X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b91255f50ba15bc43994c328c9457f6738509c0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=8f1aa46e4f5649fcc6ff38ff4a7281a63e668dca;hpb=1145380bdd6555637794c9db36624fa42a8818c8;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8f1aa46..9b91255 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,42 +1,125 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.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.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
+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.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.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.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws1.Discoverer;
+import jalview.ws.jws2.Jws2Discoverer;
+
+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.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!
@@ -81,51 +164,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
this(al, null, width, height);
}
+
/**
- * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
* @param al
* @param width
* @param height
* @param sequenceSetId
*/
- public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId)
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId)
{
this(al, null, width, height, sequenceSetId);
}
+
/**
- * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
* @param al
* @param width
* @param height
* @param sequenceSetId
* @param viewId
*/
- public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId, String viewId)
{
this(al, null, width, height, sequenceSetId, viewId);
}
+
/**
* new alignment window with hidden columns
*
* @param al
- * AlignmentI
+ * AlignmentI
* @param hiddenColumns
- * ColumnSelection or null
- * @param width Width of alignment frame
- * @param height height of frame.
+ * ColumnSelection or null
+ * @param width
+ * Width of alignment frame
+ * @param height
+ * height of frame.
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height)
{
this(al, hiddenColumns, width, height, null);
}
+
/**
- * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
* @param al
* @param hiddenColumns
* @param width
* @param height
- * @param sequenceSetId (may be null)
+ * @param sequenceSetId
+ * (may be null)
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height, String sequenceSetId)
@@ -134,16 +232,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
* @param al
* @param hiddenColumns
* @param width
* @param height
- * @param sequenceSetId (may be null)
- * @param viewId (may be null)
+ * @param sequenceSetId
+ * (may be null)
+ * @param viewId
+ * (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height,
- String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
@@ -163,9 +265,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* Make a new AlignFrame from exisiting alignmentPanels
*
* @param ap
- * AlignmentPanel
+ * AlignmentPanel
* @param av
- * AlignViewport
+ * AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
@@ -174,8 +276,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addAlignmentPanel(ap, false);
init();
}
+
/**
- * initalise the alignframe from the underlying viewport data and the configurations
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
*/
void init()
{
@@ -229,9 +333,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* button functionality.
*
* @param file
- * valid filename
+ * valid filename
* @param format
- * format of file
+ * format of file
*/
public void setFileName(String file, String format)
{
@@ -298,7 +402,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
|| evt.isShiftDown() || evt.isAltDown());
}
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)
@@ -385,39 +504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
boolean toggleSeqs = !evt.isControlDown();
boolean toggleCols = !evt.isShiftDown();
-
- boolean hide = false;
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (toggleSeqs)
- {
- if (sg != null
- && sg.getSize() != viewport.alignment.getHeight())
- {
- hideSelSequences_actionPerformed(null);
- hide = true;
- }
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- showAllSeqs_actionPerformed(null);
- }
- }
-
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- showAllColumns_actionPerformed(null);
- }
- }
+ toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
case KeyEvent.VK_PAGE_UP:
@@ -503,6 +590,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
}
}
@@ -525,32 +613,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
private void addServiceListeners()
{
final java.beans.PropertyChangeListener thisListener;
- // Do this once to get current state
- BuildWebServiceMenu();
- Desktop.discoverer
- .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+ Desktop.instance.addJalviewPropertyChangeListener("services",
+ thisListener = new java.beans.PropertyChangeListener()
{
public void propertyChange(PropertyChangeEvent evt)
{
- // System.out.println("Discoverer property change.");
- if (evt.getPropertyName().equals("services"))
+ // // System.out.println("Discoverer property change.");
+ // if (evt.getPropertyName().equals("services"))
{
- // System.out.println("Rebuilding web service menu");
- BuildWebServiceMenu();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ public void run()
+ {
+ System.err
+ .println("Rebuild WS Menu for service change");
+ BuildWebServiceMenu();
+ }
+
+ });
}
}
});
-
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- // System.out.println("deregistering discoverer listener");
- Desktop.discoverer.removePropertyChangeListener(thisListener);
