X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=79756718b4b28541db533e1f5a5dfcdc1f7def80;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=ca4a48bc665b847b5e5a70b1edbbfeb3e8bf2ce4;hpb=7ac3fac5daad2af7e538b199dc015737f12a22b1;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ca4a48b..7975671 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,44 +1,130 @@
/*
- * 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.gui;
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-import javax.swing.event.MenuEvent;
-
-import jalview.analysis.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.NJTree;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
import jalview.bin.Cache;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
+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.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HTMLOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.jbgui.GAlignFrame;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+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.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
@@ -202,7 +288,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- if (viewport.conservation == null)
+ if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
@@ -228,7 +314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
addServiceListeners();
- setGUINucleotide(viewport.alignment.isNucleotide());
+ setGUINucleotide(viewport.getAlignment().isNucleotide());
}
setMenusFromViewport(viewport);
@@ -267,6 +353,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -322,6 +409,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
break;
+ // case KeyEvent.VK_A:
+ // if (viewport.cursorMode)
+ // {
+ // alignPanel.seqPanel.insertNucAtCursor(false,"A");
+ // //System.out.println("A");
+ // }
+ // break;
+ /*
+ * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
+ * System.out.println("closing bracket"); } break;
+ */
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
@@ -436,6 +534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
@@ -488,12 +587,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (newPanel)
{
- if (ap.av.padGaps)
+ if (ap.av.isPadGaps())
{
- ap.av.alignment.padGaps();
+ ap.av.getAlignment().padGaps();
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
}
}
@@ -519,6 +619,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.instance.addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
// // System.out.println("Discoverer property change.");
@@ -541,6 +642,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -551,7 +653,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
};
});
// Finally, build the menu once to get current service state
- BuildWebServiceMenu();
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BuildWebServiceMenu();
+ }
+ }).start();
}
public void setGUINucleotide(boolean nucleotide)
@@ -560,11 +669,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
+ rnahelicesColour.setEnabled(nucleotide);
+ purinePyrimidineColour.setEnabled(nucleotide);
// Remember AlignFrame always starts as protein
- if (!nucleotide)
- {
- calculateMenu.remove(calculateMenu.getItemCount() - 2);
- }
+ // if (!nucleotide)
+ // {
+ // showTr
+ // calculateMenu.remove(calculateMenu.getItemCount() - 2);
+ // }
}
/**
@@ -586,7 +698,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void setMenusFromViewport(AlignViewport av)
{
- padGapsMenuitem.setSelected(av.padGaps);
+ padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.showColourText);
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
@@ -601,25 +713,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
- showNonconservedMenuItem.setSelected(av.showUnconserved);
- showGroupConsensus.setSelected(av.showGroupConsensus);
- showGroupConservation.setSelected(av.showGroupConservation);
- showConsensusHistogram.setSelected(av.showConsensusHistogram);
- showSequenceLogo.setSelected(av.showSequenceLogo);
+ showNonconservedMenuItem.setSelected(av.getShowUnconserved());
+ showGroupConsensus.setSelected(av.isShowGroupConsensus());
+ showGroupConservation.setSelected(av.isShowGroupConservation());
+ showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
+ showSequenceLogo.setSelected(av.isShowSequenceLogo());
+ normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
-
+ autoCalculate.setSelected(av.autoCalculateConsensus);
+ sortByTree.setSelected(av.sortByTree);
+ listenToViewSelections.setSelected(av.followSelection);
+ rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
+ rnahelicesColour
+ .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
updateEditMenuBar();
}
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
Hashtable progressBars, progressBarHandlers;
/*
@@ -627,6 +748,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
if (progressBars == null)
@@ -670,10 +792,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
progressBars.put(lId, progressPanel);
}
// update GUI
- setMenusForViewport();
+ // setMenusForViewport();
validate();
}
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
@@ -691,11 +814,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar("Cancelled "
- + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
@@ -706,6 +832,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @return true if any progress bars are still active
*/
+ @Override
public boolean operationInProgress()
{
if (progressBars != null && progressBars.size() > 0)
@@ -728,20 +855,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
+ @Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
+ @Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
{
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
if (currentFileFormat.equals("Jalview"))
@@ -750,6 +882,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int i = 0; i < frames.length; i++)
{
if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
&& ((AlignFrame) frames[i]).fileName.equals(fileName))
{
try
@@ -787,6 +920,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
nfs.frame.setBounds(fspos);
@@ -800,16 +934,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
}
+ @Override
public void addFromURL_actionPerformed(ActionEvent e)
{
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
@@ -831,10 +968,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAs_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"),
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
currentFileFormat, false);
@@ -905,7 +1043,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
int reply = JOptionPane
.showInternalConfirmDialog(
@@ -923,9 +1061,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
FormatAdapter f = new FormatAdapter();
String output = f.formatSequences(format,
- (Alignment) viewport.alignment, // class cast exceptions will
+ viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
+ omitHidden, f.getCacheSuffixDefault(format),
+ viewport.getColumnSelection());
if (output == null)
{
@@ -981,11 +1120,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
int reply = JOptionPane
.showInternalConfirmDialog(
@@ -1004,11 +1144,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + e.getActionCommand(), 600, 500);
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.alignment, omitHidden, viewport.colSel));
+ try
+ {
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ viewport.getAlignment(), omitHidden,
+ viewport.getColumnSelection()));
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ cap.dispose();
+ }
+
}
/**
@@ -1017,11 +1166,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
- .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer());
+ new HTMLOutput(alignPanel,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
