X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=01353d893f56dfd4803356249fd9db4fff83586d;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=b20314bb8bebefe6499d12cfc19f02b17c3092c2;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
old mode 100755
new mode 100644
index b20314b..01353d8
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,44 +1,149 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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 .
+ * 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.AlignmentUtils;
+import jalview.analysis.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.Dna;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
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.EditCommand.Action;
+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.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AlignmentProperties;
+import jalview.io.AnnotationFile;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HtmlSvgOutput;
+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.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+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.ItemEvent;
+import java.awt.event.ItemListener;
+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.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
@@ -47,20 +152,23 @@ import jalview.ws.jws2.Jws2Discoverer;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
+ IProgressIndicator, AlignViewControllerGuiI
{
- /** DOCUMENT ME!! */
public static final int DEFAULT_WIDTH = 700;
- /** DOCUMENT ME!! */
public static final int DEFAULT_HEIGHT = 500;
+ /*
+ * The currently displayed panel (selected tabbed view if more than one)
+ */
public AlignmentPanel alignPanel;
AlignViewport viewport;
- Vector alignPanels = new Vector();
+ public AlignViewControllerI avc;
+
+ List alignPanels = new ArrayList();
/**
* Last format used to load or save alignments in this window
@@ -133,6 +241,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
this(al, hiddenColumns, width, height, null);
}
+
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
@@ -167,21 +276,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
+
+ if (al.getDataset() == null)
+ {
+ al.setDataset(null);
+ }
+
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
alignPanel = new AlignmentPanel(this, viewport);
+
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection hiddenColumns, int width, int height)
+ {
+ setSize(width, height);
+
if (al.getDataset() == null)
{
al.setDataset(null);
}
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
init();
}
+
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
@@ -202,7 +335,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- if (viewport.conservation == null)
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
+ if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
@@ -228,12 +365,14 @@ 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);
buildSortByAnnotationScoresMenu();
- if (viewport.wrapAlignment)
+ buildTreeMenu();
+
+ if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
}
@@ -245,6 +384,76 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addKeyListener();
+ final List selviews = new ArrayList();
+ final List origview = new ArrayList();
+ final String menuLabel = MessageManager
+ .getString("label.copy_format_from");
+ ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
+ new ViewSetProvider()
+ {
+
+ @Override
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ origview.clear();
+ origview.add(alignPanel);
+ // make an array of all alignment panels except for this one
+ List aps = new ArrayList(
+ Arrays.asList(Desktop.getAlignmentPanels(null)));
+ aps.remove(AlignFrame.this.alignPanel);
+ return aps.toArray(new AlignmentPanel[aps.size()]);
+ }
+ }, selviews, new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (origview.size() > 0)
+ {
+ final AlignmentPanel ap = origview.get(0);
+
+ /*
+ * Copy the ViewStyle of the selected panel to 'this one'.
+ * Don't change value of 'scaleProteinAsCdna' unless copying
+ * from a SplitFrame.
+ */
+ ViewStyleI vs = selviews.get(0).getAlignViewport()
+ .getViewStyle();
+ boolean fromSplitFrame = selviews.get(0)
+ .getAlignViewport().getCodingComplement() != null;
+ if (!fromSplitFrame)
+ {
+ vs.setScaleProteinAsCdna(ap.getAlignViewport()
+ .getViewStyle().isScaleProteinAsCdna());
+ }
+ ap.getAlignViewport().setViewStyle(vs);
+
+ /*
+ * Also rescale ViewStyle of SplitFrame complement if there is
+ * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
+ * the whole ViewStyle (allow cDNA protein to have different
+ * fonts)
+ */
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ if (complement != null && vs.isScaleProteinAsCdna())
+ {
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ ((SplitFrame) af.getSplitViewContainer())
+ .adjustLayout();
+ af.setMenusForViewport();
+ }
+
+ ap.updateLayout();
+ ap.setSelected(true);
+ ap.alignFrame.setMenusForViewport();
+
+ }
+ }
+ });
+ formatMenu.add(vsel);
+
}
/**
@@ -259,14 +468,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void setFileName(String file, String format)
{
fileName = file;
- currentFileFormat = format;
+ setFileFormat(format);
reload.setEnabled(true);
}
+ /**
+ * Add a KeyListener with handlers for various KeyPressed and KeyReleased
+ * events
+ */
void addKeyListener()
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -274,7 +488,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ {
+ alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
@@ -286,42 +502,69 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_DOWN:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(false);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, 1);
+ }
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(true);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, -1);
+ }
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(-1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
|| 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)
@@ -330,7 +573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
@@ -339,19 +582,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_S:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRow();
+ alignPanel.getSeqPanel().setCursorRow();
}
break;
case KeyEvent.VK_C:
if (viewport.cursorMode && !evt.isControlDown())
{
- alignPanel.seqPanel.setCursorColumn();
+ alignPanel.getSeqPanel().setCursorColumn();
}
break;
case KeyEvent.VK_P:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorPosition();
+ alignPanel.getSeqPanel().setCursorPosition();
}
break;
@@ -359,46 +602,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_COMMA:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRowAndColumn();
+ alignPanel.getSeqPanel().setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+ alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
}
- alignPanel.seqPanel.seqCanvas.repaint();
+ alignPanel.getSeqPanel().seqCanvas.repaint();
break;
case KeyEvent.VK_F1:
try
{
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
- "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
ex.printStackTrace();
@@ -412,7 +649,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
break;
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
@@ -423,7 +660,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
@@ -436,20 +673,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
}
}
@@ -459,8 +701,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
- alignPanels.addElement(ap);
+ alignPanels.add(ap);
PaintRefresher.Register(ap, ap.av.getSequenceSetId());
@@ -488,12 +732,13 @@ 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);
}
}
@@ -502,7 +747,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
- AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ AlignmentPanel first = alignPanels.get(0);
tabbedPane.addTab(first.av.viewName, first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
@@ -519,6 +764,7 @@ 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.");
@@ -527,6 +773,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
System.err
@@ -540,6 +787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -552,6 +800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
+ @Override
public void run()
{
BuildWebServiceMenu();
@@ -559,21 +808,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}).start();
}
+ /**
+ * Configure menu items that vary according to whether the alignment is
+ * nucleotide or protein
+ *
+ * @param nucleotide
+ */
public void setGUINucleotide(boolean nucleotide)
{
showTranslation.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
- // Remember AlignFrame always starts as protein
- if (!nucleotide)
- {
- calculateMenu.remove(calculateMenu.getItemCount() - 2);
- }
+ rnahelicesColour.setEnabled(nucleotide);
+ purinePyrimidineColour.setEnabled(nucleotide);
+ showComplementMenuItem.setText(MessageManager
+ .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+ setColourSelected(jalview.bin.Cache.getDefault(
+ nucleotide ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
- * set up menus for the currently viewport. This may be called after any
+ * set up menus for the current viewport. This may be called after any
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
@@ -591,135 +848,87 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void setMenusFromViewport(AlignViewport av)
{
- padGapsMenuitem.setSelected(av.padGaps);
- colourTextMenuItem.setSelected(av.showColourText);
+ padGapsMenuitem.setSelected(av.isPadGaps());
+ colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
- idRightAlign.setSelected(av.rightAlignIds);
- centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
- renderGapsMenuItem.setSelected(av.renderGaps);
- wrapMenuItem.setSelected(av.wrapAlignment);
- scaleAbove.setVisible(av.wrapAlignment);
- scaleLeft.setVisible(av.wrapAlignment);
- scaleRight.setVisible(av.wrapAlignment);
- 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);
+ idRightAlign.setSelected(av.isRightAlignIds());
+ centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
+ renderGapsMenuItem.setSelected(av.isRenderGaps());
+ wrapMenuItem.setSelected(av.getWrapAlignment());
+ scaleAbove.setVisible(av.getWrapAlignment());
+ scaleLeft.setVisible(av.getWrapAlignment());
+ scaleRight.setVisible(av.getWrapAlignment());
+ annotationPanelMenuItem.setState(av.isShowAnnotation());
+ /*
+ * Show/hide annotations only enabled if annotation panel is shown
+ */
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ viewBoxesMenuItem.setSelected(av.getShowBoxes());
+ viewTextMenuItem.setSelected(av.getShowText());
+ 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);
- showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
- showDbRefsMenuitem.setSelected(av.isShowDbRefs());
-
+ showSeqFeatures.setSelected(av.isShowSequenceFeatures());
+ hiddenMarkers.setState(av.getShowHiddenMarkers());
+ 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();
}
- Hashtable progressBars, progressBarHandlers;
+ private IProgressIndicator progressBar;
/*
* (non-Javadoc)
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
- if (progressBars == null)
- {
- progressBars = new Hashtable();
- progressBarHandlers = new Hashtable();
- }
-
- JPanel progressPanel;
- Long lId = new Long(id);
- GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(lId) != null)
- {
- progressPanel = (JPanel) progressBars.get(new Long(id));
- statusPanel.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
- {
- progressPanel = new JPanel(new BorderLayout(10, 5));
-
- JProgressBar progressBar = new JProgressBar();
- progressBar.setIndeterminate(true);
-
- progressPanel.add(new JLabel(message), BorderLayout.WEST);
- progressPanel.add(progressBar, BorderLayout.CENTER);
-
- layout.setRows(layout.getRows() + 1);
- statusPanel.add(progressPanel);
-
- progressBars.put(lId, progressPanel);
- }
- // update GUI
- setMenusForViewport();
- validate();
+ progressBar.setProgressBar(message, id);
}
+ @Override
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);
- }
+ progressBar.registerHandler(id, handler);
}
/**
*
* @return true if any progress bars are still active
*/
+ @Override
public boolean operationInProgress()
{
- if (progressBars != null && progressBars.size() > 0)
- {
- return true;
- }
- return false;
+ return progressBar.operationInProgress();
+ }
+
+ @Override
+ public void setStatus(String text)
+ {
+ statusBar.setText(text);
}
/*
@@ -732,23 +941,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureRenderer getFeatureRenderer()
{
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ return alignPanel.getSeqPanel().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"))
@@ -757,6 +971,7 @@ 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
@@ -794,6 +1009,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
nfs.frame.setBounds(fspos);
@@ -807,16 +1023,19 @@ 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
@@ -838,6 +1057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAs_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
@@ -847,21 +1067,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
currentFileFormat = chooser.getSelectedFormat();
- if (currentFileFormat == null)
+ while (currentFileFormat == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified", JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager
+ .getString("label.file_format_not_specified"),
+ JOptionPane.WARNING_MESSAGE);
+ currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
- return;
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
}
fileName = chooser.getSelectedFile().getPath();
@@ -893,10 +1122,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().SaveAlignment(this, file, shortName);
+ success = new Jalview2XML().saveAlignment(this, file, shortName);
- statusBar.setText("Successfully saved to file: " + fileName + " in "
- + format + " format.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format }));
}
else
@@ -910,29 +1140,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return false;
}
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns)
- {
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to save only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
- }
- FormatAdapter f = new FormatAdapter();
+ ExportData exportData = getAlignmentForExport(format);
+ FormatAdapter f = new FormatAdapter(alignPanel);
String output = f.formatSequences(format,
- (Alignment) viewport.alignment, // class cast exceptions will
+ exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ f.getCacheSuffixDefault(format),
+ viewport.getColumnSelection());
if (output == null)
{
@@ -948,8 +1163,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText("Successfully saved to file: " + fileName
- + " in " + format + " format.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format }));
} catch (Exception ex)
{
success = false;
@@ -960,13 +1177,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
- + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { fileName }), MessageManager
+ .getString("label.error_saving_file"),
+ JOptionPane.WARNING_MESSAGE);
}
return success;
}
+
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
@@ -988,36 +1209,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
- String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ ExportData exportData = getAlignmentForExport(e.getActionCommand());
+ if (exportData.getSettings().isCancelled())
{