+ System.out.println("deregistering discoverer listener");
+ Desktop.instance.removeJalviewPropertyChangeListener("services",
+ thisListener);
closeMenuItem_actionPerformed(true);
};
});
+ // Finally, build the menu once to get current service state
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ BuildWebServiceMenu();
+ }
+ }).start();
}
public void setGUINucleotide(boolean nucleotide)
@@ -558,12 +661,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
showTranslation.setVisible(nucleotide);
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);
+ // }
}
/**
@@ -581,7 +687,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* loading from Jalview2XML.java
*
* @param av
- * AlignViewport
+ * AlignViewport
*/
void setMenusFromViewport(AlignViewport av)
{
@@ -600,7 +706,11 @@ 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);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
@@ -609,13 +719,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
applyToAllGroups.setState(av.colourAppliesToAllGroups);
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
-
+ autoCalculate.setSelected(av.autoCalculateConsensus);
+ sortByTree.setSelected(av.sortByTree);
+ listenToViewSelections.setSelected(av.followSelection);
+ rnahelicesColour.setEnabled(av.alignment.hasRNAStructure());
+ rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
updateEditMenuBar();
}
- Hashtable progressBars;
+ Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
@@ -627,21 +741,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (progressBars == null)
{
progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
}
JPanel progressPanel;
+ Long lId = new Long(id);
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(new Long(id)) != null)
+ if (progressBars.get(lId) != null)
{
progressPanel = (JPanel) progressBars.get(new Long(id));
statusPanel.remove(progressPanel);
- progressBars.remove(progressPanel);
+ progressBars.remove(lId);
progressPanel = null;
if (message != null)
{
statusBar.setText(message);
}
-
+ if (progressBarHandlers.contains(lId))
+ {
+ progressBarHandlers.remove(lId);
+ }
layout.setRows(layout.getRows() - 1);
}
else
@@ -657,13 +776,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
layout.setRows(layout.getRows() + 1);
statusPanel.add(progressPanel);
- progressBars.put(new Long(id), progressPanel);
+ progressBars.put(lId, progressPanel);
}
// update GUI
- setMenusForViewport();
+ // setMenusForViewport();
validate();
}
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
/**
*
* @return true if any progress bars are still active
@@ -704,6 +853,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (fileName != null)
{
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
if (currentFileFormat.equals("Jalview"))
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -738,7 +889,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
protocol, currentFileFormat);
newframe.setBounds(bounds);
-
+ if (featureSettings != null && featureSettings.isShowing())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
+ }
this.closeMenuItem_actionPerformed(true);
}
}
@@ -757,8 +924,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
- || (currentFileFormat == null
- || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true))
+ || (currentFileFormat == null || !jalview.io.FormatAdapter
+ .isValidIOFormat(currentFileFormat, true))
|| fileName.startsWith("http"))
{
saveAs_actionPerformed(null);
@@ -773,12 +940,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
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);
@@ -840,12 +1007,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
{
- // JBPNote need to have a raise_gui flag here
- JOptionPane.showInternalMessageDialog(this, "Cannot save file "
- + fileName + " using format " + format,
- "Alignment output format not supported",
- JOptionPane.WARNING_MESSAGE);
+ warningMessage("Cannot save file " + fileName + " using format "
+ + format, "Alignment output format not supported");
saveAs_actionPerformed(null);
+ // JBPNote need to have a raise_gui flag here
return false;
}
@@ -906,11 +1071,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return success;
}
+ private void warningMessage(String warning, String title)
+ {
+ if (new jalview.util.Platform().isHeadless())
+ {
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void outputText_actionPerformed(ActionEvent e)
{
@@ -935,24 +1115,32 @@ 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.alignment, omitHidden, viewport.colSel));
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ cap.dispose();
+ }
+
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
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)
@@ -964,7 +1152,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void createPNG(File f)
{
@@ -975,7 +1163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void createEPS(File f)
{
@@ -992,7 +1180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printMenuItem_actionPerformed(ActionEvent e)
{
@@ -1008,7 +1196,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(alignPanel,
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
viewport.showAnnotation ? viewport.alignment
.getAlignmentAnnotation() : null, viewport.alignment
.getGroups(),
@@ -1018,8 +1207,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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");
@@ -1030,16 +1219,16 @@ 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);
}
}
/**
- * Close the current view or all views in the alignment frame.