}
public void createImageMap(File file, String image)
@@ -1035,6 +1185,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -1046,11 +1197,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1063,6 +1216,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
@@ -1070,25 +1224,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
thread.start();
}
+ @Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportFeatures(alignPanel);
}
+ @Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportAnnotations(alignPanel,
- 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);
}
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Load Jalview Annotations or Features File");
chooser.setToolTipText("Load Jalview Annotations / Features file");
@@ -1099,7 +1256,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice);
+ loadJalviewDataFile(choice, null, null, null);
}
}
@@ -1110,6 +1267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @param closeAllTabs
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
@@ -1219,9 +1377,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = (viewport.colSel != null
- && viewport.colSel.getHiddenColumns() != null && viewport.colSel
- .getHiddenColumns().size() > 0);
+ viewport.updateHiddenColumns();
+ // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
}
}
@@ -1244,7 +1404,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport != null)
{
return new AlignmentI[]
- { viewport.alignment };
+ { viewport.getAlignment() };
}
return null;
}
@@ -1255,6 +1415,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
@@ -1268,11 +1429,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- originalSource.hasHiddenColumns = (viewport.colSel != null
- && viewport.colSel.getHiddenColumns() != null && viewport.colSel
- .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ if (originalSource != viewport)
+ {
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for undo");
+ }
+ originalSource.updateHiddenColumns();
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
}
@@ -1282,6 +1451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.redoList.size() < 1)
@@ -1298,11 +1468,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- originalSource.hasHiddenColumns = (viewport.colSel != null
- && viewport.colSel.getHiddenColumns() != null && viewport.colSel
- .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+
+ if (originalSource != viewport)
+ {
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for redo");
+ }
+ originalSource.updateHiddenColumns();
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
}
@@ -1324,7 +1503,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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;
@@ -1339,7 +1518,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
@@ -1362,69 +1541,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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(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);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ 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)
@@ -1434,15 +1569,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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.add(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ invertGroup.add(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[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
@@ -1501,6 +1634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1513,7 +1647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
omitHidden = viewport.getViewAsString(true);
}
@@ -1528,11 +1662,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.gui.Desktop.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
- new StringSelection(""), null);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
@@ -1540,7 +1674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
Vector hiddenColumns = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
hiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
@@ -1559,7 +1693,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
Desktop.jalviewClipboard = new Object[]
- { seqs, viewport.alignment.getDataset(), hiddenColumns };
+ { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
}
@@ -1569,6 +1703,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1580,6 +1715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1648,6 +1784,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
+ ArrayList newGraphGroups = new ArrayList();
+ int fgroup = -1;
if (newAlignment)
{
@@ -1715,6 +1853,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
newDs.clear(); // tidy up
}
+ if (alignment.getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation alan : alignment
+ .getAlignmentAnnotation())
+ {
+ if (alan.graphGroup > fgroup)
+ {
+ fgroup = alan.graphGroup;
+ }
+ }
+ }
if (pastedal.getAlignmentAnnotation() != null)
{
// Add any annotation attached to alignment.
@@ -1725,6 +1874,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ if (newann.graphGroup > -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
+ }
+
newann.padAnnotation(alwidth);
alignment.addAnnotation(newann);
}
@@ -1744,11 +1909,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (sequences[i].getAnnotation() != null)
{
+ AlignmentAnnotation newann;
for (int a = 0; a < sequences[i].getAnnotation().length; a++)
{
annotationAdded = true;
- sequences[i].getAnnotation()[a].adjustForAlignment();
- sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+ newann = sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup > -1)
+ {
+ if (newann.graphGroup > -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
+ }
+ }
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
// was
// duplicated
@@ -1788,6 +1973,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newann.padAnnotation(avwidth);
alview[avnum].addAnnotation(newann); // annotation was
// duplicated earlier
+ // TODO JAL-1145 graphGroups are not updated for sequence
+ // annotation added to several views. This may cause
+ // strangeness
alview[avnum].setAnnotationIndex(newann, a);
}
}
@@ -1795,8 +1983,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildSortByAnnotationScoresMenu();
}
- viewport.firePropertyChange("alignment", null, alignment
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ alignment.getSequences());
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : ((Vector) alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
+ {
+ alignPanel.validateAnnotationDimensions(false);
+ }
}
else
@@ -1860,6 +2059,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
@@ -1872,6 +2072,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -1890,7 +2091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
// 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);
@@ -1907,11 +2108,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
viewport.sendSelection();
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
@@ -1932,9 +2133,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- viewport.alignment.deleteAllGroups();
+ viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
@@ -1948,6 +2150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
@@ -1957,7 +2160,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth() - 1);
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
viewport.sendSelection();
alignPanel.paintAlignment(true);
@@ -1970,6 +2173,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
@@ -1984,6 +2188,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
/**
@@ -1992,6 +2197,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2009,14 +2215,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
alignPanel.paintAlignment(true);