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to output only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
+ return;
}
-
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
-
try
{
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.alignment, omitHidden, viewport.colSel));
- Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+ .formatSequences(
+ e.getActionCommand(),
+ exportData.getAlignment(),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ viewport.getColumnSelection()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1026,19 +1239,123 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
+ public ExportData getAlignmentForExport(String exportFomat)
+ {
+ AlignmentI alignmentToExport = null;
+ String[] omitHidden = null;
+ int[] alignmentStartEnd = new int[2];
+
+ HiddenSequences hiddenSeqs = viewport.getAlignment()
+ .getHiddenSequences();
+
+
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = new int[]
+ { 0, alignmentToExport.getWidth() - 1 };
+
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFomat);
+ settings.isExportAnnotations();
+
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
+ }
+ return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+ settings);
+ }
+
+ private static int[] getStartEnd(int[] aligmentStartEnd,
+ List hiddenCols)
+ {
+ int startPos = aligmentStartEnd[0];
+ int endPos = aligmentStartEnd[1];
+
+ int[] lowestRange = new int[2];
+ int[] higestRange = new int[2];
+
+ for (int[] hiddenCol : hiddenCols)
+ {
+ // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
+
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+ // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
+ // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
+
+ if (lowestRange[0] == 0 && lowestRange[1] == 0)
+ {
+ startPos = aligmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == 0 && higestRange[1] == 0)
+ {
+ endPos = aligmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0];
+ }
+
+ // System.out.println("Export range : " + minPos + " - " + maxPos);
+ return new int[]
+ { startPos, endPos };
+ }
+
+ public static void main(String[] args)
+ {
+ ArrayList hiddenCols = new ArrayList();
+ hiddenCols.add(new int[]
+ { 0, 4 });
+ hiddenCols.add(new int[]
+ { 6, 9 });
+ hiddenCols.add(new int[]
+ { 11, 12 });
+ hiddenCols.add(new int[]
+ { 33, 33 });
+ hiddenCols.add(new int[]
+ { 45, 50 });
+
+ int[] x = getStartEnd(new int[]
+ { 0, 50 }, hiddenCols);
+ // System.out.println("Export range : " + x[0] + " - " + x[1]);
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel,
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ new HtmlSvgOutput(null, alignPanel);
}
+ @Override
+ public void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+ }
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
@@ -1050,6 +1367,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -1061,11 +1379,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1078,6 +1402,7 @@ 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
@@ -1085,29 +1410,29 @@ 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);
+ new AnnotationExporter().exportAnnotations(alignPanel);
}
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
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");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
@@ -1115,7 +1440,7 @@ 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);
}
}
@@ -1126,6 +1451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @param closeAllTabs
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
@@ -1145,7 +1471,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// setClosed(true) is called
for (int i = 0; i < alignPanels.size(); i++)
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ AlignmentPanel ap = alignPanels.get(i);
ap.closePanel();
}
}
@@ -1167,22 +1493,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * close alignPanel2 and shuffle tabs appropriately.
+ * Close the specified panel and close up tabs appropriately.
*
- * @param alignPanel2
+ * @param panelToClose
*/
- public void closeView(AlignmentPanel alignPanel2)
+ public void closeView(AlignmentPanel panelToClose)
{
int index = tabbedPane.getSelectedIndex();
- int closedindex = tabbedPane.indexOfComponent(alignPanel2);
- alignPanels.removeElement(alignPanel2);
- // Unnecessary
- // if (viewport == alignPanel2.av)
- // {
- // viewport = null;
- // }
- alignPanel2.closePanel();
- alignPanel2 = null;
+ int closedindex = tabbedPane.indexOfComponent(panelToClose);
+ alignPanels.remove(panelToClose);
+ panelToClose.closePanel();
+ panelToClose = null;
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
@@ -1202,29 +1523,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
void updateEditMenuBar()
{
- if (viewport.historyList.size() > 0)
+ if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText("Undo " + command.getDescription());
+ CommandI command = viewport.getHistoryList().peek();
+ undoMenuItem.setText(MessageManager.formatMessage(
+ "label.undo_command", new Object[]
+ { command.getDescription() }));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
}
- if (viewport.redoList.size() > 0)
+ if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText("Redo " + command.getDescription());
+ CommandI command = viewport.getRedoList().peek();
+ redoMenuItem.setText(MessageManager.formatMessage(
+ "label.redo_command", new Object[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
}
}
@@ -1232,12 +1557,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.clear();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
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);
}
}
@@ -1249,18 +1576,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (alignPanels != null)
{
- Enumeration e = alignPanels.elements();
AlignmentI[] als = new AlignmentI[alignPanels.size()];
- for (int i = 0; e.hasMoreElements(); i++)
+ int i = 0;
+ for (AlignmentPanel ap : alignPanels)
{
- als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
+ als[i++] = ap.av.getAlignment();
}
return als;
}
if (viewport != null)
{
return new AlignmentI[]
- { viewport.alignment };
+ { viewport.getAlignment() };
}
return null;
}
@@ -1271,24 +1598,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.historyList.empty())
+ if (viewport.getHistoryList().isEmpty())
+ {
return;
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
+ }
+ CommandI command = viewport.getHistoryList().pop();
+ viewport.addToRedoList(command);
command.undoCommand(getViewAlignments());
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
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());
}
}
@@ -1298,33 +1636,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.redoList.size() < 1)
+ if (viewport.getRedoList().size() < 1)
{
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
+ CommandI command = viewport.getRedoList().pop();
+ viewport.addToHistoryList(command);
command.doCommand(getViewAlignments());
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
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());
}
}
- AlignViewport getOriginatingSource(CommandI command)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
+ AlignmentViewport originalSource = null;
// For sequence removal and addition, we need to fire
// the property change event FROM the viewport where the
// original alignment was altered
@@ -1333,16 +1681,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ List comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- for (int i = 0; i < comps.size(); i++)
+ for (Component comp : comps)
{
- if (comps.elementAt(i) instanceof AlignmentPanel)
+ if (comp instanceof AlignmentPanel)
{
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
+ if (al == ((AlignmentPanel) comp).av.getAlignment())
