X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ab99e065edd79a2053a65ca1de46f243d9e88ccc;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=0aefe9b01b51d544ce42103ceb58fea4f0c904a2;hpb=6b544d4a85673db44b7f75f40c22d9b7425d444e;p=jalview.git
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
old mode 100755
new mode 100644
index 0aefe9b..ab99e06
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,35 +1,94 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
- *
+ *
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener
@@ -47,7 +106,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
String title, boolean embedded)
{
-
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -68,7 +126,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.updateConsensus(alignPanel);
annotationPanelMenuItem.setState(viewport.showAnnotation);
- displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+ displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
+ followMouseOverFlag.setState(viewport.getFollowHighlight());
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());
+ showGroupConservation.setState(viewport.isShowGroupConservation());
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
seqLimits.setState(viewport.showJVSuffix);
@@ -125,7 +189,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
-
+ if (viewport.getAlignment().isNucleotide())
+ {
+ viewport.updateStrucConsensus(alignPanel);
+ if (viewport.getAlignment().hasRNAStructure())
+ {
+ RNAHelixColour.setEnabled(true);
+ }
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ }
+ }
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ purinePyrimidineColour.setEnabled(false);
+ }
// Some JVMS send keyevents to Top frame or lowest panel,
// Havent worked out why yet. So add to both this frame and seqCanvas for
// now
@@ -134,8 +214,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.idPanel.idCanvas.addKeyListener(this);
alignPanel.scalePanel.addKeyListener(this);
alignPanel.annotationPanel.addKeyListener(this);
+ alignPanel.annotationPanelHolder.addKeyListener(this);
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+ alignPanel.alabels.addKeyListener(this);
createAlignFrameWindow(embedded, title);
- alignPanel.validate();
+
+ validate();
+ alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
}
@@ -150,22 +235,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/**
- * DOCUMENT ME!
+ * Load a features file onto the alignment
*
- * @param String
- * DOCUMENT ME!
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
*/
- public void parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, String type)
+ {
+ return parseFeaturesFile(file, type, true);
+ }
+
+ /**
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
+ * @param autoenabledisplay
+ * when true, display features flag will be automatically enabled if
+ * features are loaded
+ * @return true if data parsed as a features file
+ */
+ public boolean parseFeaturesFile(String file, String type,
+ boolean autoenabledisplay)
{
+ // TODO: test if importing a features file onto an alignment which already
+ // has features with links overwrites the original links.
+
Hashtable featureLinks = new Hashtable();
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file, type).parse(
- viewport.alignment, alignPanel.seqPanel.seqCanvas
+ featuresFile = new jalview.io.FeaturesFile(file, type)
+ .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().featureColours, featureLinks,
- true);
+ true, viewport.applet.getDefaultParameter(
+ "relaxedidmatch", false));
} catch (Exception ex)
{
ex.printStackTrace();
@@ -177,17 +286,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
}
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
+ if (autoenabledisplay)
+ {
+ viewport.showSequenceFeatures = true;
+ sequenceFeatures.setState(true);
+ }
if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true);
+ statusBar.setText("Successfully added features to alignment.");
}
-
+ return featuresFile;
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -201,6 +315,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed();
+
+ alignPanel.alabels.cancelDrag();
break;
case KeyEvent.VK_X:
if (evt.isControlDown() || evt.isMetaDown())
@@ -460,8 +576,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
- .getSelected().size() > 0)
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
@@ -484,12 +601,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (toggleSeqs)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
{
viewport.showAllHiddenSeqs();
}
@@ -497,12 +615,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (toggleCols)
{
- if (viewport.colSel.getSelected().size() > 0)
+ if (viewport.getColumnSelection().getSelected().size() > 0)
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
{
- viewport.selectionGroup = sg;
+ viewport.setSelectionGroup(sg);
}
}
else if (!hide)
@@ -512,14 +630,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == displayNonconservedMenuItem)
@@ -586,7 +707,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
else if (evt.getSource() == autoCalculate)
{
- viewport.autocalculateConsensus = autoCalculate.getState();
+ viewport.autoCalculateConsensus = autoCalculate.getState();
+ }
+ else if (evt.getSource() == sortByTree)
+ {
+ viewport.sortByTree = sortByTree.getState();
}
else if (evt.getSource() == this.centreColumnLabelFlag)
{
@@ -596,7 +721,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
mouseOverFlag_stateChanged();
}
-
+ else if (evt.getSource() == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (evt.getSource() == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (evt.getSource() == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (evt.getSource() == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (evt.getSource() == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (evt.getSource() == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
alignPanel.paintAlignment(true);
}
@@ -613,6 +761,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
this.alignPanel.annotationPanel.repaint();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
@@ -786,44 +935,38 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
}
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
else if (source == featureSettings)
{
new FeatureSettings(alignPanel);
}
else if (source == alProperties)
{