- viewport.sendSelection();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
+ @Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/**
@@ -2025,6 +2233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
@@ -2036,6 +2245,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
@@ -2061,11 +2271,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
@@ -2073,32 +2283,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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.get(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
@@ -2113,25 +2319,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
- 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);
@@ -2140,7 +2348,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// 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());
@@ -2159,30 +2367,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
- 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);
@@ -2197,9 +2406,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
- viewport.padGaps = padGapsMenuitem.isSelected();
+ viewport.setPadGaps(padGapsMenuitem.isSelected());
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
@@ -2220,15 +2430,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder();
}
+ @Override
public void newView_actionPerformed(ActionEvent e)
{
+ newView(true);
+ }
+
+ /**
+ *
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(boolean copyAnnotation)
+ {
+ return newView(null, copyAnnotation);
+ }
+
+ /**
+ *
+ * @param viewTitle
+ * title of newly created view
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle)
+ {
+ return newView(viewTitle, true);
+ }
+
+ /**
+ *
+ * @param viewTitle
+ * title of newly created view
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+ {
AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
true);
+ if (!copyAnnotation)
+ {
+ // just remove all the current annotation except for the automatic stuff
+ newap.av.getAlignment().deleteAllGroups();
+ for (AlignmentAnnotation alan : newap.av.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated)
+ {
+ newap.av.getAlignment().deleteAnnotation(alan);
+ }
+ ;
+ }
+ }
newap.av.gatherViewsHere = false;
@@ -2241,8 +2502,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.av.redoList = viewport.redoList;
int index = Desktop.getViewCount(viewport.getSequenceSetId());
- String newViewName = "View " + index;
-
+ // make sure the new view has a unique name - this is essential for Jalview
+ // 2 archives
+ boolean addFirstIndex = false;
+ if (viewTitle == null || viewTitle.trim().length() == 0)
+ {
+ viewTitle = "View";
+ addFirstIndex = true;
+ }
+ else
+ {
+ index = 1;// we count from 1 if given a specific name
+ }
+ String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
Vector comps = (Vector) PaintRefresher.components.get(viewport
.getSequenceSetId());
Vector existingNames = new Vector();
@@ -2260,7 +2532,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
while (existingNames.contains(newViewName))
{
- newViewName = "View " + (++index);
+ newViewName = viewTitle + " " + (++index);
}
newap.av.viewName = newViewName;
@@ -2272,13 +2544,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.gatherViewsHere = true;
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
}
+ @Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.instance.explodeViews(this);
}
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
@@ -2290,6 +2565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
@@ -2301,6 +2577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
@@ -2310,12 +2587,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ @Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.rightAlignIds = idRightAlign.isSelected();
alignPanel.paintAlignment(true);
}
+ @Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
@@ -2327,6 +2606,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+ @Override
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
@@ -2342,6 +2622,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2354,6 +2635,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
@@ -2363,17 +2645,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
}
+ @Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
+ @Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
repaint();
}
+ @Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
@@ -2396,8 +2681,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// 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()))
{
@@ -2420,12 +2706,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (toggleSeqs)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hideSelSequences_actionPerformed(null);
hide = true;
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
{
showAllSeqs_actionPerformed(null);
}
@@ -2433,12 +2720,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (toggleCols)
{
- if (viewport.colSel.getSelected().size() > 0)
+ if (viewport.getColumnSelection().getSelected().size() > 0)
{
hideSelColumns_actionPerformed(null);
if (!toggleSeqs)
{
- viewport.selectionGroup = sg;
+ viewport.setSelectionGroup(sg);
}
}
else if (!hide)
@@ -2455,6 +2742,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
+ @Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
@@ -2467,6 +2755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2483,6 +2772,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
@@ -2490,12 +2780,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ @Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
+ @Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
@@ -2508,6 +2800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2520,6 +2813,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2532,6 +2826,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2544,6 +2839,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2556,6 +2852,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2568,6 +2865,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2576,6 +2874,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureSettings featureSettings;
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
@@ -2598,6 +2897,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2614,6 +2914,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
@@ -2637,68 +2938,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
}
+ @Override
public void alignmentProperties()
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
- 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("
Sequences: " + viewport.alignment.getHeight());
- contents.append("
Minimum Sequence Length: " + min);
- contents.append("
Maximum Sequence Length: " + max);
- contents.append("
Average Length: " + (int) avg);
-
- if (((Alignment) viewport.alignment).getProperties() != null)
- {
- Hashtable props = ((Alignment) viewport.alignment).getProperties();
- Enumeration en = props.keys();
- contents.append("
");
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- StringBuffer val = new StringBuffer();
- String vals = props.get(key).toString();
- int pos = 0, npos;
- do
- {
- npos = vals.indexOf("\n", pos);
- if (npos == -1)
- {
- val.append(vals.substring(pos));
- }
- else
- {
- val.append(vals.substring(pos, npos));
- val.append("
");
- }
- pos = npos + 1;
- } while (npos != -1);
- contents
- .append("| " + key + " | " + val + " |
");
- }
- contents.append("
");
- }
- editPane.setText(contents.toString() + "");
+ StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+ .formatAsHtml();
+ editPane.setText("" + contents.toString() + "");
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
@@ -2712,6 +2966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
@@ -2722,23 +2977,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