- * If the frame only contains one view then the alignment will be removed from memory.
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
*
- * @param closeAllTabs
+ * @param closeAllTabs
*/
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
@@ -1054,24 +1243,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (closeAllTabs)
{
- for (int i = 0; i < alignPanels.size(); i++)
+ if (this.isClosed())
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- jalview.structure.StructureSelectionManager ssm =
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager();
- ssm.removeStructureViewerListener(ap.seqPanel, null);
- ssm.removeSelectionListener(ap.seqPanel);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
- ap.av.alignment = null;
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ ap.closePanel();
+ }
}
}
else
{
closeView(alignPanel);
- viewport = null;
}
}
@@ -1085,22 +1270,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ /**
+ * close alignPanel2 and shuffle tabs appropriately.
+ *
+ * @param alignPanel2
+ */
public void closeView(AlignmentPanel alignPanel2)
{
int index = tabbedPane.getSelectedIndex();
int closedindex = tabbedPane.indexOfComponent(alignPanel2);
alignPanels.removeElement(alignPanel2);
- PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel2);
- alignPanel2.av.alignment = null;
-
- if (viewport == alignPanel2.av)
- {
- viewport = null;
- }
+ // Unnecessary
+ // if (viewport == alignPanel2.av)
+ // {
+ // viewport = null;
+ // }
+ alignPanel2.closePanel();
alignPanel2 = null;
-
+
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
@@ -1110,7 +1297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
index--;
}
- this.tabSelectionChanged(index);
+ this.tabSelectionChanged(index);
}
/**
@@ -1152,7 +1339,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
}
}
@@ -1184,7 +1373,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
@@ -1199,7 +1388,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
@@ -1209,7 +1400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
@@ -1227,7 +1418,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
@@ -1279,7 +1472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param up
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
@@ -1426,7 +1619,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void copy_actionPerformed(ActionEvent e)
{
@@ -1455,11 +1648,11 @@ 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);
@@ -1470,15 +1663,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.hasHiddenColumns)
{
hiddenColumns = new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+ .getSelectionGroup().getEndRes();
for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
.size(); i++)
{
int[] region = (int[]) viewport.getColumnSelection()
.getHiddenColumns().elementAt(i);
-
- hiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+ {
+ hiddenColumns.addElement(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ }
}
}
@@ -1491,7 +1687,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void pasteNew_actionPerformed(ActionEvent e)
{
@@ -1502,7 +1698,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
@@ -1513,7 +1709,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* Paste contents of Jalview clipboard
*
* @param newAlignment
- * true to paste to a new alignment, otherwise add to this.