- StringBuffer contents = new StringBuffer();
-
- float avg = 0;
- int min = Integer.MAX_VALUE, max = 0;
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
- {
- int size = viewport.alignment.getSequenceAt(i).getEnd()
- - viewport.alignment.getSequenceAt(i).getStart();
- avg += size;
- if (size > max)
- max = size;
- if (size < min)
- min = size;
- }
- avg = avg / (float) viewport.alignment.getHeight();
-
- contents.append("\nSequences: " + viewport.alignment.getHeight());
- contents.append("\nMinimum Sequence Length: " + min);
- contents.append("\nMaximum Sequence Length: " + max);
- contents.append("\nAverage Length: " + (int) avg);
-
- if (((Alignment) viewport.alignment).alignmentProperties != null)
- {
- Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
- Enumeration en = props.keys();
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- contents.append("\n" + key + "\t" + props.get(key));
- }
- }
-
+ StringBuffer contents = new jalview.io.AlignmentProperties(
+ viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
@@ -842,8 +985,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
else if (source == clustalColour)
{
abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(viewport.alignment
- .getSequences(), viewport.alignment.getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
}
else if (source == zappoColour)
{
@@ -877,6 +1019,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
changeColour(new NucleotideColourScheme());
}
+ else if (source == purinePyrimidineColour)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ else if (source == RNAHelixColour)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
else if (source == modifyPID)
{
modifyPID_actionPerformed();
@@ -897,6 +1047,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
changeColour(new Blosum62ColourScheme());
}
+ else if (source == tcoffeeColour)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
else if (source == annotationColour)
{
new AnnotationColourChooser(viewport, alignPanel);
@@ -969,17 +1123,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
- + e.getActionCommand(), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(e
- .getActionCommand(), viewport.getAlignment(),
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
+ cap.setText(new AppletFormatAdapter().formatSequences(
+ e.getActionCommand(), viewport.getAlignment(),
viewport.showJVSuffix));
}
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations file here.");
+ cap.setText("Paste your features / annotations / T-coffee score file here.");
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
@@ -990,10 +1144,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public String outputAnnotations(boolean displayTextbox)
{
String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.alignment
- .getAlignmentAnnotation() : null, viewport.alignment
- .getGroups(),
- ((Alignment) viewport.alignment).alignmentProperties);
+ viewport.showAnnotation ? viewport.getAlignment()
+ .getAlignmentAnnotation() : null, viewport
+ .getAlignment().getGroups(), ((Alignment) viewport
+ .getAlignment()).alignmentProperties);
if (displayTextbox)
{
@@ -1009,7 +1163,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
private Hashtable getDisplayedFeatureCols()
{
- if (alignPanel.getFeatureRenderer() != null)
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.featuresDisplayed != null)
{
FeatureRenderer fr = alignPanel.getFeatureRenderer();
Hashtable fcols = new Hashtable();
@@ -1029,24 +1184,40 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
String features;
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(viewport.alignment
- .getSequencesArray(), getDisplayedFeatureCols());
+ features = new FeaturesFile().printJalviewFormat(viewport
+ .getAlignment().getSequencesArray(),
+ getDisplayedFeatureCols());
}
else
{
- features = new FeaturesFile().printGFFFormat(viewport.alignment
+ features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
.getSequencesArray(), getDisplayedFeatureCols());
}
if (displayTextbox)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ boolean frimport = false;
+ if (features == null || features.equals("No Features Visible"))
+ {
+ features = "# No features visible - paste some and import them here.";
+ frimport = true;
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
+ if (frimport)
+ {
+ cap.setAnnotationImport();
+ }
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
-
cap.setText(features);
}
+ else
+ {
+ if (features == null)
+ features = "";
+ }
return features;
}
@@ -1067,9 +1238,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.applet.getParameter("annotations") != null)
{
url.append("&annotations=");
- url
- .append(appendProtocol(viewport.applet
- .getParameter("annotations")));
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));
}
if (viewport.applet.getParameter("jnetfile") != null)
@@ -1147,19 +1316,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void closeMenuItem_actionPerformed()
{
PaintRefresher.RemoveComponent(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+ if (alignPanel.seqPanel != null
+ && alignPanel.seqPanel.seqCanvas != null)
+ {
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+ }
+ if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
+ {
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+ }
if (PaintRefresher.components.size() == 0 && viewport.applet == null)
{
System.exit(0);
}
-
+ else
+ {
+ }
+ viewport = null;
+ alignPanel = null;
this.dispose();
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104
*/
void updateEditMenuBar()
{
@@ -1190,6 +1370,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
+ /**
+ * TODO: JAL-1104
+ */
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
@@ -1197,12 +1380,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.historyList.push(command);
viewport.redoList.removeAllElements();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.updateHiddenColumns();
}
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
@@ -1219,15 +1402,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
command.undoCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst undoing");
+ }
+ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
@@ -1244,11 +1434,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
command.doCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst re-doing");