- .getWidth(), frame.getHeight());
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2750,6 +3006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2761,11 +3018,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void clustalColour_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(), viewport.alignment
- .getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+ viewport.getHiddenRepSequences()));
}
/**
@@ -2774,6 +3031,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
@@ -2785,6 +3043,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
@@ -2796,6 +3055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
@@ -2807,6 +3067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
@@ -2818,6 +3079,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
@@ -2829,6 +3091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
@@ -2840,6 +3103,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
@@ -2851,22 +3115,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void nucleotideColour_actionPerformed(ActionEvent e)
{
changeColour(new NucleotideColourScheme());
}
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+
+ /*
+ * public void covariationColour_actionPerformed(ActionEvent e) {
+ * changeColour(new
+ * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
+ * ()[0])); }
+ */
+ @Override
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+ @Override
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -2880,6 +3165,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
public void changeColour(ColourSchemeI cs)
{
+ // TODO: compare with applet and pull up to model method
int threshold = 0;
if (cs != null)
@@ -2901,13 +3187,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -2919,19 +3205,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
if (cs == null)
{
sg.cs = null;
@@ -2940,8 +3223,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(viewport.hiddenRepSequences), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg,
+ viewport.getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
@@ -2951,7 +3234,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ sg.cs = cs.getClass().newInstance();
} catch (Exception ex)
{
}
@@ -2963,9 +3246,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(viewport.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
else
{
@@ -2975,11 +3258,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(viewport.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
+ ResidueProperties.propHash, 3, sg.getSequences(viewport
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
sg.cs.setConservation(c);
}
else
@@ -3003,13 +3286,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyPID_actionPerformed(ActionEvent e)
{
if (viewport.getAbovePIDThreshold()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport
- .getGlobalColourScheme(), "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
@@ -3020,13 +3304,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
if (viewport.getConservationSelected()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme, "Background");
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
@@ -3037,6 +3322,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3055,6 +3341,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3073,6 +3360,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
if (e.getActionCommand().equals("User Defined..."))
@@ -3114,13 +3402,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
|| SwingUtilities.isRightMouseButton(evt))
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
@@ -3137,6 +3425,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3148,6 +3437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3166,6 +3456,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
@@ -3177,6 +3468,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
@@ -3188,13 +3480,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3204,11 +3497,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
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);
}
@@ -3218,12 +3513,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3233,12 +3529,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3249,6 +3546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
@@ -3260,6 +3558,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ((viewport.getSelectionGroup() == null)
@@ -3283,6 +3582,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if (((viewport.getSelectionGroup() != null)
@@ -3302,6 +3602,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3312,12 +3613,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+ viewport.sortByTree = sortByTree.isSelected();
+ }
+
+ @Override
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ viewport.followSelection = listenToViewSelections.isSelected();
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3329,6 +3643,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
@@ -3340,6 +3655,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -3351,6 +3667,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
@@ -3370,7 +3687,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null)
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0)
{
if (viewport.getSelectionGroup().getSize() < 3)
{
@@ -3382,14 +3700,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize())
+ for (SequenceI _s : sg.getSequences())
{
- if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
- .getEndRes())
+ if (_s.getLength() < sg.getEndRes())
{
JOptionPane
.showMessageDialog(
@@ -3410,7 +3726,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
else
{
// are the visible sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
JOptionPane
.showMessageDialog(
@@ -3424,7 +3740,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- if (viewport.alignment.getHeight() < 2)
+ if (viewport.getAlignment().getHeight() < 2)
{
return;
}
@@ -3459,6 +3775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3467,8 +3784,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
- addHistoryItem(new OrderCommand(order.getName(), oldOrder,
- viewport.alignment));
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
+ .getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3491,13 +3808,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
- .getAlignment());// ,viewport.getSelectionGroup());
+ AlignmentSorter.sortByAnnotationScore(scoreLabel,
+ viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
});
@@ -3515,23 +3833,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* rebuilding in subsequence calls.
*
*/
+ @Override
public void buildSortByAnnotationScoresMenu()
{
- if (viewport.alignment.getAlignmentAnnotation() == null)
+ if (viewport.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
- if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
+ if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
- Enumeration sq = viewport.alignment.getSequences().elements();
- while (sq.hasMoreElements())
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
- aann = ((SequenceI) sq.nextElement()).getAnnotation();
+ aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
{
if (aann[i].hasScore() && aann[i].sequenceRef != null)
@@ -3543,13 +3861,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Enumeration labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
- .nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore,
+ (String) labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
- _annotationScoreVectorHash = viewport.alignment
+ _annotationScoreVectorHash = viewport.getAlignment()
.getAlignmentAnnotation().hashCode();
}
}
@@ -3566,6 +3884,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param title
* SortBy menu item title.