{
- originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
+ originalSource = ((AlignmentPanel) comp).av;
break;
}
}
@@ -1355,7 +1703,7 @@ 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;
@@ -1378,69 +1726,25 @@ 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 ArrayList();
if (viewport.cursorMode)
{
- sg.addElement(viewport.alignment
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().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)
@@ -1448,44 +1752,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- Vector invertGroup = new Vector();
+ List invertGroup = new ArrayList();
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ for (SequenceI seq : viewport.getAlignment().getSequences())
{
- if (!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.add(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(seq))
+ {
+ invertGroup.add(seq);
+ }
}
- 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++)
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ {
+ seqs2[i] = invertGroup.get(i);
+ }
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(-size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
@@ -1497,16 +1815,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque historyList = viewport.getHistoryList();
+ if (historyList != null
+ && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .appendSlideCommand((SlideSequencesCommand) historyList
.peek());
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
@@ -1517,6 +1839,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1529,13 +1852,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
omitHidden = viewport.getViewAsString(true);
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
@@ -1555,28 +1878,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- Vector hiddenColumns = null;
- if (viewport.hasHiddenColumns)
+ ArrayList hiddenColumns = null;
+ if (viewport.hasHiddenColumns())
{
- hiddenColumns = new Vector();
+ hiddenColumns = new ArrayList();
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
.getSelectionGroup().getEndRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
- hiddenColumns.addElement(new int[]
+ hiddenColumns.add(new int[]
{ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
}
Desktop.jalviewClipboard = new Object[]
- { seqs, viewport.alignment.getDataset(), hiddenColumns };
- statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
+ { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new Object[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
@@ -1585,6 +1907,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1596,6 +1919,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1664,6 +1988,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
+ ArrayList newGraphGroups = new ArrayList();
+ int fgroup = -1;
if (newAlignment)
{
@@ -1731,6 +2057,17 @@ 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.
@@ -1741,6 +2078,22 @@ 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);
}
@@ -1752,7 +2105,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
@@ -1760,15 +2115,35 @@ 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);
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
- // earlier
+ 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
+ // earlier
alignment
.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
}
@@ -1787,7 +2162,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
AlignmentAnnotation sann[] = sequences[i].getAnnotation();
if (sann == null)
+ {
continue;
+ }
for (int avnum = 0; avnum < alview.length; avnum++)
{
if (alview[avnum] != alignment)
@@ -1804,6 +2181,9 @@ 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);
}
}
@@ -1813,6 +2193,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : alignPanels)
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
+ {
+ alignPanel.validateAnnotationDimensions(false);
+ }
}
else
@@ -1824,19 +2215,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ List hc = (List) Desktop.jalviewClipboard[2];
+ for (int[] region : hc)
{
- int[] region = (int[]) hc.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
@@ -1870,12 +2260,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
+ @Override
+ protected void expand_newalign(ActionEvent e)
+ {
+ try
+ {
+ AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
+ .getAlignment(), -1);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Flanking alignment");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
+ {
+ List hc = (List) Desktop.jalviewClipboard[2];
+ for (int region[] : hc)
+ {
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
+ {
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+ }
+
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Viewing flanking region of alignment", oom);
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
@@ -1888,6 +2332,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -1897,37 +2342,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- Vector seqs = new Vector();
- SequenceI seq;
- for (int i = 0; i < sg.getSize(); i++)
+ /*
+ * If the cut affects all sequences, warn, remove highlighted columns
+ */
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
- seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
- }
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
- {
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
- SequenceI[] cut = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- cut[i] = (SequenceI) seqs.elementAt(i);
- }
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
- /*
- * //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
viewport.sendSelection();
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
@@ -1948,14 +2392,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ if (avc.deleteGroups())
+ {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
}
/**
@@ -1964,6 +2409,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
@@ -1973,7 +2419,7 @@ 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);
@@ -1986,20 +2432,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
{
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
+ alignPanel.getSeqPanel().keyboardNo1 = null;
+ alignPanel.getSeqPanel().keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+ alignPanel.getIdPanel().getIdCanvas().searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
/**
@@ -2008,6 +2456,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2025,14 +2474,16 @@ 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();
}
/**
@@ -2041,6 +2492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
@@ -2052,6 +2504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
@@ -2077,11 +2530,11 @@ 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;
@@ -2089,32 +2542,30 @@ 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.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
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);
}
}
@@ -2129,34 +2580,37 @@ 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);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns", new Object[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// 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());
@@ -2175,30 +2629,31 @@ 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);
@@ -2213,88 +2668,161 @@ 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());
}
- // else
- {
- // if (justifySeqs>0)
- {
- // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
- }
- }
-
- // }
-
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder();
}
+ /**
+ * Create a new view of the current alignment.
+ */
+ @Override
public void newView_actionPerformed(ActionEvent e)
{
+ newView(null, true);
+ }
+
+ /**
+ * Creates and shows a new view of the current alignment.
