageManager
- .getString("label.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(MessageManager.getString("action.format"));
- selectMenu.setLabel(MessageManager.getString("action.select"));
- newView.setLabel(MessageManager.getString("action.new_view"));
- newView.addActionListener(this);
+ /*
+ * Add top level menus to frame
+ */
alignFrameMenuBar.add(fileMenu);
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
alignFrameMenuBar.add(editMenu);
+ Menu selectMenu = new Menu(MessageManager.getString("action.select"));
alignFrameMenuBar.add(selectMenu);
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
alignFrameMenuBar.add(viewMenu);
+ Menu annotationsMenu = new Menu(
+ MessageManager.getString("action.annotations"));
+ alignFrameMenuBar.add(annotationsMenu);
+ Menu formatMenu = new Menu(MessageManager.getString("action.format"));
alignFrameMenuBar.add(formatMenu);
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
alignFrameMenuBar.add(colourMenu);
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(helpMenu);
+ /*
+ * File menu
+ */
fileMenu.add(inputText);
fileMenu.add(loadTree);
fileMenu.add(loadAnnotations);
-
fileMenu.addSeparator();
fileMenu.add(outputTextboxMenu);
fileMenu.add(outputFeatures);
fileMenu.add(outputAnnotations);
-
if (jalviewServletURL != null)
{
fileMenu.add(loadApplication);
}
-
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+ /*
+ * Edit menu
+ */
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
+
+ /*
+ * Select menu
+ */
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumnSelection);
+
+ /*
+ * View menu
+ */
viewMenu.add(newView);
viewMenu.addSeparator();
- viewMenu.add(menu1);
- viewMenu.add(menu2);
+ showMenu.add(showColumns);
+ showMenu.add(showSeqs);
+ showMenu.add(showAllHidden);
+ viewMenu.add(showMenu);
+ hideMenu.add(hideColumns);
+ hideMenu.add(hideSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+ viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(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);
viewMenu.add(alProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
+
+ /*
+ * Annotations menu
+ */
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAlignmentAnnotations);
+ annotationsMenu.add(showSequenceAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ annotationsMenu.add(autoAnnMenu);
+
+ /*
+ * Format menu
+ */
+ formatMenu.add(font);
+ formatMenu.add(seqLimits);
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(displayNonconservedMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelFlag);
+
+ /*
+ * Colour menu
+ */
colourMenu.add(applyToAllGroups);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(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(createGroup);
- selectMenu.add(unGroup);
- 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);
}
public void setStatus(String string)
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();
MenuItem showAllHidden = new MenuItem();
- Menu formatMenu = new Menu();
+ MenuItem newView = new MenuItem();
+
+ private CheckboxMenuItem showAlignmentAnnotations;
- Menu selectMenu = new Menu();
+ private CheckboxMenuItem showSequenceAnnotations;
- MenuItem newView = new MenuItem();
+ 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
* 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, 11, 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
{
//
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
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 :"
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;
boolean needtoadd = false;
if (toaddpdb != null)
{
- Vector pdbe = toaddpdb.getPDBId();
+ Vector pdbe = toaddpdb.getAllPDBEntries();
PDBEntry pdbentry = null;
if (pdbe != null && pdbe.size() > 0)
{
{
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()];
chains[i] = (String) oj[1];
}
}
- return new Object[]
- { seqs, chains };
+ return new Object[] { seqs, chains };
}
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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff