X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=9fe2456fcf58c2313fbf5724cc8407c7fcda1361;hb=b9fbdac95abae11673f09be76494032ec0bbca74;hp=83870895d0bd2d61b0d09396f28c0e852b4d2e82;hpb=37b210ecad3c132b87c525f84e3b754a4edf12a6;p=jalview.git
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8387089..9fe2456 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,39 +1,98 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
* 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
+ * 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
+ *
+ * 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 .
*/
package jalview.appletgui;
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
+import jalview.analysis.AAFrequency;
+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.SequenceCollectionI;
+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;
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+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.io.InputStreamReader;
+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
{
public AlignmentPanel alignPanel;
@@ -45,10 +104,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
String jalviewServletURL;
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
- String title, boolean embedded)
- {
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -69,12 +127,13 @@ 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.showGroupConsensus);
- showGroupConservation.setState(viewport.showGroupConservation);
- showConsensusHistogram.setState(viewport.showConsensusHistogram);
- showSequenceLogo.setState(viewport.showSequenceLogo);
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());
+ showGroupConservation.setState(viewport.isShowGroupConservation());
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
seqLimits.setState(viewport.showJVSuffix);
@@ -131,7 +190,20 @@ 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
@@ -144,7 +216,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
createAlignFrameWindow(embedded, title);
- alignPanel.validate();
+
+ validate();
alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
}
@@ -160,20 +233,35 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/**
- * DOCUMENT ME!
- *
- * @param String
- * DOCUMENT ME!
+ * 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
*/
- 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,
+ .parse(viewport.getAlignment(),
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
} catch (Exception ex)
@@ -187,17 +275,22 @@ 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
@@ -211,8 +304,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed();
-
- alignPanel.alabels.cancelDrag();
+
+ alignPanel.alabels.cancelDrag();
break;
case KeyEvent.VK_X:
if (evt.isControlDown() || evt.isMetaDown())
@@ -459,7 +552,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* called by key handler and the hide all/show all menu items
- *
+ *
* @param toggleSeqs
* @param toggleCols
*/
@@ -472,7 +565,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
+ if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
.getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
@@ -496,12 +589,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (toggleSeqs)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
{
viewport.showAllHiddenSeqs();
}
@@ -509,12 +602,12 @@ 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)
@@ -524,14 +617,17 @@ 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)
@@ -598,7 +694,11 @@ 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)
{
@@ -620,6 +720,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
showSequenceLogo_actionPerformed();
}
+ else if (evt.getSource() == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
else if (evt.getSource() == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
@@ -644,6 +748,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
this.alignPanel.annotationPanel.repaint();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
@@ -829,6 +934,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
showSequenceLogo_actionPerformed();
}
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
else if (source == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
@@ -844,7 +953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
else if (source == alProperties)
{
StringBuffer contents = new jalview.io.AlignmentProperties(
- viewport.alignment).formatAsString();
+ viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
@@ -863,9 +972,7 @@ 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)
{
@@ -899,6 +1006,14 @@ 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();
@@ -919,6 +1034,9 @@ 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);
@@ -1001,7 +1119,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
@@ -1012,10 +1130,10 @@ 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
+ viewport.showAnnotation ? viewport.getAlignment()
+ .getAlignmentAnnotation() : null, viewport.getAlignment()
.getGroups(),
- ((Alignment) viewport.alignment).alignmentProperties);
+ ((Alignment) viewport.getAlignment()).alignmentProperties);
if (displayTextbox)
{
@@ -1031,7 +1149,7 @@ 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();
@@ -1052,24 +1170,37 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (format.equalsIgnoreCase("Jalview"))
{
features = new FeaturesFile().printJalviewFormat(
- viewport.alignment.getSequencesArray(),
+ viewport.getAlignment().getSequencesArray(),
getDisplayedFeatureCols());
}
else
{
features = new FeaturesFile().printGFFFormat(
- viewport.alignment.getSequencesArray(),
+ 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;
@@ -1169,8 +1300,13 @@ 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)
{
@@ -1183,7 +1319,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/**
- * DOCUMENT ME!