*/
+ @Override
public void buildTreeMenu()
{
sortByTreeMenu.removeAll();
@@ -3594,21 +3913,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (i = 0; i < treePanels.size(); i++)
{
- TreePanel tp = (TreePanel) treePanels.elementAt(i);
+ final TreePanel tp = (TreePanel) treePanels.elementAt(i);
final JMenuItem item = new JMenuItem(tp.getTitle());
final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
- AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+ tp.sortByTree_actionPerformed(null);
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));
- addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
- viewport.alignment));
-
- alignPanel.paintAlignment(true);
}
});
@@ -3616,6 +3931,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
@@ -3677,9 +4005,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
// limit sequences - JBPNote in future - could spawn multiple prediction
// jobs
- // TODO: viewport.alignment.isAligned is a global state - the local
+ // TODO: viewport.getAlignment().isAligned is a global state - the local
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
- if (!viewport.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
seqs.setSequences(new SeqCigar[]
{ seqs.getSequences()[0] });
@@ -3696,11 +4024,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Select a newick-like tree file");
chooser.setToolTipText("Load a tree file");
@@ -3724,13 +4053,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop, fin
- .getWarningMessage(), "Possible problem with tree file",
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(), "Possible problem with tree file",
JOptionPane.WARNING_MESSAGE);
}
}
}
+ @Override
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
+
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
@@ -3817,127 +4152,178 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
;
}
+ final AlignFrame me = this;
buildingMenu = true;
- try
+ new Thread(new Runnable()
{
- System.err
- .println("Building ws menu again " + Thread.currentThread());
- // TODO: add support for context dependent disabling of services based on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract
- // handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or introduce
- // object broker mechanism.
- Vector wsmenu = new Vector();
- final IProgressIndicator af = this;
- if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
- && Discoverer.services != null
- && (Discoverer.services.size() > 0))
+ @Override
+ public void run()
{
- // TODO: refactor to allow list of AbstractName/Handler bindings to be
- // stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
- Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
- // TODO: move GUI generation code onto service implementation - so a
- // client instance attaches itself to the GUI with method call like
- // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
- // alignframe)
- if (msaws != null)
+ try
{
- // Add any Multiple Sequence Alignment Services
+ System.err.println("Building ws menu again "
+ + Thread.currentThread());
+ // TODO: add support for context dependent disabling of services based
+ // on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract
+ // handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or
+ // introduce
+ // object broker mechanism.
+ final Vector wsmenu = new Vector();
+ final IProgressIndicator af = me;
final JMenu msawsmenu = new JMenu("Alignment");
- for (int i = 0, j = msaws.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, this);
-
- }
- wsmenu.add(msawsmenu);
- }
- if (secstrpr != null)
- {
- // Add any secondary structure prediction services
final JMenu secstrmenu = new JMenu(
"Secondary Structure Prediction");
- for (int i = 0, j = secstrpr.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(secstrmenu, this);
- }
- wsmenu.add(secstrmenu);
- }
- if (seqsrch != null)
- {
- // Add any sequence search services
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- for (int i = 0, j = seqsrch.size(); i < j; i++)
+ final JMenu analymenu = new JMenu("Analysis");
+ final JMenu dismenu = new JMenu("Protein Disorder");
+ // JAL-940 - only show secondary structure prediction services from
+ // the legacy server
+ if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ // &&
+ Discoverer.services != null && (Discoverer.services.size() > 0))
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, this);
+ // TODO: refactor to allow list of AbstractName/Handler bindings to
+ // be
+ // stored or retrieved from elsewhere
+ Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services
+ .get("SecStrPred");
+ Vector seqsrch = null; // (Vector)
+ // Discoverer.services.get("SeqSearch");
+ // TODO: move GUI generation code onto service implementation - so a
+ // client instance attaches itself to the GUI with method call like
+ // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+ // alignframe)
+ if (msaws != null)
+ {
+ // Add any Multiple Sequence Alignment Services
+ for (int i = 0, j = msaws.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(msawsmenu, me);
+
+ }
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(secstrmenu, me);
+ }
+ }
+ if (seqsrch != null)
+ {
+ // Add any sequence search services
+ for (int i = 0, j = seqsrch.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+ .elementAt(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(seqsrchmenu, me);
+ }
+ }
}
- wsmenu.add(seqsrchmenu);
- }
- }
- // TODO: move into separate menu builder class.
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
+ // Add all submenus in the order they should appear on the web
+ // services menu
+ wsmenu.add(msawsmenu);
+ wsmenu.add(secstrmenu);
+ wsmenu.add(dismenu);
+ wsmenu.add(analymenu);
+ // final ArrayList submens=new ArrayList();
+ // submens.add(msawsmenu);
+ // submens.add(secstrmenu);
+ // submens.add(dismenu);
+ // submens.add(analymenu);
+
+ // No search services yet
+ // wsmenu.add(seqsrchmenu);
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- JMenu jws2men = new JMenu("Jalview 2 Services");
- jws2servs.attachWSMenuEntry(jws2men, this);
- for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
+ @Override
+ public void run()
{
- wsmenu.add(jws2men.getMenuComponent(i));
+ try
+ {
+ webService.removeAll();
+ // first, add discovered services onto the webservices menu
+ if (wsmenu.size() > 0)
+ {
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add(wsmenu.get(i));
+ }
+ }
+ else
+ {
+ webService.add(me.webServiceNoServices);
+ }
+ // TODO: move into separate menu builder class.
