<mapID target="alwEdit" url="html/menus/alwedit.html"/>
<mapID target="alwSelect" url="html/menus/alwselect.html"/>
<mapID target="alwView" url="html/menus/alwview.html"/>
+ <mapID target="alwAnnotations" url="html/menus/alwannotation.html"/>
<mapID target="alwFormat" url="html/menus/alwformat.html"/>
<mapID target="alwColour" url="html/menus/alwcolour.html"/>
<mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
<mapID target="wsMenu" url="html/menus/wsmenu.html"/>
<mapID target="popMenu" url="html/menus/popupMenu.html"/>
- <mapID target="annotMenus" url="html/menus/alwannotations.html"/>
+ <mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
<mapID target="memory" url="html/memory.html" />
<mapID target="jalviewjnlp" url="html/jalviewjnlp.html" />
<tocitem text="Window Menus" target="menus" expand="false">
<tocitem text="Desktop Window" target="desktopMenu"/>
<tocitem text="Alignment Window" target="alMenu">
- <tocitem text="File Menu" target="alwFile"/>
- <tocitem text="Edit Menu" target="alwEdit"/>
- <tocitem text="Select Menu" target="alwSelect"/>
- <tocitem text="View Menu" target="alwView"/>
- <tocitem text="Format Menu" target="alwFormat"/>
- <tocitem text="Colour Menu" target="alwColour"/>
- <tocitem text="Calculation Menu" target="alwCalc"/>
- <tocitem text="Web Service Menu" target="wsMenu"/>
- <tocitem text="Annotation Menus" target="annotMenus"/>
- <tocitem text="Popup Menu" target="popMenu"/>
- </tocitem>
+ <tocitem text="File Menu" target="alwFile"/>
+ <tocitem text="Edit Menu" target="alwEdit"/>
+ <tocitem text="Select Menu" target="alwSelect"/>
+ <tocitem text="View Menu" target="alwView"/>
+ <tocitem text="Annotations Menu" target="alwAnnotations"/>
+ <tocitem text="Format Menu" target="alwFormat"/>
+ <tocitem text="Colour Menu" target="alwColour"/>
+ <tocitem text="Calculation Menu" target="alwCalc"/>
+ <tocitem text="Web Service Menu" target="wsMenu"/>
+ <tocitem text="Annotation Panel Menu" target="annotPanelMenu"/>
+ <tocitem text="Popup Menu" target="popMenu"/>
+ </tocitem>
</tocitem>
<tocitem text="Preferences" target="preferences"/>
<tocitem text="Memory Settings" target="memory" expand="false">
selected, the view will automatically scroll to display the
highlighted sequence position corresponding to the position under
the mouse pointer in a linked alignment or structure view.</em></li>
- <li><strong>Show Annotations<br> </strong><em>If this
- is selected the "Annotation Panel" will be displayed
- below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values
- as bar charts. </em>
- </li>
- <li><strong>Show All Annotations</strong><em><br>
- Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a>
- or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
- <li><strong>Hide All Annotations</strong><em><br>
- Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
- <li><strong>Autocalculated Annotation<br> </strong><em>Settings
- for the display of autocalculated annotation.</em>
- <ul>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, any modification to the current settings will be applied
- to all autocalculated annotation.</em></li>
- <li><strong>Show Consensus Histogram<br> </strong><em>
- Enable or disable the display of the histogram above the
- consensus sequence.</em></li>
- <li><strong>Show Consensus Logo<br> </strong><em> Enable
- or disable the display of the Consensus Logo above the consensus
- sequence.</em></li>
- <li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
- <li><strong>Group Conservation<br> </strong><em> When
- ticked, display a conservation row for all groups (only available
- for protein alignments).</em></li>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, display a consensus row for all groups.</em></li>
- </ul></li>
<li><strong>Show Sequence Features</strong><br> <em>Show
or hide sequence features on this alignment.</em>
</li>
using the mouse. </em>
</li>
</ul></li>
+ <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+ <ul>
+ <li><strong>Show Annotations<br> </strong><em>If this
+ is selected the "Annotation Panel" will be displayed
+ below the alignment. The default setting is to display the
+ conservation calculation, quality calculation and consensus values
+ as bar charts. </em>
+ </li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for example, Consensus,
+ or secondary structure prediction from alignment).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
+ (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+ allowing you to make a manual ordering of the annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+ for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em>
+ Show autocalculated annotations above sequence-specific annotations.
+ Note this also applies to other annotations for the alignment, for example secondary
+ structure prediction from alignment.</em></li>
+ <li><strong>Show last<br></strong><em>
+ Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br> </strong><em> When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br> </strong><em>
+ Enable or disable the display of the histogram above the
+ consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br> </strong><em> Enable
+ or disable the display of the Consensus Logo above the consensus
+ sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.</em></li>
+ <li><strong>Group Conservation<br> </strong><em> When
+ ticked, display a conservation row for all groups (only available
+ for protein alignments).</em></li>
+ <li><strong>Group Consensus<br> </strong><em> When
+ ticked, display a consensus row for all groups.</em></li>
+ </ul>
+ </li>
+ </ul>
+ </li>
<li><strong>Alignment Window Format Menu</strong>
<ul>
<li><strong>Font...<br> </strong><em>Opens the
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+<p><strong>Alignment Window Annotations Menu</strong> (Since Jalview 2.8.2)</p>
+<ul>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for example, Consensus,
+ or secondary structure prediction from alignment)).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for example, Consensus).</em></li>
+ <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
+ (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+ allowing you to make a manual ordering of the annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+ for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em>
+ Show autocalculated annotations above sequence-specific annotations.