+ }
+ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
AlignViewport getOriginatingSource(CommandI command)
@@ -1268,7 +1466,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
if (comps.elementAt(i) instanceof AlignmentPanel)
{
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
{
originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
break;
@@ -1283,7 +1481,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
@@ -1299,65 +1497,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ up ? null : viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
+ List sg = new Vector();
if (viewport.cursorMode)
{
- sg.addElement(viewport.alignment
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.alignment
- .getHeight())
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
@@ -1365,21 +1523,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
return;
}
- Vector invertGroup = new Vector();
+ Vector invertGroup = new Vector();
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
- if (!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
- SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
+ .size()]);
for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ seqs2[i] = invertGroup.elementAt(i);
SlideSequencesCommand ssc;
if (right)
@@ -1445,14 +1602,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
+ int index = viewport.getAlignment().findIndex(seq);
orderedSeqs.put(index + "", seq);
}
int index = 0, startRes, endRes;
char ch;
- if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
+ if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
@@ -1599,16 +1756,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
for (int i = 0; i < seqs.length; i++)
{
- viewport.alignment.addSequence(seqs[i]);
+ viewport.getAlignment().addSequence(seqs[i]);
}
// !newAlignment
addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
+ seqs, 0, viewport.getAlignment().getWidth(),
+ viewport.getAlignment()));
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.firePropertyChange("alignment", null, viewport.alignment
+ viewport.setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getAlignment().getWidth();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
@@ -1637,7 +1795,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
// If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
@@ -1654,10 +1812,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
*/
addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
@@ -1666,6 +1824,66 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
this.setVisible(false);
}
+ viewport.sendSelection();
+ }
+
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /**
+ * group conservation toggled.
+ */
+ protected void showGroupConservation_actionPerformed()
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed()
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed()
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void normSequenceLogo_actionPerformed()
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed()
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void makeGrpsFromSelection_actionPerformed()
@@ -1673,10 +1891,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.getSelectionGroup() != null)
{
SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(), viewport.getAlignmentView(
- true).getSequenceStrings(viewport.getGapCharacter()),
- viewport.alignment.getGroups());
- viewport.alignment.deleteAllGroups();
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()), viewport.getAlignment()
+ .getGroups());
+ viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
// set view properties for each group
@@ -1684,24 +1903,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.alignment.addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255), (int) (Math
- .random() * 255), (int) (Math.random() * 255));
+ viewport.getAlignment().addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq
- .hasMoreElements(); viewport.setSequenceColour(
- (SequenceI) sq.nextElement(), col))
- ;
+ for (SequenceI sq : gps[g].getSequences(null))
+ viewport.setSequenceColour(sq, col);
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- // alignPanel.updateAnnotation();
+ alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
protected void deleteGroups_actionPerformed()
{
- viewport.alignment.deleteAllGroups();
+ viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
@@ -1715,10 +1932,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth() - 1);
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void deselectAllSequenceMenuItem_actionPerformed()
@@ -1735,6 +1953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertSequenceMenuItem_actionPerformed()
@@ -1746,6 +1965,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertColSel_actionPerformed()
@@ -1753,6 +1973,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
void trimAlignment(boolean trimLeft)
@@ -1775,11 +1996,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
@@ -1787,32 +2008,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
trimRegion = new TrimRegionCommand("Remove Left",
TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
viewport.setStartRes(0);
}
else
{
trimRegion = new TrimRegionCommand("Remove Right",
TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
}
statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
addHistoryItem(trimRegion);
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
@@ -1823,23 +2040,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void removeGappedColumnMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
- "Remove Gapped Columns", seqs, start, end, viewport.alignment);
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
addHistoryItem(removeGapCols);
@@ -1848,7 +2066,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// This is to maintain viewport position on first residue
// of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
@@ -1863,28 +2081,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void removeAllGapsMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
// This is to maintain viewport position on first residue
// of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.alignment));
+ viewport.getAlignment()));
viewport.setStartRes(seq.findIndex(startRes) - 1);
@@ -1907,35 +2125,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public AlignFrame newView(String viewtitle)