+ * true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
@@ -1719,8 +1915,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildSortByAnnotationScoresMenu();
}
- viewport.firePropertyChange("alignment", null, alignment
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ alignment.getSequences());
}
else
@@ -1782,7 +1978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void cut_actionPerformed(ActionEvent e)
{
@@ -1794,7 +1990,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -1854,7 +2050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
@@ -1862,6 +2058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
@@ -1869,7 +2066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
@@ -1891,7 +2088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
@@ -1907,13 +2104,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
@@ -1932,21 +2130,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
alignPanel.paintAlignment(true);
- viewport.sendSelection();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
@@ -1957,7 +2156,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
@@ -2034,7 +2233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
@@ -2080,7 +2279,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
@@ -2118,21 +2317,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.padGaps = padGapsMenuitem.isSelected();
-
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
+ // else
+ {
+ // if (justifySeqs>0)
+ {
+ // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
+ }
+ }
+
+ // }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findMenuItem_actionPerformed(ActionEvent e)
{
@@ -2141,8 +2349,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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.alignment.deleteAllGroups();
+ for (AlignmentAnnotation alan : newap.av.alignment
+ .getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated)
+ {
+ newap.av.alignment.deleteAnnotation(alan);
+ }
+ ;
+ }
+ }
newap.av.gatherViewsHere = false;
@@ -2155,8 +2412,19 @@ 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();
@@ -2174,7 +2442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
while (existingNames.contains(newViewName))
{
- newViewName = "View " + (++index);
+ newViewName = viewTitle + " " + (++index);
}
newap.av.viewName = newViewName;
@@ -2186,6 +2454,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.gatherViewsHere = true;
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
}
public void expandViews_actionPerformed(ActionEvent e)
@@ -2202,7 +2471,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
@@ -2213,7 +2482,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void seqLimit_actionPerformed(ActionEvent e)
{
@@ -2235,14 +2504,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
alignPanel.paintAlignment(true);
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
{
- alignPanel.scrollToPosition(alignPanel.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.scrollToPosition(
+ alignPanel.seqPanel.seqCanvas.searchResults, false);
}
}
@@ -2250,7 +2523,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
@@ -2262,7 +2535,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
@@ -2290,6 +2563,116 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // 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)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
+ {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
+ * event.ActionEvent)
+ */
+ public void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ toggleHiddenRegions(false, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ public void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ public void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
@@ -2306,7 +2689,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleAbove_actionPerformed(ActionEvent e)
{
@@ -2318,7 +2701,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleLeft_actionPerformed(ActionEvent e)
{
@@ -2330,7 +2713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleRight_actionPerformed(ActionEvent e)
{
@@ -2342,7 +2725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
@@ -2354,7 +2737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
@@ -2366,7 +2749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
@@ -2383,14 +2766,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
featureSettings.close();
featureSettings = null;
}
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
featureSettings = new FeatureSettings(this);
}
/**
- * DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
@@ -2403,10 +2792,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
+ .isSelected());
+ if (viewport.getShowSequenceFeaturesHeight())
+ {
+ // ensure we're actually displaying features
+ viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(true);
+ }
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
@@ -2418,58 +2830,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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.alignment)
+ .formatAsHtml();
+ editPane.setText("" + contents.toString() + "");
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
@@ -2481,7 +2844,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
@@ -2493,19 +2856,18 @@ 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()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
alignPanel.setOverviewPanel(overview);
}
@@ -2519,7 +2881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
@@ -2530,20 +2892,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void clustalColour_actionPerformed(ActionEvent e)
{
changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(), viewport.alignment
- .getWidth()));
+ viewport.alignment.getSequences(),
+ viewport.alignment.getWidth()));
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void zappoColour_actionPerformed(ActionEvent e)
{
@@ -2554,7 +2916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void taylorColour_actionPerformed(ActionEvent e)
{
@@ -2565,7 +2927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
@@ -2576,7 +2938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void helixColour_actionPerformed(ActionEvent e)
{
@@ -2587,7 +2949,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void strandColour_actionPerformed(ActionEvent e)
{
@@ -2598,7 +2960,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void turnColour_actionPerformed(ActionEvent e)
{
@@ -2609,7 +2971,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void buriedColour_actionPerformed(ActionEvent e)
{
@@ -2620,23 +2982,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void nucleotideColour_actionPerformed(ActionEvent e)