+ Note this also applies to other annotations for the alignment, for example secondary
+ structure prediction from alignment.</em></li>
+ <li><strong>Show last<br></strong><em>
+ Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br> </strong><em> When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br> </strong><em>
+ Enable or disable the display of the histogram above the
+ consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br> </strong><em> Enable
+ or disable the display of the Consensus Logo above the consensus
+ sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.</em></li>
+ <li><strong>Group Conservation<br> </strong><em> When
+ ticked, display a conservation row for all groups (only available
+ for protein alignments).</em></li>
+ <li><strong>Group Consensus<br> </strong><em> When
+ ticked, display a consensus row for all groups.</em></li>
+ </ul>
+ </li>
+</ul>
+<p> </p>
+</body>
+</html>
All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
<li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region)</strong><em><br>
Hides the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
- <li><strong>Show Annotations<br>
- </strong><em>If this is selected the "Annotation Panel" will be
- displayed below the alignment. The default setting is to display the conservation
- calculation, quality calculation and consensus values as bar charts. </em></li>
- <li><strong>Show All Annotations</strong><em><br>
- Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a>
- or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
- <li><strong>Hide All Annotations</strong><em><br>
- Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
- <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
- <ul><li>
- <strong>Apply to all groups<br></strong>
- When ticked, any modification to the current settings will be applied to all autocalculated annotation.
- </li>
- <li>
- <strong>Show Consensus Histogram<br></strong>
- Enable or disable the display of the histogram above the consensus sequence.
- </li>
- <li>
- <strong>Show Consensus Logo<br></strong>
- Enable or disable the display of the sequence logo above the consensus sequence.
- </li>
- <li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
-
- <li>
- <strong>Group Conservation<br></strong>
- When ticked, display a conservation row for all groups (only available for protein alignments).
- </li>
- <li>
- <strong>Apply to all groups<br></strong>
- When ticked, display a consensus row for all groups.
- </li>
- </ul>
- </li>
<li><strong>Automatic Scrolling<br>
</strong><em>When selected, the view will automatically scroll to display the
highlighted sequence position corresponding to the position under the mouse
<p>The <a href="popupMenu.html">Popup Menus</a> are opened by
clicking with the right mouse button in the alignment display area or on
a sequence label in the alignment window.</p>
-<p>The <a href="alwannotations.html">Annotations Menu</a> is opened
+<p>The <a href="alwannotationpanel.html">Annotations Menu</a> is opened
by right-clicking on an annotation row label or in an annotation row.</p>
</body>
label.sequence_details = Sequence Details
label.jmol_help = Jmol Help
label.all = All
-label.sort_by = Sort by
+label.sort_by = Sort alignment by
label.sort_by_score = Sort by Score
label.sort_by_density = Sort by Density
label.sequence_sort_by_density = Sequence sort by Density
+label.sort_ann_by = Sort annotations by
label.sort_annotations_by_sequence = Sort by sequence
label.sort_annotations_by_label = Sort by label
label.reveal = Reveal
public class AnnotationSorter
{
+ /**
+ * enum for annotation sort options. The text description is used in the
+ * Preferences drop-down options. The enum name is saved in the preferences
+ * file.