{
AlignmentI newal;
- if (viewport.hasHiddenRows)
+ if (viewport.hasHiddenRows())
{
newal = new Alignment(viewport.getAlignment().getHiddenSequences()
.getFullAlignment().getSequencesArray());
}
else
{
- newal = new Alignment(viewport.alignment.getSequencesArray());
+ newal = new Alignment(viewport.getAlignment().getSequencesArray());
}
- if (viewport.alignment.getAlignmentAnnotation() != null)
+ if (viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
{
- if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
{
- newal
- .addAnnotation(viewport.alignment
- .getAlignmentAnnotation()[i]);
+ newal.addAnnotation(viewport.getAlignment()
+ .getAlignmentAnnotation()[i]);
}
}
}
AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
- newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+ newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
- .getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel,
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
newaf.alignPanel.av.getSequenceSetId());
@@ -2077,11 +2294,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
overview.getPreferredSize().height + 50);
frame.pack();
+ final AlignmentPanel ap = alignPanel;
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
- alignPanel.setOverviewPanel(null);
+ if (ap != null)
+ {
+ ap.setOverviewPanel(null);
+ }
};
});
@@ -2112,13 +2334,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.getConservationSelected())
{
- Alignment al = (Alignment) viewport.alignment;
+ Alignment al = (Alignment) viewport.getAlignment();
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
cs.setConservation(c);
@@ -2131,81 +2353,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
cs.setConservation(null);
}
- cs.setConsensus(viewport.hconsensus);
+ cs.setConsensus(viewport.getSequenceConsensusHash());
}
viewport.setGlobalColourScheme(cs);
- if (viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(viewport.hiddenRepSequences), sg.getWidth());
- }
- else
- {
- try
- {
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(viewport.hiddenRepSequences), 0, sg
- .getWidth()));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(viewport.hiddenRepSequences), 0,
- viewport.alignment.getWidth() - 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- }
- }
-
if (alignPanel.getOverviewPanel() != null)
{
alignPanel.getOverviewPanel().updateOverviewImage();
}
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sequenceColoursChanged(
- alignPanel);
+ .getStructureSelectionManager(viewport.applet)
+ .sequenceColoursChanged(alignPanel);
alignPanel.paintAlignment(true);
}
@@ -2213,10 +2373,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void modifyPID_actionPerformed()
{
if (viewport.getAbovePIDThreshold()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport
- .getGlobalColourScheme(), "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
@@ -2224,10 +2384,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void modifyConservation_actionPerformed()
{
if (viewport.getConservationSelected()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme, "Background");
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
@@ -2263,7 +2423,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2271,7 +2431,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2279,7 +2440,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2288,7 +2450,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2313,7 +2475,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void PCAMenuItem_actionPerformed()
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
@@ -2370,7 +2532,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
void NewTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
@@ -2390,10 +2552,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if ((viewport.getSelectionGroup() != null && viewport
.getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null && viewport.alignment
- .getHeight() > 1))
+ || (viewport.getAlignment().getHeight() > 1))
{
- final TreePanel tp = new TreePanel(viewport, type, pwType);
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
addTreeMenuItem(tp, title);
@@ -2413,7 +2574,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
@@ -2434,7 +2595,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2452,6 +2613,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
sortByTreeMenu.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
sortByTree(treePanel, title); // treePanel.getTitle());
@@ -2460,6 +2622,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
treePanel.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowOpened(WindowEvent e)
{
if (viewport.sortByTree)
@@ -2469,6 +2632,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
super.windowOpened(e);
}
+ @Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
@@ -2476,9 +2640,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
});
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting " + alorder.getOrder().size()
+ + " in alignment '" + getTitle() + "'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
protected void documentation_actionPerformed()
{
- showURL("http://www.jalview.org/help.html", "HELP");
+ alignPanel.av.applet.openJalviewHelpUrl();
}
protected void about_actionPerformed()
@@ -2496,6 +2678,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
this.builddate = builddate;
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.white);
@@ -2512,28 +2695,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
g.setFont(new Font("Helvetica", Font.BOLD, 12));
g.drawString("Build date: " + builddate, x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g
- .drawString(
- "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
- x, y += fh * 1.5);
- g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
- g
- .drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- x, y += fh);
- g
- .drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
- x, y += fh);
+ g.drawString(
+ "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
+ x, y += fh * 1.5);
+ g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
+ g.drawString(
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ x, y += fh);
+ g.drawString(
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ x, y += fh);
g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g