+ *
+ * @param viewTitle
+ * title of newly created view; if null, one will be generated
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+ {
+ /*
+ * Create a new AlignmentPanel (with its own, new Viewport)
+ */
AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
true);
+ if (!copyAnnotation)
+ {
+ /*
+ * remove all groups and annotation except for the automatic stuff
+ */
+ newap.av.getAlignment().deleteAllGroups();
+ newap.av.getAlignment().deleteAllAnnotations(false);
+ }
- newap.av.gatherViewsHere = false;
+ newap.av.setGatherViewsHere(false);
if (viewport.viewName == null)
{
- viewport.viewName = "Original";
+ viewport.viewName = MessageManager
+ .getString("label.view_name_original");
}
- newap.av.historyList = viewport.historyList;
- newap.av.redoList = viewport.redoList;
+ /*
+ * Views share the same edits, undo and redo stacks, mappings.
+ */
+ newap.av.setHistoryList(viewport.getHistoryList());
+ newap.av.setRedoList(viewport.getRedoList());
+ newap.av.getAlignment().setCodonFrames(
+ viewport.getAlignment().getCodonFrames());
+
+ newap.av.viewName = getNewViewName(viewTitle);
- int index = Desktop.getViewCount(viewport.getSequenceSetId());
- String newViewName = "View " + index;
+ addAlignmentPanel(newap, true);
+ newap.alignmentChanged();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- Vector existingNames = new Vector();
- for (int i = 0; i < comps.size(); i++)
+ if (alignPanels.size() == 2)
{
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
- if (!existingNames.contains(ap.av.viewName))
- {
- existingNames.addElement(ap.av.viewName);
- }
- }
+ viewport.setGatherViewsHere(true);
}
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
+ }
- while (existingNames.contains(newViewName))
+ /**
+ * Make a new name for the view, ensuring it is unique within the current
+ * sequenceSetId. (This used to be essential for Jalview Project archives, but
+ * these now use viewId. Unique view names are still desirable for usability.)
+ *
+ * @param viewTitle
+ * @return
+ */
+ protected String getNewViewName(String viewTitle)
+ {
+ int index = Desktop.getViewCount(viewport.getSequenceSetId());
+ boolean addFirstIndex = false;
+ if (viewTitle == null || viewTitle.trim().length() == 0)
+ {
+ viewTitle = MessageManager.getString("action.view");
+ addFirstIndex = true;
+ }
+ else
{
- newViewName = "View " + (++index);
+ index = 1;// we count from 1 if given a specific name
}
+ String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
- newap.av.viewName = newViewName;
+ List comps = PaintRefresher.components.get(viewport
+ .getSequenceSetId());
- addAlignmentPanel(newap, true);
+ List existingNames = getExistingViewNames(comps);
- if (alignPanels.size() == 2)
+ while (existingNames.contains(newViewName))
{
- viewport.gatherViewsHere = true;
+ newViewName = viewTitle + " " + (++index);
}
- tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newViewName;
+ }
+
+ /**
+ * Returns a list of distinct view names found in the given list of
+ * components. View names are held on the viewport of an AlignmentPanel.
+ *
+ * @param comps
+ * @return
+ */
+ protected List getExistingViewNames(List comps)
+ {
+ List existingNames = new ArrayList();
+ for (Component comp : comps)
+ {
+ if (comp instanceof AlignmentPanel)
+ {
+ AlignmentPanel ap = (AlignmentPanel) comp;
+ if (!existingNames.contains(ap.av.viewName))
+ {
+ existingNames.add(ap.av.viewName);
+ }
+ }
+ }
+ return existingNames;
}
+ /**
+ * Explode tabbed views into separate windows.
+ */
+ @Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.instance.explodeViews(this);
}
+ /**
+ * Gather views in separate windows back into a tabbed presentation.
+ */
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
@@ -2306,6 +2834,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
@@ -2317,24 +2846,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+ alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
.calculateIdWidth());
alignPanel.paintAlignment(true);
}
+ @Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
- viewport.rightAlignIds = idRightAlign.isSelected();
+ viewport.setRightAlignIds(idRightAlign.isSelected());
alignPanel.paintAlignment(true);
}
+ @Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
- viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
alignPanel.paintAlignment(true);
}
@@ -2343,12 +2875,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+ @Override
protected void followHighlight_actionPerformed()
{
- if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+ /*
+ * Set the 'follow' flag on the Viewport (and scroll to position if now
+ * true).
+ */
+ final boolean state = this.followHighlightMenuItem.getState();
+ viewport.setFollowHighlight(state);
+ if (state)
{
alignPanel.scrollToPosition(
- alignPanel.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.getSeqPanel().seqCanvas.searchResults, false);
}
}
@@ -2358,6 +2897,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2370,30 +2910,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
scaleLeft.setVisible(wrapMenuItem.isSelected());
scaleRight.setVisible(wrapMenuItem.isSelected());
viewport.setWrapAlignment(wrapMenuItem.isSelected());
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.updateLayout();
}
+ @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();
- alignPanel.paintAlignment(true);
+// alignPanel.paintAlignment(true);
}
/**
@@ -2412,8 +2956,9 @@ 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()))
{
@@ -2436,12 +2981,13 @@ 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);
}
@@ -2449,12 +2995,12 @@ 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)
@@ -2471,6 +3017,7 @@ 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);
@@ -2483,6 +3030,7 @@ 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();
@@ -2499,6 +3047,7 @@ 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();
@@ -2506,12 +3055,14 @@ 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());
@@ -2524,6 +3075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2536,6 +3088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2548,6 +3101,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2560,6 +3114,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2572,6 +3127,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2584,6 +3140,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2592,6 +3149,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureSettings featureSettings;
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
@@ -2614,6 +3178,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2630,11 +3195,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
.isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
+ if (viewport.isShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
viewport.setShowSequenceFeatures(true);
@@ -2648,77 +3214,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * DOCUMENT ME!
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
*
* @param e
- * DOCUMENT ME!