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ jws2servs.attachWSMenuEntry(webService, me);
+ }
+ if (jws2servs.isRunning())
+ {
+ JMenuItem tm = new JMenuItem(
+ "Still discovering JABA Services");
+ tm.setEnabled(false);
+ webService.add(tm);
+ }
+ }
+ }
+
+ build_urlServiceMenu(me.webService);
+ build_fetchdbmenu(webService);
+ for (JMenu item : wsmenu)
+ {
+ if (item.getItemCount() == 0)
+ {
+ item.setEnabled(false);
+ }
+ else
+ {
+ item.setEnabled(true);
+ }
+ }
+ } catch (Exception e)
+ {
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
+ }
+ ;
}
- }
- }
- }
- resetWebServiceMenu();
- // finally, add the whole shebang onto the webservices menu
- if (wsmenu.size() > 0)
- {
- for (int i = 0, j = wsmenu.size(); i < j; i++)
+ });
+ } catch (Exception e)
{
- webService.add((JMenu) wsmenu.get(i));
}
+ ;
+
+ buildingMenu = false;
}
- else
- {
- this.webService.add(this.webServiceNoServices);
- }
- } catch (Exception e)
- {
- }
- ;
- buildingMenu = false;
- }
+ }).start();
- /**
- * empty the web service menu and add any ad-hoc functions not dynamically
- * discovered.
- *
- */
- private void resetWebServiceMenu()
- {
- webService.removeAll();
- build_fetchdbmenu(webService);
- build_urlServiceMenu(webService);
}
/**
@@ -3947,6 +4333,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
private void build_urlServiceMenu(JMenu webService)
{
+ // TODO: remove this code when 2.7 is released
+ // DEBUG - alignmentView
+ /*
+ * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
+ * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent e) {
+ * jalview.datamodel.AlignmentView
+ * .testSelectionViews(af.viewport.getAlignment(),
+ * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
+ *
+ * }); webService.add(testAlView);
+ */
+ // TODO: refactor to RestClient discoverer and merge menu entries for
+ // rest-style services with other types of analysis/calculation service
+ // SHmmr test client - still being implemented.
+ // DEBUG - alignmentView
+
+ for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+ .getRestClients())
+ {
+ client.attachWSMenuEntry(
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+ this);
+ }
+
if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
{
jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
@@ -4021,6 +4433,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
xtype.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: new thread for this call with vis-delay
@@ -4036,8 +4449,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception e)
{
jalview.bin.Cache.log
- .warn(
- "canTranslate threw an exception - please report to help@jalview.org",
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
e);
return false;
}
@@ -4055,13 +4467,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
try
{
- Alignment ds = ths.getViewport().alignment.getDataset(); // update
+ Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
// our local
// dataset
// reference
@@ -4127,18 +4540,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// old way
try
{
- return (jalview.analysis.Dna.canTranslate(selection, viewport
- .getViewAsVisibleContigs(true)));
+ return (jalview.analysis.Dna.canTranslate(selection,
+ viewport.getViewAsVisibleContigs(true)));
} catch (Exception e)
{
jalview.bin.Cache.log
- .warn(
- "canTranslate threw an exception - please report to help@jalview.org",
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
e);
return false;
}
}
+ @Override
public void showProducts_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4172,6 +4585,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void showTranslation_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4184,13 +4598,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
viewport.getViewAsVisibleContigs(true), viewport
- .getGapCharacter(), viewport.alignment
- .getAlignmentAnnotation(), viewport.alignment
+ .getGapCharacter(), viewport.getAlignment()
+ .getAlignmentAnnotation(), viewport.getAlignment()
.getWidth(), viewport.getAlignment().getDataset());
} catch (Exception ex)
{
al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", ex);
+ jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.",
+ "Implementation error: Translation Failed", JOptionPane.ERROR_MESSAGE);
+ return;
}
if (al == null)
{
@@ -4222,9 +4642,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
- .getDataset(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, false);
+ featuresFile = new FeaturesFile(file, type).parse(viewport
+ .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, false,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
ex.printStackTrace();
@@ -4249,22 +4670,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return featuresFile;
}
+ @Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+ @Override
public void dragExit(DropTargetEvent evt)
{
}
+ @Override
public void dragOver(DropTargetDragEvent evt)
{
}
+ @Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
+ @Override
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
@@ -4319,10 +4745,127 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
try
{
-
+ // check to see if any of these files have names matching sequences in
+ // the alignment
+ SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ .getAlignment().getSequencesArray());
+ /**
+ * Object[] { String,SequenceI}
+ */
+ ArrayList filesmatched = new ArrayList();
+ ArrayList filesnotmatched = new ArrayList();
for (int i = 0; i < files.size(); i++)
{
- loadJalviewDataFile(files.get(i).toString());
+ String file = files.get(i).toString();
+ String pdbfn = "";
+ String protocol = FormatAdapter.checkProtocol(file);
+ if (protocol == jalview.io.FormatAdapter.FILE)
+ {
+ File fl = new File(file);
+ pdbfn = fl.getName();
+ }
+ else if (protocol == jalview.io.FormatAdapter.URL)
+ {
+ URL url = new URL(file);
+ pdbfn = url.getFile();
+ }
+ if (pdbfn.length() > 0)
+ {
+ // attempt to find a match in the alignment
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+ int l = 0, c = pdbfn.indexOf(".");
+ while (mtch == null && c != -1)
+ {
+ do
+ {
+ l = c;
+ } while ((c = pdbfn.indexOf(".", l)) > l);
+ if (l > -1)
+ {
+ pdbfn = pdbfn.substring(0, l);
+ }
+ mtch = idm.findAllIdMatches(pdbfn);
+ }
+ if (mtch != null)
+ {
+ String type = null;
+ try
+ {
+ type = new IdentifyFile().Identify(file, protocol);
+ } catch (Exception ex)
+ {
+ type = null;
+ }
+ if (type != null)
+ {
+ if (type.equalsIgnoreCase("PDB"))
+ {
+ filesmatched.add(new Object[]
+ { file, protocol, mtch });
+ continue;
+ }
+ }
+ }
+ // File wasn't named like one of the sequences or wasn't a PDB file.