- .drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
- x, y += fh);
- g
- .drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
- x, y += fh);
+ g.drawString(
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ x, y += fh);
+ g.drawString(
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ x, y += fh);
g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
x, y += fh);
}
@@ -2554,35 +2732,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
else
{
- try
- {
- if (url.indexOf(":") == -1)
- {
- // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
- // form valid URL
- if (url.indexOf("/") == 0)
- {
- String codebase = viewport.applet.getCodeBase().toString();
- url = codebase.substring(0, codebase.length()
- - viewport.applet.getCodeBase().getFile().length())
- + url;
- }
- else
- {
- url = viewport.applet.getCodeBase() + url;
- }
- System.out.println("Show url (prepended codebase): " + url);
- }
- else
- {
- System.out.println("Show url: " + url);
- }
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url), target);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ viewport.applet.showURL(url, target);
}
}
@@ -2671,12 +2821,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
MenuItem buriedColour = new MenuItem();
+ MenuItem purinePyrimidineColour = new MenuItem();
+
+ MenuItem RNAHelixColour = new MenuItem();
+
MenuItem userDefinedColour = new MenuItem();
MenuItem PIDColour = new MenuItem();
MenuItem BLOSUM62Colour = new MenuItem();
+ MenuItem tcoffeeColour = new MenuItem();
+
MenuItem njTreeBlosumMenuItem = new MenuItem();
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
@@ -2742,6 +2898,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
"Autocalculate Consensus", true);
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+ "Sort Alignment With New Tree", true);
+
Menu sortByTreeMenu = new Menu();
Menu sort = new Menu();
@@ -2762,6 +2921,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+ Menu autoAnnMenu = new Menu();
+
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
+
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
+
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+
private void jbInit() throws Exception
{
@@ -2778,6 +2951,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
@@ -2850,12 +3024,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
turnColour.addActionListener(this);
buriedColour.setLabel("Buried Index");
buriedColour.addActionListener(this);
+ purinePyrimidineColour.setLabel("Purine/Pyrimidine");
+ purinePyrimidineColour.addActionListener(this);
+ RNAHelixColour.setLabel("by RNA Helices");
+ RNAHelixColour.addActionListener(this);
userDefinedColour.setLabel("User Defined...");
userDefinedColour.addActionListener(this);
PIDColour.setLabel("Percentage Identity");
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62 Score");
BLOSUM62Colour.addActionListener(this);
+ tcoffeeColour.setLabel("T-Coffee Scores");
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
+ // provided
+ tcoffeeColour.addActionListener(this);
avDistanceTreeBlosumMenuItem
.setLabel("Average Distance Using BLOSUM62");
avDistanceTreeBlosumMenuItem.addActionListener(this);
@@ -2931,6 +3113,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
sort.setLabel("Sort");
calculate.setLabel("Calculate Tree");
autoCalculate.addItemListener(this);
+ sortByTree.addItemListener(this);
inputText.setLabel("Input from textbox");
inputText.addActionListener(this);
centreColumnLabelFlag.setLabel("Centre column labels");
@@ -2964,6 +3147,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
hideAllSelection.setLabel("Selected Region");
showAllHidden.setLabel("All Sequences and Columns");
+ showGroupConsensus.setLabel("Group Consensus");
+ showGroupConservation.setLabel("Group Conservation");
+ showConsensusHistogram.setLabel("Show Consensus Histogram");
+ showSequenceLogo.setLabel("Show Consensus Logo");
+ normSequenceLogo.setLabel("Normalise Consensus Logo");
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");
+ applyAutoAnnotationSettings.setState(true);
+ autoAnnMenu.setLabel("Autocalculated Annotation");
+
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
@@ -2972,6 +3164,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
hideAllButSelection.addActionListener(this);
hideAllSelection.addActionListener(this);
showAllHidden.addActionListener(this);
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+
+ applyAutoAnnotationSettings.addItemListener(this);
formatMenu.setLabel("Format");
selectMenu.setLabel("Select");
newView.setLabel("New View");
@@ -3021,6 +3220,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
@@ -3042,6 +3249,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
@@ -3049,12 +3258,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(RNAHelixColour);
calculateMenu.add(sort);
calculateMenu.add(calculate);
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);
@@ -3156,10 +3367,29 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
+ 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();
}
else
@@ -3180,4 +3410,345 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
DEFAULT_HEIGHT);
}
}
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note This method doesn't work
+ * without an additional javascript library to exchange messages between the
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ */
+ public SequenceStructureBinding addStructureViewInstance(
+ Object jmolviewer, String[] sequenceIds)
+ {
+ org.jmol.api.JmolViewer viewer = null;
+ try
+ {
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ } catch (ClassCastException ex)
+ {
+ System.err.println("Unsupported viewer object :"
+ + jmolviewer.getClass());
+ }
+ if (viewer == null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs = null;
+ if (sequenceIds == null || sequenceIds.length == 0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ Vector sqi = new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid = 0; sid < sequenceIds.length; sid++)
+ {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq != null)
+ {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size() > 0)
+ {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ }
+ else
+ {
+ return null;
+ }
+ }
+ ExtJmol jmv = null;
+ // TODO: search for a jmv that involves viewer
+ if (jmv == null)
+ { // create a new viewer/jalview binding.
