label.consensus = Consensus
label.histogram = Histogram
label.logo = Logo
-label.non_positional_features = Non-positional Features
-label.database_references = Database References
+label.non_positional_features = List Non-positional Features
+label.database_references = List Database References
label.share_selection_across_views = Share selection across views
label.scroll_highlighted_regions = Scroll to highlighted regions
label.gap_symbol = Gap Symbol
label.use_modeller_output = Use Modeller Output
label.wrap_alignment = Wrap Alignment
label.right_align_ids = Right Align Ids
-label.sequence_name_italics = Sequence Name Italics
+label.sequence_name_italics = Italic Sequence Ids
label.open_overview = Open Overview
label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment
label.annotation_shading_default = Annotation Shading Default
info.associate_wit_sequence = Associate with Sequence
label.search_result = Search Result
label.found_structures_summary = Found Structures Summary
-label.configure_displayed_columns = Configure Displayed Columns
\ No newline at end of file
+label.configure_displayed_columns = Configure Displayed Columns
+label.scale_as_cdna = Scale residues to width of codons
+label.scale_protein_to_cdna = Scale Protein to cDNA
+label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
*/
void setShowNPFeats(boolean shownpfeats);
+ /**
+ * Get flag to scale protein residues 3 times the width of cDNA bases (only
+ * applicable in SplitFrame views)
+ *
+ * @return
+ */
+ boolean isScaleProteinAsCdna();
+
+ /**
+ * Set flag to scale protein residues 3 times the width of cDNA bases (only
+ * applicable in SplitFrame views)
+ *
+ * @return
+ */
+ void setScaleProteinAsCdna(boolean b);
}
private CheckboxMenuItem showAutoLast;
+ private SplitFrame splitFrame;
+
/**
* Attach the alignFrame panels after embedding menus, if necessary. This used
* to be called setEmbedded, but is now creates the dropdown menus in a
return false;
}
+ public SplitFrame getSplitFrame()
+ {
+ return this.splitFrame;
+ }
+
+ public void setSplitFrame(SplitFrame sf)
+ {
+ this.splitFrame = sf;
+ }
}
setShowUnconserved(applet.getDefaultParameter("showUnconserved",
getShowUnconserved()));
+ setScaleProteinAsCdna(applet.getDefaultParameter(
+ "scaleProteinAsCdna", isScaleProteinAsCdna()));
+
String param = applet.getParameter("upperCase");
if (param != null)
{
*/
package jalview.appletgui;
-import jalview.api.ViewStyleI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Button;
+import java.awt.Checkbox;
import java.awt.Choice;
import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-public class FontChooser extends Panel implements ActionListener,
- ItemListener
+import jalview.api.ViewStyleI;
+import jalview.util.MessageManager;
+
+/**
+ * This dialog allows the user to try different font settings and related
+ * options. Changes are immediately visible on the alignment or tree. The user
+ * can dismiss the dialog by confirming changes with 'OK', or reverting to
+ * previous settings with 'Cancel'.