*/
+ @Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
+ alignPanel.updateLayout();
}
+ @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(MessageManager.formatMessage("label.html_content",
+ new Object[]
+ { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
- + getTitle(), 500, 400);
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new Object[]
+ { getTitle() }), 500, 400);
}
/**
@@ -2727,6 +3258,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
@@ -2737,12 +3269,14 @@ 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, MessageManager.formatMessage(
+ "label.overview_params", new Object[]
+ { this.getTitle() }), frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -2753,6 +3287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2764,6 +3299,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2775,11 +3311,11 @@ 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()));
}
/**
@@ -2788,6 +3324,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
@@ -2799,6 +3336,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
@@ -2810,6 +3348,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
@@ -2821,6 +3360,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
@@ -2832,6 +3372,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
@@ -2843,6 +3384,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
@@ -2854,6 +3396,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
@@ -2865,22 +3408,49 @@ 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 annotationColumn_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColumnChooser(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());
@@ -2894,6 +3464,7 @@ 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)
@@ -2902,26 +3473,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
+ cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
}
else
{
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
}
if (viewport.getConservationSelected())
{
- Alignment al = (Alignment) viewport.alignment;
+ Alignment al = (Alignment) viewport.getAlignment();
Conservation c = new Conservation("All",
ResidueProperties.propHash, 3, al.getSequences(), 0,
al.getWidth() - 1);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
cs.setConservation(c);
@@ -2933,19 +3501,16 @@ 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;
@@ -2954,9 +3519,8 @@ 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)
{
@@ -2966,7 +3530,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ sg.cs = cs.getClass().newInstance();
} catch (Exception ex)
{
}
@@ -2976,25 +3540,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
|| cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.hiddenRepSequences),
+ sg.getSequences(viewport.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
}
else
{
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
}
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
@@ -3018,10 +3582,11 @@ 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");
@@ -3035,13 +3600,14 @@ 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();
}
}
@@ -3052,6 +3618,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3070,6 +3637,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3088,9 +3656,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
new UserDefinedColours(alignPanel, null);
}
@@ -3107,8 +3677,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
Component[] menuItems = colourMenu.getMenuComponents();
- int i, iSize = menuItems.length;
- for (i = 0; i < iSize; i++)
+ int iSize = menuItems.length;
+ for (int i = 0; i < iSize; i++)
{
if (menuItems[i].getName() != null
&& menuItems[i].getName().equals("USER_DEFINED"))
@@ -3129,6 +3699,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
@@ -3138,8 +3709,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
@@ -3151,6 +3724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3162,6 +3736,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3180,6 +3755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
@@ -3191,6 +3767,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
@@ -3202,13 +3779,14 @@ 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);
}
@@ -3218,11 +3796,13 @@ 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);
}
@@ -3232,12 +3812,13 @@ 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);
}
@@ -3247,12 +3828,13 @@ 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);
}
@@ -3263,6 +3845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
@@ -3274,20 +3857,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this,
- "You must select at least 2 sequences.", "Invalid Selection",
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .getString("label.you_must_select_least_two_sequences"),
+ MessageManager.getString("label.invalid_selection"),
JOptionPane.WARNING_MESSAGE);
}
else
{
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
@@ -3297,6 +3884,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if (((viewport.getSelectionGroup() != null)
@@ -3304,11 +3892,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane.showInternalMessageDialog(this,
- "Principal component analysis must take\n"
- + "at least 4 input sequences.",
- "Sequence selection insufficient",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ this,
+ MessageManager
+ .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
@@ -3316,6 +3907,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3326,15 +3918,28 @@ 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");
+ newTreePanel("AV", "PID", "Average distance tree using PID");
}
/**
@@ -3343,9 +3948,10 @@ 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");
+ newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
}
/**
@@ -3354,9 +3960,10 @@ 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");
+ newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
}
/**
@@ -3365,9 +3972,10 @@ 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");
+ newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
/**
@@ -3380,38 +3988,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param title
* DOCUMENT ME!
*/
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null)
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0)
{
if (viewport.getSelectionGroup().getSize() < 3)
{
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "You need to have more than two sequences selected to build a tree!",
- "Not enough sequences", JOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.you_need_more_two_sequences_selected_build_tree"),
+ MessageManager
+ .getString("label.not_enough_sequences"),
+ JOptionPane.WARNING_MESSAGE);
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(
Desktop.desktop,
- "The selected region to create a tree may\nonly contain residues or gaps.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences in selection are not aligned",
+ MessageManager
+ .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager
+ .getString("label.sequences_selection_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -3424,21 +4034,21 @@ 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(
Desktop.desktop,
- "The sequences must be aligned before creating a tree.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences not aligned",
+ MessageManager
+ .getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager
+ .getString("label.sequences_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
}
- if (viewport.alignment.getHeight() < 2)
+ if (viewport.getAlignment().getHeight() < 2)
{
return;
}
@@ -3469,10 +4079,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem("by " + title);
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3481,8 +4092,8 @@ 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);
}
@@ -3505,13 +4116,14 @@ 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());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
});
@@ -3529,23 +4141,23 @@ 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)
@@ -3563,7 +4175,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
- _annotationScoreVectorHash = viewport.alignment
+ _annotationScoreVectorHash = viewport.getAlignment()
.getAlignmentAnnotation().hashCode();
}
}
@@ -3580,25 +4192,55 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param title
* SortBy menu item title.