+ * TODO: JAL-1104
*/
void updateEditMenuBar()
{
@@ -1214,6 +1350,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
+ /**
+ * TODO: JAL-1104
+ */
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
@@ -1221,13 +1360,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.historyList.push(command);
viewport.redoList.removeAllElements();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.updateHiddenColumns();
}
}
/**
+ * TODO: JAL-1104
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1243,16 +1383,20 @@ 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.getAlignment().getSequences());
}
/**
+ * TODO: JAL-1104
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1268,11 +1412,15 @@ 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.getAlignment().getSequences());
}
AlignViewport getOriginatingSource(CommandI command)
@@ -1292,7 +1440,7 @@ 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;
@@ -1307,7 +1455,7 @@ 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;
@@ -1323,65 +1471,24 @@ 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();
+ Listsg = new Vector();
if (viewport.cursorMode)
{
- sg.addElement(viewport.alignment
+ sg.add(viewport.getAlignment()
.getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.alignment
+ && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
.getHeight())
{
sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
@@ -1389,21 +1496,19 @@ 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)
@@ -1469,14 +1574,14 @@ 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();
@@ -1623,17 +1728,17 @@ 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.setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null,
- viewport.alignment.getSequences());
+ viewport.getAlignment().getSequences());
}
@@ -1661,7 +1766,7 @@ 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);
@@ -1678,10 +1783,10 @@ 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());
@@ -1695,7 +1800,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* group consensus toggled
- *
+ *
*/
protected void showGroupConsensus_actionPerformed()
{
@@ -1715,7 +1820,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
@@ -1727,7 +1832,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
@@ -1737,6 +1842,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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()
{
@@ -1751,8 +1863,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
viewport.getSequenceSelection(),
viewport.getAlignmentView(true).getSequenceStrings(
viewport.getGapCharacter()),
- viewport.alignment.getGroups());
- viewport.alignment.deleteAllGroups();
+ viewport.getAlignment().getGroups());
+ viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
// set view properties for each group
@@ -1760,13 +1872,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.alignment.addGroup(gps[g]);
+ 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());
@@ -1777,7 +1889,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
protected void deleteGroups_actionPerformed()
{
- viewport.alignment.deleteAllGroups();
+ viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
@@ -1791,7 +1903,7 @@ 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());
@@ -1855,11 +1967,11 @@ 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;
@@ -1867,32 +1979,30 @@ 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++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ for (SequenceGroup sg:viewport.getAlignment().getGroups())
+ {
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
@@ -1903,23 +2013,23 @@ 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);
@@ -1928,7 +2038,7 @@ 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());
@@ -1943,28 +2053,28 @@ 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);
@@ -1980,37 +2090,37 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* create a new view derived from the current view
- *
+ *
* @param viewtitle
* @return frame for the new view
*/
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());
@@ -2053,7 +2163,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/**
- *
+ *
* @return list of feature groups on the view
*/
public String[] getFeatureGroups()
@@ -2069,7 +2179,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* get sequence feature groups that are hidden or shown
- *
+ *
* @param visible
* true is visible
* @return list
@@ -2087,7 +2197,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* Change the display state for the given feature groups
- *
+ *
* @param groups
* list of group strings
* @param state
@@ -2155,11 +2265,15 @@ 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);
+ }
};
});
@@ -2190,13 +2304,13 @@ 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);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
cs.setConservation(c);
@@ -2209,73 +2323,11 @@ 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)
{
@@ -2292,7 +2344,7 @@ 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");
@@ -2303,10 +2355,10 @@ 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();
}
}
@@ -2342,7 +2394,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2350,7 +2402,7 @@ 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);
}
@@ -2359,7 +2411,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2368,7 +2420,7 @@ 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);
}
@@ -2393,7 +2445,7 @@ 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();
@@ -2450,7 +2502,7 @@ 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();
@@ -2470,7 +2522,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
if ((viewport.getSelectionGroup() != null && viewport
.getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null && viewport.alignment
+ || (viewport.getSelectionGroup() == null && viewport.getAlignment()
.getHeight() > 1))
{
final TreePanel tp = new TreePanel(alignPanel, type, pwType);
@@ -2500,7 +2552,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* sort the alignment using the given treePanel
- *
+ *
* @param treePanel
* tree used to sort view
* @param title
@@ -2514,14 +2566,14 @@ 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);
}
/**
* Do any automatic reordering of the alignment and add the necessary bits to
* the menu structure for the new tree
- *
+ *
* @param treePanel
* @param title
*/
@@ -2532,6 +2584,7 @@ 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());
@@ -2540,6 +2593,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
treePanel.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowOpened(WindowEvent e)
{
if (viewport.sortByTree)
@@ -2549,6 +2603,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
super.windowOpened(e);
}
+ @Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
@@ -2566,14 +2621,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
if (undoname!=null)
{
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+ 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()
@@ -2591,6 +2647,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
this.builddate = builddate;
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.white);
@@ -2644,45 +2701,7 @@ 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
- // Should really use docbase, not codebase.