+ filesnotmatched.add(file);
+ }
+ }
+ int assocfiles = 0;
+ if (filesmatched.size() > 0)
+ {
+ if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
+ || JOptionPane
+ .showConfirmDialog(
+ this,
+ "Do you want to automatically associate the "
+ + filesmatched.size()
+ + " PDB files with sequences in the alignment that have the same name ?",
+ "Automatically Associate PDB files by name",
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+
+ {
+ for (Object[] fm : filesmatched)
+ {
+ // try and associate
+ // TODO: may want to set a standard ID naming formalism for
+ // associating PDB files which have no IDs.
+ for (SequenceI toassoc : (SequenceI[]) fm[2])
+ {
+ PDBEntry pe = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq((String) fm[0],
+ (String) fm[1], toassoc, false);
+ if (pe != null)
+ {
+ System.err.println("Associated file : "
+ + ((String) fm[0]) + " with "
+ + toassoc.getDisplayId(true));
+ assocfiles++;
+ }
+ }
+ alignPanel.paintAlignment(true);
+ }
+ }
+ }
+ if (filesnotmatched.size() > 0)
+ {
+ if (assocfiles > 0
+ && (Cache.getDefault(
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+ .showConfirmDialog(
+ this,
+ "Do you want to ignore the "
+ + filesnotmatched.size()
+ + " files whose names did not match any sequence IDs ?",
+ "Ignore unmatched dropped files ?",
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+ {
+ return;
+ }
+ for (String fn : filesnotmatched)
+ {
+ loadJalviewDataFile(fn, null, null, null);
+ }
+
}
} catch (Exception ex)
{
@@ -4340,47 +4883,117 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param file
* either a filename or a URL string.
*/
- public void loadJalviewDataFile(String file)
+ public void loadJalviewDataFile(String file, String protocol,
+ String format, SequenceI assocSeq)
{
try
{
- String protocol = jalview.io.FormatAdapter.FILE;
- String f = file.toLowerCase();
- if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
- || f.indexOf("file:") == 0)
+ if (protocol == null)
{
- protocol = jalview.io.FormatAdapter.URL;
+ protocol = jalview.io.FormatAdapter.checkProtocol(file);
}
-
- boolean isAnnotation = new AnnotationFile().readAnnotationFile(
- viewport.alignment, file, protocol);
+ // if the file isn't identified, or not positively identified as some
+ // other filetype (PFAM is default unidentified alignment file type) then
+ // try to parse as annotation.
+ boolean isAnnotation = (format == null || format
+ .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
+ .readAnnotationFile(viewport.getAlignment(), file, protocol)
+ : false;
if (!isAnnotation)
{
- // try to see if its a JNet 'concise' style annotation file *before* we
- // try to parse it as a features file
- String format = new IdentifyFile().Identify(file, protocol);
- if (format.equalsIgnoreCase("JnetFile"))
+ // first see if its a T-COFFEE score file
+ TCoffeeScoreFile tcf = null;
+ try
+ {
+ tcf = new TCoffeeScoreFile(file, protocol);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ isAnnotation = true;
+ statusBar
+ .setText("Successfully pasted T-Coffee scores to alignment.");
+ }
+ else
+ {
+ // some problem - if no warning its probable that the ID matching
+ // process didn't work
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+ : tcf.getWarningMessage(),
+ "Problem reading T-COFFEE score file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
- protocol);
- new JnetAnnotationMaker().add_annotation(predictions, viewport
- .getAlignment(), 0, false);
- isAnnotation = true;
+ Cache.log
+ .debug("Exception when processing data source as T-COFFEE score file",
+ x);
+ tcf = null;
}
- else
+ if (tcf == null)
{
+ // try to see if its a JNet 'concise' style annotation file *before*
+ // we
// try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
+ if (format == null)
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ if (format.equalsIgnoreCase("JnetFile"))
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
+ isAnnotation = true;
}
else
{
- alignPanel.paintAlignment(true);
+ /*
+ * if (format.equalsIgnoreCase("PDB")) {
+ *
+ * String pdbfn = ""; // try to match up filename with sequence id
+ * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+ * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+ * // attempt to find a match in the alignment SequenceI mtch =
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+ * { System.err.println("Associated file : " + file + " with " +
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+ * TODO: maybe need to load as normal otherwise return; } }
+ */
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ else
+ {
+ alignPanel.paintAlignment(true);
+ }
}
}
}
@@ -4395,9 +5008,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception ex)
{
ex.printStackTrace();
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "loading data "
+ + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+ : "using " + protocol + " from " + file)
+ : ".")