{
changeColour(new NucleotideColourScheme());
}
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ /*
+ public void covariationColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0]));
+ }
+ */
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
@@ -2647,7 +3024,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void changeColour(ColourSchemeI cs)
{
@@ -2674,8 +3051,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Alignment al = (Alignment) viewport.alignment;
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);
@@ -2711,8 +3088,9 @@ 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.getSequences(viewport.hiddenRepSequences),
+ sg.getWidth());
}
else if (cs instanceof UserColourScheme)
{
@@ -2734,9 +3112,9 @@ 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.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
else
{
@@ -2746,9 +3124,9 @@ 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.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
sg.cs.setConservation(c);
@@ -2772,15 +3150,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void modifyPID_actionPerformed(ActionEvent e)
{
if (viewport.getAbovePIDThreshold()
&& viewport.globalColourScheme != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport
- .getGlobalColourScheme(), "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
@@ -2789,7 +3167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void modifyConservation_actionPerformed(ActionEvent e)
{
@@ -2806,7 +3184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
@@ -2824,7 +3202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
@@ -2842,7 +3220,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void userDefinedColour_actionPerformed(ActionEvent e)
{
@@ -2890,8 +3268,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (evt.isControlDown()
|| SwingUtilities.isRightMouseButton(evt))
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
@@ -2935,7 +3312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void PIDColour_actionPerformed(ActionEvent e)
{
@@ -2946,7 +3323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
@@ -2957,7 +3334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
@@ -2973,7 +3350,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
@@ -2987,7 +3364,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
+ */
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
@@ -3003,7 +3395,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
@@ -3014,7 +3406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
@@ -3037,7 +3429,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
@@ -3067,12 +3459,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getAlignment().getSequences());
}
}
+ 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!
+ * DOCUMENT ME!
*/
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
@@ -3083,7 +3484,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
@@ -3094,7 +3495,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
@@ -3105,7 +3506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
@@ -3116,11 +3517,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwType
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void NewTreePanel(String type, String pwType, String title)
{
@@ -3165,8 +3566,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
- // are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the visible sequences aligned?
+ if (!viewport.alignment.isAligned(false))
{
JOptionPane
.showMessageDialog(
@@ -3204,9 +3605,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param order
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
@@ -3235,10 +3636,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* Add a new sort by annotation score menu item
*
* @param sort
- * the menu to add the option to
+ * the menu to add the option to
* @param scoreLabel
- * the label used to retrieve scores for each sequence on the
- * alignment
+ * the label used to retrieve scores for each sequence on the
+ * alignment
*/
public void addSortByAnnotScoreMenuItem(JMenu sort,
final String scoreLabel)
@@ -3250,8 +3651,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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));
alignPanel.paintAlignment(true);
@@ -3299,8 +3700,8 @@ 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();
@@ -3318,9 +3719,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* modified.
*
* @param treePanel
- * Displayed tree window.
+ * Displayed tree window.
* @param title
- * SortBy menu item title.
+ * SortBy menu item title.
*/
public void buildTreeMenu()
{
@@ -3350,21 +3751,16 @@ 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()
{
public void actionPerformed(ActionEvent e)
{
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
- AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
-
- addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
- viewport.alignment));
-
- alignPanel.paintAlignment(true);
+ tp.sortByTree_actionPerformed(null);
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));
+
}
});
@@ -3372,6 +3768,19 @@ 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.alignment));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
@@ -3435,10 +3844,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// jobs
// TODO: viewport.alignment.isAligned is a global state - the local
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
seqs.setSequences(new SeqCigar[]
{ seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned
+ // user!
+
}
return seqs;
}
@@ -3447,13 +3859,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
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");
@@ -3477,8 +3889,8 @@ 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);
}
}
@@ -3506,19 +3918,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* current alignment view
*
* @param nf
- * the tree
+ * the tree
* @param title
- * tree viewer title
+ * tree viewer title
* @param input
- * Associated alignment input data (or null)
+ * Associated alignment input data (or null)
* @param w
- * width
+ * width
* @param h
- * height
+ * height
* @param x
- * position
+ * position
* @param y
- * position
+ * position
* @return TreePanel handle
*/
public TreePanel ShowNewickTree(NewickFile nf, String title,
@@ -3551,98 +3963,201 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return tp;
}
+ private boolean buildingMenu = false;
+
/**
* Generates menu items and listener event actions for web service clients
*
*/
public void BuildWebServiceMenu()
{
- // 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.