- if (url.indexOf("/") == 0)
- {
- String codebase = viewport.applet.getCodeBase().toString();
- url = codebase.substring(0, codebase.length()
- - viewport.applet.getCodeBase().getFile().length())
- + url;
- }
- else
- {
- url = viewport.applet.getCodeBase() + url;
- }
- System.out.println("Show url (prepended codebase): " + url);
- }
- else
- {
- System.out.println("Show url: " + url);
- }
- if (url.indexOf("javascript:") == 0)
- {
- // no target for the javascript context
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url));
- }
- else
- {
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url), target);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ viewport.applet.showURL(url, target);
}
}
@@ -2771,12 +2790,17 @@ 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();
@@ -2842,6 +2866,9 @@ 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();
@@ -2859,7 +2886,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem seqLimits = new CheckboxMenuItem();
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
+
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
Menu autoAnnMenu=new Menu();
CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
@@ -2867,6 +2894,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
private void jbInit() throws Exception
{
@@ -2884,6 +2912,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
@@ -2956,14 +2985,20 @@ 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);
- avDistanceTreeBlosumMenuItem
- .setLabel("Average Distance Using BLOSUM62");
+ 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);
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
njTreeBlosumMenuItem.addActionListener(this);
@@ -3037,6 +3072,7 @@ 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");
@@ -3074,10 +3110,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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);
@@ -3090,6 +3127,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
showGroupConservation.addItemListener(this);
showConsensusHistogram.addItemListener(this);
showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+
applyAutoAnnotationSettings.addItemListener(this);
formatMenu.setLabel("Format");
selectMenu.setLabel("Select");
@@ -3143,6 +3182,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
@@ -3168,6 +3208,8 @@ 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);
@@ -3175,12 +3217,14 @@ 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);
@@ -3261,7 +3305,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
* Attach the alignFrame panels after embedding menus, if necessary. This used
* to be called setEmbedded, but is now creates the dropdown menus in a
* platform independent manner to avoid OSX/Mac menu appendage daftness.
- *
+ *
* @param reallyEmbedded
* true to attach the view to the applet area on the page rather than
* in a new window
@@ -3289,14 +3333,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
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)
{
@@ -3331,7 +3375,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
* 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
@@ -3396,7 +3440,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
/**
* bind a pdb file to a sequence in the current view
- *
+ *
* @param sequenceId
* - sequenceId within the dataset.
* @param pdbEntryString
@@ -3568,7 +3612,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
/**
* modify the current selection, providing the user has not made a selection already.
- * @param sel - sequences from this alignment
+ * @param sel - sequences from this alignment
* @param csel - columns to be selected on the alignment
*/
public void select(SequenceGroup sel, ColumnSelection csel)
@@ -3578,6 +3622,67 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void scrollTo(int row, int column)
{
- alignPanel.seqPanel.scrollTo(row, 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;
+ }
+
+
}