+ */
+@SuppressWarnings("serial")
+public class FontChooser extends Panel implements ItemListener
{
- AlignmentPanel ap;
+ private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
+
+ private Choice fontSize = new Choice();
+
+ private Choice fontStyle = new Choice();
+
+ private Choice fontName = new Choice();
+
+ private Checkbox scaleAsCdna = new Checkbox();
+
+ private Button ok = new Button();
- TreePanel tp;
+ private Button cancel = new Button();
- Font oldFont;
+ private AlignmentPanel ap;
- int oldCharWidth = 0;
+ private TreePanel tp;
- boolean init = true;
+ private Font oldFont;
- Frame frame;
+ private int oldCharWidth = 0;
+ private boolean oldScaleProtein = false;
+
+ private Font lastSelected = null;
+
+ private int lastSelStyle = 0;
+
+ private int lastSelSize = 0;
+
+ private boolean init = true;
+
+ private Frame frame;
+
+ /**
+ * Constructor for a TreePanel font chooser
+ *
+ * @param tp
+ */
public FontChooser(TreePanel tp)
{
try
init();
}
+ /**
+ * Constructor for an AlignmentPanel font chooser
+ *
+ * @param ap
+ */
public FontChooser(AlignmentPanel ap)
{
+ this.ap = ap;
+ oldFont = ap.av.getFont();
+ oldCharWidth = ap.av.getViewStyle().getCharWidth();
+ oldScaleProtein = ap.av.getViewStyle().isScaleProteinAsCdna();
+
try
{
jbInit();
{
e.printStackTrace();
}
-
- this.ap = ap;
- oldFont = ap.av.getFont();
- oldCharWidth = ap.av.getViewStyle().getCharWidth();
init();
}
+ /**
+ * Populate choice lists and open this dialog
+ */
void init()
{
String fonts[] = Toolkit.getDefaultToolkit().getFontList();
fontSize.select(oldFont.getSize() + "");
fontStyle.select(oldFont.getStyle());
- Frame frame = new Frame();
- this.frame = frame;
+ this.frame = new Frame();
frame.add(this);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("action.change_font"), 440, 115);
init = false;
}
- public void actionPerformed(ActionEvent evt)
- {
- if (evt.getSource() == ok)
- {
- ok_actionPerformed();
- }
- else if (evt.getSource() == cancel)
- {
- cancel_actionPerformed();
- }
- }
-
+ /**
+ * Actions on change of font name, size or style.
+ */
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == fontName)
+ final Object source = evt.getSource();
+ if (source == fontName)
{
fontName_actionPerformed();
}
- else if (evt.getSource() == fontSize)
+ else if (source == fontSize)
{
fontSize_actionPerformed();
}
- else if (evt.getSource() == fontStyle)
+ else if (source == fontStyle)
{
fontStyle_actionPerformed();
}
+ else if (source == scaleAsCdna)
+ {
+ scaleAsCdna_actionPerformed();
+ }
}
+ /**
+ * Close this dialog on OK to confirm any changes. Also updates the overview
+ * window if displayed.
+ */
protected void ok_actionPerformed()
{
frame.setVisible(false);
ap.getOverviewPanel().updateOverviewImage();
}
}
-
}
+ /**
+ * Close this dialog on Cancel, reverting to previous font settings.
+ */
protected void cancel_actionPerformed()
{
if (ap != null)
frame.setVisible(false);
}
- private Font lastSelected = null;
-
- private int lastSelStyle = 0;
-
- private int lastSelSize = 0;
-
/**
* DOCUMENT ME!
*/
changeFont();
}
- Label label1 = new Label();
-
- protected Choice fontSize = new Choice();
-
- protected Choice fontStyle = new Choice();
-
- Label label2 = new Label();
-
- Label label3 = new Label();
-
- protected Choice fontName = new Choice();
-
- Button ok = new Button();
-
- Button cancel = new Button();
-
- Panel panel1 = new Panel();
-
- Panel panel2 = new Panel();
-
- Panel panel3 = new Panel();
-
- BorderLayout borderLayout1 = new BorderLayout();
+ /**
+ * Construct this panel's contents
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ this.setLayout(new BorderLayout());
+ this.setBackground(Color.white);
- BorderLayout borderLayout2 = new BorderLayout();
+ Label fontLabel = new Label(MessageManager.getString("label.font"));
+ fontLabel.setFont(VERDANA_11PT);
+ fontLabel.setAlignment(Label.RIGHT);