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
+ { seqs });
+ }
+ return jmv;
+
+ }
+
+ /**
+ * bind a pdb file to a sequence in the current view
+ *
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or sequenceId location
+ * fails.
+ */
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,
+ String pdbFile)
+ {
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector pdbe = toaddpdb.getPDBId();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ // make a note of the access mode and add
+ if (pdbentry.getProperty() == null)
+ {
+ pdbentry.setProperty(new Hashtable());
+ }
+ pdbentry.getProperty().put("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ }
+ }
+ return true;
+ }
+
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
+ {
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[]
+ { seqs[i], (chains != null) ? chains[i] : null });
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
+ }
+ return new Object[]
+ { seqs, chains };
+
+ }
+
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
+ {
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ }
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
+ {
+ protocol = (String) pdb.getProperty().get("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
+ }
+ if (applet.useXtrnalSviewer)
+ {
+ // register the association(s) and quit, don't create any windows.
+ if (StructureSelectionManager.getStructureSelectionManager(applet)
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ {
+ System.err.println("Failed to map " + pdb.getFile() + " ("
+ + protocol + ") to any sequences");
+ }
+ return;
+ }
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+ {
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm != null)
+ {
+ System.err
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ // try and add the pdb structure
+ // ajm.addS
+ ajm = null;
+ }
+ }
+ // otherwise, create a new window
+ if (applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ }
+
+ }
+
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
+ }
+
+ /**
+ * modify the current selection, providing the user has not made a selection
+ * already.
+ *
+ * @param sel
+ * - sequences from this alignment
+ * @param csel
+ * - columns to be selected on the alignment
+ */
+ public void select(SequenceGroup sel, ColumnSelection csel)
+ {
+ alignPanel.seqPanel.selection(sel, csel, null);
+ }
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.seqPanel.scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.seqPanel.scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.seqPanel.scrollToColumn(column);
+ }
+
+ /**
+ * @return the alignments unique ID.
+ */
+ public String getSequenceSetId()
+ {
+ return viewport.getSequenceSetId();
+ }
+
+ /**
+ * Load the (T-Coffee) score file from the specified url
+ *
+ * @param source
+ * File/URL/T-COFFEE score file contents
+ * @throws IOException
+ * @return true if alignment was annotated with data from source
+ */
+ public boolean loadScoreFile(String source) throws IOException
+ {
+
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,
+ AppletFormatAdapter.checkProtocol(source));
+ if (!file.isValid())
+ {
+ // TODO: raise dialog for gui
+ System.err.println("Problems parsing T-Coffee scores: "
+ + file.getWarningMessage());
+ System.err.println("Origin was:\n" + source);
+ return false;
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if ((aln = viewport.getAlignment()) != null
+ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
+ .getWidth()))
+ {
+ // TODO: raise a dialog box here rather than bomb out.
+ System.err
+ .println("The scores matrix does not match the alignment dimensions");
+
+ }
+
+ // TODO add parameter to indicate if matching should be done
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))
+ {
+ alignPanel.fontChanged();
+ tcoffeeColour.setEnabled(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ return true;
+ }
+ else
+ {
+ System.err.println("Problems resolving T-Coffee scores:");
+ if (file.getWarningMessage() != null)
+ {
+ System.err.println(file.getWarningMessage());
+ }
+ }
+ return false;
+ }
+
}