*/
+ @Override
public void buildTreeMenu()
{
+ calculateTree.removeAll();
+ // build the calculate menu
+
+ for (final String type : new String[]
+ { "NJ", "AV" })
+ {
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + type.toLowerCase());
+ for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
+ {
+ JMenuItem tm = new JMenuItem();
+ ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
+ if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+ {
+ String smn = MessageManager.getStringOrReturn(
+ "label.score_model_", sm.getName());
+ final String title = MessageManager.formatMessage(
+ "label.treecalc_title", treecalcnm, smn);
+ tm.setText(title);//
+ tm.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newTreePanel(type, pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
+
+ }
+ }
sortByTreeMenu.removeAll();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ List comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- Vector treePanels = new Vector();
- int i, iSize = comps.size();
- for (i = 0; i < iSize; i++)
+ List treePanels = new ArrayList();
+ for (Component comp : comps)
{
- if (comps.elementAt(i) instanceof TreePanel)
+ if (comp instanceof TreePanel)
{
- treePanels.add(comps.elementAt(i));
+ treePanels.add((TreePanel) comp);
}
}
- iSize = treePanels.size();
-
- if (iSize < 1)
+ if (treePanels.size() < 1)
{
sortByTreeMenu.setVisible(false);
return;
@@ -3606,23 +4248,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sortByTreeMenu.setVisible(true);
- for (i = 0; i < treePanels.size(); i++)
+ for (final TreePanel tp : treePanels)
{
- 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);
-
- addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
- viewport.alignment));
+ tp.sortByTree_actionPerformed();
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));
- alignPanel.paintAlignment(true);
}
});
@@ -3630,6 +4266,19 @@ 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.
@@ -3654,16 +4303,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
msa = viewport.getAlignmentView(true);
}
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
+ {
+ int option = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.oneseq_msainput_selection"),
+ MessageManager.getString("label.invalid_selection"),
+ JOptionPane.OK_CANCEL_OPTION);
+ if (option == JOptionPane.OK_OPTION)
+ {
+ msa = viewport.getAlignmentView(false);
+ }
+ }
else
{
- /*
- * Vector seqs = viewport.getAlignment().getSequences();
- *
- * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
- *
- * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
- * seqs.elementAt(i); } }
- */
msa = viewport.getAlignmentView(false);
}
return msa;
@@ -3691,9 +4344,9 @@ 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] });
@@ -3710,14 +4363,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ @Override
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
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");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_newick_like_tree_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
int value = chooser.showOpenDialog(null);
@@ -3732,19 +4387,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(), "Possible problem with tree file",
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), MessageManager
+ .getString("label.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);
@@ -3829,14 +4496,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception e)
{
}
- ;
}
final AlignFrame me = this;
buildingMenu = true;
new Thread(new Runnable()
{
+ @Override
public void run()
{
+ final List legacyItems = new ArrayList();
try
{
System.err.println("Building ws menu again "
@@ -3851,119 +4519,142 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// TODO: group services by location as well as function and/or
// introduce
// object broker mechanism.
- final Vector wsmenu = new Vector();
+ final Vector wsmenu = new Vector();
final IProgressIndicator af = me;
- if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
- && Discoverer.services != null
- && (Discoverer.services.size() > 0))
+ 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");
+ final JMenu dismenu = new JMenu("Protein Disorder");
+ // final JMenu msawsmenu = new
+ // JMenu(MessageManager.getString("label.alignment"));
+ // final JMenu secstrmenu = new
+ // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ // final JMenu seqsrchmenu = new
+ // JMenu(MessageManager.getString("label.sequence_database_search"));
+ // final JMenu analymenu = new
+ // JMenu(MessageManager.getString("label.analysis"));
+ // final JMenu dismenu = new
+ // JMenu(MessageManager.getString("label.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))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ // No MSAWS used any more:
+ // Vector msaws = null; // (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)
- {
- // 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.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, me);
-
- }
- 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);
+ int p = secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- }
- 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 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())
- {
- JMenu jws2men = new JMenu("Jaba Web Services");
- jws2servs.attachWSMenuEntry(jws2men, me);
- for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
+ int q = secstrmenu.getItemCount();
+ for (int litm = p; litm < q; litm++)
{
- wsmenu.add(jws2men.getMenuComponent(i));
+ legacyItems.add(secstrmenu.getItem(litm));
}
}
}
}
+ // 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);
+ // No search services yet
+ // wsmenu.add(seqsrchmenu);
+
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
try
{
-
- resetWebServiceMenu();
- // finally, add the whole shebang onto the webservices menu
+ 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));
+ webService.add(wsmenu.get(i));
}
}
else
{
- me.webService.add(me.webServiceNoServices);
+ webService.add(me.webServiceNoServices);
}
- } catch (Exception e)
- {
- }
- ;
- }
- });
- } catch (Exception e)
- {
- }
- ;
+ // TODO: move into separate menu builder class.
+ boolean new_sspred = false;
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ jws2servs.attachWSMenuEntry(webService, me);
+ for (Jws2Instance sv : jws2servs.getServices())
+ {
+ if (sv.description.toLowerCase().contains("jpred"))
+ {
+ for (JMenuItem jmi : legacyItems)
+ {
+ jmi.setVisible(false);
+ }
+ }
+ }
+ }
+ 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);
+ }
+ }
+ });
+ } catch (Exception e)
+ {
+ }
buildingMenu = false;
}
}).start();
@@ -3971,28 +4662,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * 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);
- }
-
- /**
* construct any groupURL type service menu entries.