+ fontSize.setFont(VERDANA_11PT);
+ fontSize.addItemListener(this);
+ fontStyle.setFont(VERDANA_11PT);
+ fontStyle.addItemListener(this);
- BorderLayout borderLayout3 = new BorderLayout();
+ Label sizeLabel = new Label(MessageManager.getString("label.size"));
+ sizeLabel.setAlignment(Label.RIGHT);
+ sizeLabel.setFont(VERDANA_11PT);
- Panel panel4 = new Panel();
+ Label styleLabel = new Label(MessageManager.getString("label.style"));
+ styleLabel.setAlignment(Label.RIGHT);
+ styleLabel.setFont(VERDANA_11PT);
- Panel panel5 = new Panel();
+ fontName.setFont(VERDANA_11PT);
+ fontName.addItemListener(this);
- BorderLayout borderLayout4 = new BorderLayout();
+ scaleAsCdna.setLabel(MessageManager.getString("label.scale_as_cdna"));
+ scaleAsCdna.setFont(VERDANA_11PT);
+ scaleAsCdna.addItemListener(this);
+ scaleAsCdna.setState(ap.av.isScaleProteinAsCdna());
- private void jbInit() throws Exception
- {
- label1.setFont(new java.awt.Font("Verdana", 0, 11));
- label1.setAlignment(Label.RIGHT);
- label1.setText(MessageManager.getString("label.font"));
- this.setLayout(borderLayout4);
- fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
- fontSize.addItemListener(this);
- fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
- fontStyle.addItemListener(this);
- label2.setAlignment(Label.RIGHT);
- label2.setFont(new java.awt.Font("Verdana", 0, 11));
- label2.setText(MessageManager.getString("label.size"));
- label3.setAlignment(Label.RIGHT);
- label3.setFont(new java.awt.Font("Verdana", 0, 11));
- label3.setText(MessageManager.getString("label.style"));
- fontName.setFont(new java.awt.Font("Verdana", 0, 11));
- fontName.addItemListener(this);
- ok.setFont(new java.awt.Font("Verdana", 0, 11));
+ ok.setFont(VERDANA_11PT);
ok.setLabel(MessageManager.getString("action.ok"));
- ok.addActionListener(this);
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ cancel.setFont(VERDANA_11PT);
cancel.setLabel(MessageManager.getString("action.cancel"));
- cancel.addActionListener(this);
- this.setBackground(Color.white);
- panel1.setLayout(borderLayout1);
- panel2.setLayout(borderLayout3);
- panel3.setLayout(borderLayout2);
- panel5.setBackground(Color.white);
- panel4.setBackground(Color.white);
- panel1.setBackground(Color.white);
- panel2.setBackground(Color.white);
- panel3.setBackground(Color.white);
- panel1.add(label1, BorderLayout.WEST);
- panel1.add(fontName, BorderLayout.CENTER);
- panel5.add(panel1, null);
- panel5.add(panel3, null);
- panel5.add(panel2, null);
- panel2.add(label3, BorderLayout.WEST);
- panel2.add(fontStyle, BorderLayout.CENTER);
- panel3.add(label2, BorderLayout.WEST);
- panel3.add(fontSize, BorderLayout.CENTER);
- this.add(panel4, BorderLayout.SOUTH);
- panel4.add(ok, null);
- panel4.add(cancel, null);
- this.add(panel5, BorderLayout.CENTER);
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed();
+ }
+ });
+
+ Panel fontPanel = new Panel();
+ fontPanel.setLayout(new BorderLayout());
+ Panel stylePanel = new Panel();
+ stylePanel.setLayout(new BorderLayout());
+ Panel sizePanel = new Panel();
+ sizePanel.setLayout(new BorderLayout());
+ Panel scalePanel = new Panel();
+ scalePanel.setLayout(new BorderLayout());
+ Panel okCancelPanel = new Panel();
+ Panel optionsPanel = new Panel();
+
+ fontPanel.setBackground(Color.white);
+ stylePanel.setBackground(Color.white);
+ sizePanel.setBackground(Color.white);
+ okCancelPanel.setBackground(Color.white);
+ optionsPanel.setBackground(Color.white);
+
+ fontPanel.add(fontLabel, BorderLayout.WEST);
+ fontPanel.add(fontName, BorderLayout.CENTER);
+ stylePanel.add(styleLabel, BorderLayout.WEST);
+ stylePanel.add(fontStyle, BorderLayout.CENTER);
+ sizePanel.add(sizeLabel, BorderLayout.WEST);
+ sizePanel.add(fontSize, BorderLayout.CENTER);
+ scalePanel.add(scaleAsCdna, BorderLayout.CENTER);
+ okCancelPanel.add(ok, null);
+ okCancelPanel.add(cancel, null);
+
+ optionsPanel.add(fontPanel, null);
+ optionsPanel.add(sizePanel, null);
+ optionsPanel.add(stylePanel, null);
+
+ /*
+ * Only show 'scale protein as cDNA' in protein half of a SplitFrame
+ */
+ this.add(optionsPanel, BorderLayout.NORTH);
+ if (ap.alignFrame.getSplitFrame() != null
+ && !ap.av.getAlignment().isNucleotide())
+ {
+ this.add(scalePanel, BorderLayout.CENTER);
+ }
+ this.add(okCancelPanel, BorderLayout.SOUTH);
+ }
+
+ /**
+ * Turn on/off scaling of protein characters to 3 times the width of cDNA
+ * characters
+ */
+ protected void scaleAsCdna_actionPerformed()
+ {
+ ap.av.setScaleProteinAsCdna(scaleAsCdna.getState());
+ ap.alignFrame.getSplitFrame().adjustLayout();
+ ap.paintAlignment(true);
}
}
}
/*
- * Expand protein to 3 times character width of dna
+ * Scale protein to either 1 or 3 times character width of dna
*/
if (protein != null && cdna != null)
{
ViewStyleI vs = protein.getViewStyle();
- vs.setCharWidth(3 * vs.getCharWidth());
+ int scale = vs.isScaleProteinAsCdna() ? 3 : 1;
+ vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
protein.setViewStyle(vs);
}
}
panel.add(menuPanel, BorderLayout.NORTH);
panel.add(af.statusBar, BorderLayout.SOUTH);
panel.add(af.alignPanel, BorderLayout.CENTER);
+
+ af.setSplitFrame(this);
}
/**
init();
}
+ /**
+ * Apply any settings saved in user preferences
+ */
private void applyViewProperties()
{
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
SequenceAnnotationOrder.NONE.name()));
showAutocalculatedAbove = Cache.getDefault(
Preferences.SHOW_AUTOCALC_ABOVE, false);
-
+ viewStyle.setScaleProteinAsCdna(Cache.getDefault(
+ Preferences.SCALE_PROTEIN_TO_CDNA, false));
}
void init()
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.jbgui.GFontChooser;
-import jalview.util.MessageManager;
-
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.event.ActionEvent;
import javax.swing.JLayeredPane;
import javax.swing.JOptionPane;
+import jalview.bin.Cache;
+import jalview.jbgui.GFontChooser;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
Font oldFont;
+ boolean oldProteinScale;
+
boolean init = true;
JInternalFrame frame;
public FontChooser(AlignmentPanel ap)
{
oldFont = ap.av.getFont();
+ oldProteinScale = ap.av.isScaleProteinAsCdna();
+
this.ap = ap;
init();
}
smoothFont.setSelected(ap.av.antiAlias);
+ /*
+ * Enable 'scale protein as cDNA' in protein half of a SplitFrame view. The
+ * selection is stored in the ViewStyle of the Viewport
+ */
+ if (ap.av.getCodingComplement() != null
+ && !ap.av.getAlignment().isNucleotide())
+ {
+ scaleAsCdna.setVisible(true);
+ scaleAsCdna.setSelected(ap.av.isScaleProteinAsCdna());
+ }
+
if (tp != null)
{
Desktop.addInternalFrame(frame,
MessageManager.getString("action.change_font_tree_panel"),
- 340, 170, false);
+ 400, 200, false);
}
else
{
Desktop.addInternalFrame(frame,
- MessageManager.getString("action.change_font"), 340, 170,
+ MessageManager.getString("action.change_font"), 380, 200,
false);
}
for (int i = 1; i < 51; i++)
{
- fontSize.addItem(i + "");
+ fontSize.addItem(i);
}
fontStyle.addItem("plain");
fontStyle.addItem("italic");
fontName.setSelectedItem(oldFont.getName());
- fontSize.setSelectedItem(oldFont.getSize() + "");
+ fontSize.setSelectedItem(oldFont.getSize());
fontStyle.setSelectedIndex(oldFont.getStyle());
FontMetrics fm = getGraphics().getFontMetrics(oldFont);
if (ap != null)
{
ap.av.setFont(oldFont, true);
+ ap.av.setScaleProteinAsCdna(oldProteinScale);
ap.paintAlignment(true);
}
else if (tp != null)
tp.setTreeFont(oldFont);
}
fontName.setSelectedItem(oldFont.getName());
- fontSize.setSelectedItem(oldFont.getSize() + "");
+ fontSize.setSelectedItem(oldFont.getSize());
fontStyle.setSelectedIndex(oldFont.getStyle());
try
}
Font newFont = new Font(fontName.getSelectedItem().toString(),
- fontStyle.getSelectedIndex(), Integer.parseInt(fontSize
- .getSelectedItem().toString()));