+ + (format != null ? "(parsing as '" + format
+ + "' file)" : ""), oom, Desktop.desktop);
}
}
+ @Override
public void tabSelectionChanged(int index)
{
if (index > -1)
@@ -4408,6 +5038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
@@ -4432,10 +5063,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Open the dialog for regex description parsing.
*/
+ @Override
protected void extractScores_actionPerformed(ActionEvent e)
{
ParseProperties pp = new jalview.analysis.ParseProperties(
- viewport.alignment);
+ viewport.getAlignment());
// TODO: verify regex and introduce GUI dialog for version 2.5
// if (pp.getScoresFromDescription("col", "score column ",
// "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
@@ -4454,6 +5086,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
@@ -4465,6 +5098,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
@@ -4505,22 +5139,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// TODO We probably want to store a sequence database checklist in
// preferences and have checkboxes.. rather than individual sources selected
// here
- JMenu rfetch = new JMenu("Fetch DB References");
- rfetch
- .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ final JMenu rfetch = new JMenu("Fetch DB References");
+ rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
webService.add(rfetch);
JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr
- .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -4533,62 +5167,193 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
rfetch.add(fetchr);
- JMenu dfetch = new JMenu();
- rfetch.add(dfetch);
- jalview.ws.SequenceFetcher sf = SequenceFetcher
- .getSequenceFetcherSingleton(this);
- String[] otherdb = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
- int comp = 0, mcomp = 15;
- String mname = null;
- if (otherdb != null && otherdb.length > 0)
- {
- for (int i = 0; i < otherdb.length; i++)
+ final AlignFrame me = this;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
{
- String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
- if (mname == null)
- {
- mname = "from '" + dbname + "'";
- }
- fetchr = new JMenuItem(otherdb[i]);
- final String[] dassource = new String[]
- { otherdb[i] };
- fetchr.addActionListener(new ActionListener()
+ final jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(me);
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
-
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void run()
{
- new Thread(new Runnable()
+ String[] dbclasses = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ List otherdb;
+ JMenu dfetch = new JMenu();
+ JMenu ifetch = new JMenu();
+ JMenuItem fetchr = null;
+ int comp = 0, icomp = 0, mcomp = 15;
+ String mname = null;
+ int dbi = 0;
+ for (String dbclass : dbclasses)
{
+ otherdb = sf.getSourceProxy(dbclass);
+ // add a single entry for this class, or submenu allowing 'fetch
+ // all' or pick one
+ if (otherdb == null || otherdb.size() < 1)
+ {
+ continue;
+ }
+ // List dbs=otherdb;
+ // otherdb=new ArrayList();
+ // for (DbSourceProxy db:dbs)
+ // {
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)
+ // }
+ if (mname == null)
+ {
+ mname = "From " + dbclass;
+ }
+ if (otherdb.size() == 1)
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(src.getDbSource());
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
- public void run()
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText(""
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + src.getDbName()) + "");
+ dfetch.add(fetchr);
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
+ + "'");
+ fetchr.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+ });
+
+ fetchr.setToolTipText(""
+ + JvSwingUtils.wrapTooltip("Retrieve from all "
+ + otherdb.size() + " sources in "
+ + src.getDbSource() + "
First is :"
+ + src.getDbName()) + "");
+ dfetch.add(fetchr);
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu("Sources from " + src.getDbSource());
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
+ {
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = "from '" + sname + "'";
+ }
+ fetchr = new JMenuItem(msname);
+ final DbSourceProxy[] dassrc =
+ { sproxy };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassrc)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText(""
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + dbname) + "");
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(imname + " to '" + sname + "'");
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
+ }
+ }
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
{
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame,
- dassource).fetchDBRefs(false);
+ dfetch.setText(mname + " to '" + dbclass + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
}
- }).start();
+ }
}
-
});
- fetchr.setToolTipText("Retrieve from " + dbname);
- dfetch.add(fetchr);
- if (comp++ == mcomp || i == (otherdb.length - 1))
- {
- dfetch.setText(mname + " to '" + dbname + "'");
- rfetch.add(dfetch);
- dfetch = new JMenu();
- mname = null;
- comp = 0;
- }
}
- }
+ }).start();
+
}
/**
* Left justify the whole alignment.
*/
+ @Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -4599,6 +5364,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Right justify the whole alignment.
*/
+ @Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -4619,6 +5385,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
+ @Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
@@ -4632,6 +5399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
@@ -4646,6 +5414,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
@@ -4659,6 +5428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
@@ -4672,12 +5442,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ @Override
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -4690,15 +5471,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
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
@@ -4706,20 +5489,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
gps[g].setShowNonconserved(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 s : gps[g].getSequences())
+ viewport.setSequenceColour(s, col);
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
+
+ /**
+ * make the given alignmentPanel the currently selected tab
+ *
+ * @param alignmentPanel
+ */
+ public void setDisplayedView(AlignmentPanel alignmentPanel)
+ {
+ if (!viewport.getSequenceSetId().equals(
+ alignmentPanel.av.getSequenceSetId()))
+ {
+ throw new Error(
+ "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+ }
+ if (tabbedPane != null
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane
+ .getSelectedIndex())
+ {
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+ }
+ }
}
class PrintThread extends Thread
@@ -4733,6 +5535,7 @@ class PrintThread extends Thread
static PageFormat pf;
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();