- if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
- {
- // 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)
- Vector wsmenu = new Vector();
- final IProgressIndicator af = this;
- if (msaws != null)
+ while (buildingMenu)
+ {
+ try
{
- // Add any Multiple Sequence Alignment Services
- 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.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, this);
-
- }
- wsmenu.add(msawsmenu);
- }
- if (secstrpr != null)
+ System.err.println("Waiting for building menu to finish.");
+ Thread.sleep(10);
+ } catch (Exception e)
{
- // 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.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(secstrmenu, this);
- }
- wsmenu.add(secstrmenu);
}
- if (seqsrch != null)
+ ;
+ }
+ final AlignFrame me = this;
+ buildingMenu = true;
+ new Thread(new Runnable()
+ {
+ public void run()
{
- // Add any sequence search services
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- for (int i = 0, j = seqsrch.size(); i < j; i++)
+ try
+ {
+ 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");
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ final JMenu seqsrchmenu = new JMenu(
+ "Sequence Database Search");
+ final JMenu analymenu = new JMenu(
+ "Analysis");
+ // 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))
+ {
+ // 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);
+ }
+ }
+ }
+
+ // 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(msawsmenu, me);
+ }
+ }
+ }
+ // Add all submenus in the order they should appear on the web services menu
+ wsmenu.add(msawsmenu);
+ wsmenu.add(secstrmenu);
+ wsmenu.add(analymenu);
+ // No search services yet
+ // wsmenu.add(seqsrchmenu);
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ 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((JMenu) wsmenu.get(i));
+ }
+ }
+ else
+ {
+ webService.add(me.webServiceNoServices);
+ }
+ build_urlServiceMenu(me.webService);
+ build_fetchdbmenu(webService);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ });
+ } catch (Exception e)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, this);
}
- // finally, add the whole shebang onto the webservices menu
- wsmenu.add(seqsrchmenu);
- }
- resetWebServiceMenu();
- for (int i = 0, j = wsmenu.size(); i < j; i++)
- {
- webService.add((JMenu) wsmenu.get(i));
+ ;
+
+ buildingMenu = false;
}
- }
- else
- {
- resetWebServiceMenu();
- this.webService.add(this.webServiceNoServices);
- }
+ }).start();
+
}
+
/**
- * empty the web service menu and add any ad-hoc functions not dynamically
- * discovered.
+ * construct any groupURL type service menu entries.
*
+ * @param webService
*/
- private void resetWebServiceMenu()
+ private void build_urlServiceMenu(JMenu webService)
{
- webService.removeAll();
- build_fetchdbmenu(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.alignment,
+ * af.viewport.colSel, 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(
+ webService, this);
+ }
}
/*
@@ -3696,8 +4211,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
- String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection,
- dataset);
+ String[] ptypes = (selection == null || selection.length == 0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
// Object[] prods =
// CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
// selection, dataset, true);
@@ -3727,8 +4242,7 @@ 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;
}
@@ -3818,13 +4332,12 @@ 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;
}
@@ -3903,9 +4416,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file
* @param type
- * access mode of file (see jalview.io.AlignFile)
+ * access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed corectly.
*/
public boolean parseFeaturesFile(String file, String type)
@@ -3913,9 +4426,11 @@ 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.alignment.getDataset(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
+ false, jalview.bin.Cache.getDefault(
+ "RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
ex.printStackTrace();
@@ -3925,6 +4440,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
viewport.showSequenceFeatures = true;
showSeqFeatures.setSelected(true);
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
+ if (featureSettings != null)
+ {
+ featureSettings.setTableData();
+ }
alignPanel.paintAlignment(true);
}
@@ -3980,8 +4504,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ // check to see if we can handle this kind of URI
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ files.add(file.toString());
+ }
}
}
} catch (Exception e)
@@ -3992,10 +4525,127 @@ 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