+ fontStyle.getSelectedIndex(),
+ (Integer) fontSize.getSelectedItem());
FontMetrics fm = getGraphics().getFontMetrics(newFont);
double mw = fm.getStringBounds("M", getGraphics()).getWidth(), iw = fm
.getStringBounds("I", getGraphics()).getWidth();
{
fontName.setSelectedItem(lastSelected.getName());
fontStyle.setSelectedIndex(lastSelStyle);
- fontSize.setSelectedItem("" + lastSelSize);
+ fontSize.setSelectedItem(lastSelSize);
monospaced.setSelected(lastSelMono);
JOptionPane
.showInternalMessageDialog(
Cache.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
}
+
+ /**
+ * Turn on/off scaling of protein characters to 3 times the width of cDNA
+ * characters
+ */
+ @Override
+ protected void scaleAsCdna_actionPerformed(ActionEvent e)
+ {
+ ap.av.setScaleProteinAsCdna(scaleAsCdna.isSelected());
+ ((SplitFrame) ap.alignFrame.getSplitViewContainer()).adjustLayout();
+ ap.paintAlignment(true);
+ }
}
*/
package jalview.gui;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.Help.HelpId;
-import jalview.gui.StructureViewer.ViewerType;
-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 ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
public class Preferences extends GPreferences
{
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
- int width = 500, height = 420;
+ int width = 500, height = 450;
if (new jalview.util.Platform().isAMac())
{
width = 570;
- height = 460;
+ height = 480;
}
Desktop.addInternalFrame(frame,
+ ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+ false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
Boolean.toString(showConsensLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Boolean.toString(scaleProteinToCdna.isSelected()));
Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
Boolean.toString(showNpTooltip.isSelected()));
Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
public void adjustLayout()
{
/*
- * Ensure sequence ids are the same width for good alignment.
+ * Ensure sequence ids are the same width so sequences line up
*/
int w1 = ((AlignFrame) getTopFrame()).getViewport().getIdWidth();
int w2 = ((AlignFrame) getBottomFrame()).getViewport().getIdWidth();
}
/*
- * Set the character width for protein to 3 times that for dna.
+ * Scale protein to either 1 or 3 times character width of dna
*/
- boolean scaleThreeToOne = true; // TODO a new Preference option?
- if (scaleThreeToOne)
+ final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
+ final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
+ final AlignmentI topAlignment = topViewport.getAlignment();
+ final AlignmentI bottomAlignment = bottomViewport.getAlignment();
+ AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
+ : (bottomAlignment.isNucleotide() ? bottomViewport : null);
+ AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
+ : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
+ if (protein != null && cdna != null)
{
- final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
- final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
- final AlignmentI topAlignment = topViewport.getAlignment();
- final AlignmentI bottomAlignment = bottomViewport.getAlignment();
- AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
- : (bottomAlignment.isNucleotide() ? bottomViewport : null);
- AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
- : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
- if (protein != null && cdna != null)
- {
- ViewStyleI vs = cdna.getViewStyle();
- ViewStyleI vs2 = protein.getViewStyle();
- vs2.setCharWidth(3 * vs.getCharWidth());
- protein.setViewStyle(vs2);
- }
+ ViewStyleI vs = protein.getViewStyle();
+ int scale = vs.isScaleProteinAsCdna() ? 3 : 1;
+ vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
+ protein.setViewStyle(vs);
}
}
*/
package jalview.jbgui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
/**
* DOCUMENT ME!