+ *
+ * @author gmcarstairs
+ *
+ */
public enum SequenceAnnotationOrder
{
- SEQUENCE_AND_LABEL, LABEL_AND_SEQUENCE, NONE
+ // Text descriptions surface in the Preferences Sort by... options
+ SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
+ "No sort");
+
+ private String description;
+
+ private SequenceAnnotationOrder(String s)
+ {
+ description = s;
+ }
+
+ @Override
+ public String toString()
+ {
+ return description;
+ }
+
+ public static SequenceAnnotationOrder forDescription(String d) {
+ for (SequenceAnnotationOrder order : values())
+ {
+ if (order.toString().equals(d))
+ {
+ return order;
+ }
+ }
+ return null;
+ }
}
private final AlignmentI alignment;
import java.io.InputStreamReader;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
+import java.util.Collections;
import java.util.Date;
+import java.util.Enumeration;
import java.util.Properties;
+import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+ /*
+ * Property key/value constants
+ */
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
/**
* Initialises the Jalview Application Log
*/
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new Properties();
+ public static Properties applicationProperties = new Properties() {
+ // override results in properties output in alphabetical order
+ @Override
+ public synchronized Enumeration<Object> keys() {
+ return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ }
+ };
/** Default file is ~/.jalview_properties */
static String propertiesFile;
this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ alignPanel.paintAlignment(true);
}
}
sortByTree = Cache.getDefault("SORT_BY_TREE", false);
followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- "SORT_ANNOTATIONS", SequenceAnnotationOrder.NONE.name()));
+ Cache.SORT_ANNOTATIONS, SequenceAnnotationOrder.NONE.name()));
showAutocalculatedAbove = Cache
- .getDefault("SHOW_AUTOCALC_ABOVE", false);
+.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
+ false);
}
/**
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.util.Collection;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JColorChooser;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
sortby.addItem("Pairwise Identity");
sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+
+ final boolean showAbove = Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
+ true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
+
epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
epsRendering.addItem(MessageManager.getString("label.lineart"));
epsRendering.addItem(MessageManager.getString("action.text"));
Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
.getSelectedItem().toString());
+ // convert description of sort order to enum name for save
+ SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
+ .forDescription(sortAnnBy.getSelectedItem().toString());
+ if (annSortOrder != null)
+ {
+ Cache.applicationProperties.setProperty(Cache.SORT_ANNOTATIONS,
+ annSortOrder.name());
+ }
+
+ final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+ Cache.applicationProperties.setProperty(Cache.SHOW_AUTOCALC_ABOVE,
+ Boolean.valueOf(showAutocalcFirst).toString());
+
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
hideAllAnnotations_actionPerformed(true, false);
}
});
+ SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
sortAnnBySequence.setText(MessageManager
.getString("label.sort_annotations_by_sequence"));
+ sortAnnBySequence
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
boolean newState = sortAnnBySequence.getState();
- sortAnnByLabel.setState(false);
+ sortAnnByLabel.setSelected(false);
setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
: SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
});
sortAnnByLabel.setText(MessageManager
.getString("label.sort_annotations_by_label"));
+ sortAnnByLabel
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
boolean newState = sortAnnByLabel.getState();
- sortAnnBySequence.setState(false);
+ sortAnnBySequence.setSelected(false);
setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
: SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
});
showAutoFirst.setText(MessageManager.getString("label.show_first"));
- showAutoFirst.setState(Cache.getDefault("SHOW_AUTOCALC_ABOVE", false));
+ showAutoFirst.setState(Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
+ false));
showAutoFirst.addActionListener(new ActionListener()
{
@Override
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
/**
* DOCUMENT ME!
JLabel gapLabel = new JLabel();
- protected JComboBox colour = new JComboBox();
+ protected JComboBox<String> colour = new JComboBox<String>();
JLabel colourLabel = new JLabel();
JLabel fontLabel = new JLabel();
- protected JComboBox fontSizeCB = new JComboBox();
+ protected JComboBox<String> fontSizeCB = new JComboBox<String>();
- protected JComboBox fontStyleCB = new JComboBox();
+ protected JComboBox<String> fontStyleCB = new JComboBox<String>();
- protected JComboBox fontNameCB = new JComboBox();
+ protected JComboBox<String> fontNameCB = new JComboBox<String>();
- protected JComboBox gapSymbolCB = new JComboBox();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
protected JCheckBox startupCheckbox = new JCheckBox();
GridBagLayout gridBagLayout3 = new GridBagLayout();
- protected JComboBox sortby = new JComboBox();
+ protected JComboBox<String> sortby = new JComboBox<String>();
JLabel sortLabel = new JLabel();
+ protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+
+ protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+
+ JLabel sortAnnLabel = new JLabel();
+
JPanel jPanel2 = new JPanel();
JPanel visual2panel = new JPanel();
JLabel epsLabel = new JLabel();
- protected JComboBox epsRendering = new JComboBox();
+ protected JComboBox<String> epsRendering = new JComboBox<String>();
protected JLabel userIdWidthlabel = new JLabel();
fontNameCB.setFont(verdana11);
fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
+ gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
mincolourLabel.setFont(verdana11);
mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
mincolourLabel.setText(MessageManager.getString("label.min_colour"));
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
+ startupFileTextfield.setBounds(new Rectangle(172, 287, 270, 20));
startupFileTextfield.addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
jPanel1.setBorder(titledBorder1);
jPanel1.setLayout(gridBagLayout1);
sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 249, 155, 21));
+ sortby.setBounds(new Rectangle(172, 240, 155, 21));
sortLabel.setFont(verdana11);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText(MessageManager.getString("label.sort_by"));
- jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
+ sortAnnBy.setFont(verdana11);
+ sortAnnBy.setBounds(new Rectangle(172, 264, 120, 21));
+ sortAnnLabel.setFont(verdana11);
+ sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
+ sortAutocalc.setFont(verdana11);
+ sortAutocalc.setBounds(new Rectangle(300, 264, 185, 21));
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(12);
+ gridLayout2.setRows(13);
exportTab.setLayout(null);
epsLabel.setFont(verdana11);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
jPanel2.add(sortLabel);
+ jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);
visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
+ visualTab.add(sortAnnBy);
+ visualTab.add(sortAutocalc);
visualTab.add(gapSymbolCB);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
git://source.jalview.org / jalview.git / commitdiff