*
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
{
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ // 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())
{
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
+ client.attachWSMenuEntry(
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+ this);
}
}
@@ -4063,10 +4762,11 @@ 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
- af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+ af.showProductsFor(af.viewport.getSequenceSelection(),
isRegSel, dna, source);
}
@@ -4085,29 +4785,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return showp;
}
- protected void showProductsFor(SequenceI[] sel, Alignment ds,
- boolean isRegSel, boolean dna, String source)
+ protected void showProductsFor(final SequenceI[] sel,
+ final boolean isRegSel, final boolean dna, final String source)
{
- final boolean fisRegSel = isRegSel;
- final boolean fdna = dna;
- final String fsrc = source;
- final AlignFrame ths = this;
- final SequenceI[] fsel = sel;
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
- ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.searching_for_sequences_from", new Object[]
+ { source }), sttime);
try
{
- Alignment ds = ths.getViewport().alignment.getDataset(); // update
- // our local
- // dataset
- // reference
+ // update our local dataset reference
+ Alignment ds = AlignFrame.this.getViewport().getAlignment()
+ .getDataset();
Alignment prods = CrossRef
- .findXrefSequences(fsel, fdna, fsrc, ds);
+ .findXrefSequences(sel, dna, source, ds);
if (prods != null)
{
SequenceI[] sprods = new SequenceI[prods.getHeight()];
@@ -4117,29 +4814,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (ds.getSequences() == null
|| !ds.getSequences().contains(
sprods[s].getDatasetSequence()))
+ {
ds.addSequence(sprods[s].getDatasetSequence());
+ }
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
- AlignedCodonFrame[] cf = prods.getCodonFrames();
al.setDataset(ds);
- for (int s = 0; cf != null && s < cf.length; s++)
+
+ /*
+ * Copy dna-to-protein mappings to new alignment
+ */
+ // TODO 1: no mappings are set up for EMBL product
+ // TODO 2: if they were, should add them to protein alignment, not
+ // dna
+ Set cf = prods.getCodonFrames();
+ for (AlignedCodonFrame acf : cf)
{
- al.addCodonFrame(cf[s]);
- cf[s] = null;
+ al.addCodonFrame(acf);
}
AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
- String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
- + " for " + ((fisRegSel) ? "selected region of " : "")
+ String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
+ + " for " + ((isRegSel) ? "selected region of " : "")
+ getTitle();
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ naf.setTitle(newtitle);
+
+ // temporary flag until SplitFrame is released
+ boolean asSplitFrame = Cache.getDefault(
+ Preferences.ENABLE_SPLIT_FRAME, false);
+ if (asSplitFrame)
+ {
+ /*
+ * Make a copy of this alignment (sharing the same dataset
+ * sequences). If we are DNA, drop introns and update mappings
+ */
+ AlignmentI copyAlignment = null;
+ final SequenceI[] sequenceSelection = AlignFrame.this.viewport
+ .getSequenceSelection();
+ if (dna)
+ {
+ copyAlignment = AlignmentUtils.makeExonAlignment(
+ sequenceSelection, cf);
+ al.getCodonFrames().clear();
+ al.getCodonFrames().addAll(cf);
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addMappings(cf);
+ }
+ else
+ {
+ copyAlignment = new Alignment(new Alignment(
+ sequenceSelection));
+ }
+ AlignFrame copyThis = new AlignFrame(copyAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyThis.setTitle(AlignFrame.this.getTitle());
+ // SplitFrame with dna above, protein below
+ SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
+ dna ? naf : copyThis);
+ naf.setVisible(true);
+ copyThis.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ }
+ else
+ {
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
}
else
{
System.err.println("No Sequences generated for xRef type "
- + fsrc);
+ + source);
}
} catch (Exception e)
{
@@ -4153,7 +4902,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.bin.Cache.log.error("Error when finding crossreferences",
e);
}
- ths.setProgressBar("Finished searching for sequences from " + fsrc,
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.finished_searching_for_sequences_from",
+ new Object[]
+ { source }),
sttime);
}
@@ -4179,73 +4931,71 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
- public void showProducts_actionPerformed(ActionEvent e)
+ /**
+ * Construct and display a new frame containing the translation of this
+ * frame's DNA sequences to their aligned protein (amino acid) equivalents.
+ */
+ @Override
+ public void showTranslation_actionPerformed(ActionEvent e)
{
- // /////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI[] selection = viewport.getSequenceSelection();
AlignmentI al = null;
try
{
- al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
- .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
- viewport.getAlignment().getDataset());
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.translateCdna();
} 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);
+ final String msg = MessageManager
+ .getString("label.error_when_translating_sequences_submit_bug_report");
+ final String title = MessageManager
+ .getString("label.implementation_error")
+ + MessageManager.getString("translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.ERROR_MESSAGE);
+ return;
}
- if (al == null)
+ if (al == null || al.getHeight() == 0)
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
- "Translation Failed", JOptionPane.WARNING_MESSAGE);
+ final String msg = MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+ final String title = MessageManager
+ .getString("label.translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.WARNING_MESSAGE);
}
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ af.setFileFormat(this.currentFileFormat);
+ final String newTitle = MessageManager.formatMessage(
+ "label.translation_of_params", new Object[]
+ { this.getTitle() });
+ af.setTitle(newTitle);
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+ {
+ final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+ viewport.openSplitFrame(af, new Alignment(seqs),
+ al.getCodonFrames());
+ }
+ else
+ {
+ Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
}
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ /**
+ * Set the file format
+ *
+ * @param fileFormat
+ */
+ public void setFileFormat(String fileFormat)
{
- // /////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI[] selection = viewport.getSequenceSelection();
- String[] seqstring = viewport.getViewAsString(true);
- AlignmentI al = null;
- try
- {
- al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
- viewport.getViewAsVisibleContigs(true), viewport
- .getGapCharacter(), viewport.alignment
- .getAlignmentAnnotation(), viewport.alignment
- .getWidth(), viewport.getAlignment().getDataset());
- } catch (Exception ex)
- {
- al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", ex);
- }
- if (al == null)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
- "Translation Failed", JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
- }
+ this.currentFileFormat = fileFormat;
}
/**
@@ -4255,57 +5005,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* contents or path to retrieve file
* @param type
* access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
+ * @return true if features file was parsed correctly.
*/
public boolean parseFeaturesFile(String file, String type)
{
- boolean featuresFile = false;
- try
- {
- featuresFile = new FeaturesFile(file, type)
- .parse(viewport.alignment.getDataset(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- false);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ return avc.parseFeaturesFile(file, type,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+
+ }
- if (featuresFile)
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ // note - currently this is only still here rather than in the controller
+ // because of the featureSettings hard reference that is yet to be
+ // abstracted
+ if (enableIfNecessary)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(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);
}
- 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();
@@ -4360,10 +5103,140 @@ 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