*
*/
public class GFontChooser extends JPanel
{
- JLabel jLabel1 = new JLabel();
-
- protected JComboBox fontSize = new JComboBox();
-
- protected JComboBox fontStyle = new JComboBox();
-
- JLabel jLabel2 = new JLabel();
-
- JLabel jLabel3 = new JLabel();
-
- protected JComboBox fontName = new JComboBox();
+ private static final Font VERDANA_11PT = new java.awt.Font("Verdana", 0, 11);
- JButton ok = new JButton();
+ protected JComboBox<Integer> fontSize = new JComboBox<Integer>();
- JButton cancel = new JButton();
+ protected JComboBox<String> fontStyle = new JComboBox<String>();
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- JPanel jPanel3 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
+ protected JComboBox<String> fontName = new JComboBox<String>();
protected JButton defaultButton = new JButton();
protected JCheckBox smoothFont = new JCheckBox();
- BorderLayout borderLayout4 = new BorderLayout();
-
protected JCheckBox monospaced = new JCheckBox();
- JPanel jPanel4 = new JPanel();
+ protected JCheckBox scaleAsCdna = new JCheckBox();
/**
* Creates a new GFontChooser object.
*/
private void jbInit() throws Exception
{
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
- jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
- jLabel1.setText(MessageManager.getString("label.font"));
- jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
this.setLayout(null);
- fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
+ this.setBackground(Color.white);
+
+ JLabel fontLabel = new JLabel(MessageManager.getString("label.font"));
+ fontLabel.setFont(VERDANA_11PT);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+
+ fontSize.setFont(VERDANA_11PT);
fontSize.setOpaque(false);
fontSize.setPreferredSize(new Dimension(50, 21));
fontSize.addActionListener(new java.awt.event.ActionListener()
fontSize_actionPerformed(e);
}
});
- fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
+
+ fontStyle.setFont(VERDANA_11PT);
fontStyle.setOpaque(false);
fontStyle.setPreferredSize(new Dimension(90, 21));
fontStyle.addActionListener(new java.awt.event.ActionListener()
fontStyle_actionPerformed(e);
}
});
- jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));
- jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
- jLabel2.setText(MessageManager.getString("label.size"));
- jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
- jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));
- jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
- jLabel3.setText(MessageManager.getString("label.style"));
- jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
- fontName.setFont(new java.awt.Font("Verdana", 0, 11));
+
+ JLabel sizeLabel = new JLabel(MessageManager.getString("label.size"));
+ sizeLabel.setFont(VERDANA_11PT);
+ sizeLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sizeLabel.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+
+ JLabel styleLabel = new JLabel(MessageManager.getString("label.style"));
+ styleLabel.setFont(VERDANA_11PT);
+ styleLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ styleLabel.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+
+ fontName.setFont(VERDANA_11PT);
fontName.setMaximumSize(new Dimension(32767, 32767));
fontName.setMinimumSize(new Dimension(300, 21));
fontName.setOpaque(false);
fontName_actionPerformed(e);
}
});
- ok.setFont(new java.awt.Font("Verdana", 0, 11));
- ok.setText(MessageManager.getString("action.ok"));
+
+ JButton ok = new JButton(MessageManager.getString("action.ok"));
+ ok.setFont(VERDANA_11PT);
ok.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
ok_actionPerformed(e);
}
});
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));
- cancel.setText(MessageManager.getString("action.cancel"));
+
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ cancel.setFont(VERDANA_11PT);
cancel.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
cancel_actionPerformed(e);
}
});
- this.setBackground(Color.white);
- jPanel1.setOpaque(false);
- jPanel1.setBounds(new Rectangle(5, 6, 308, 23));
- jPanel1.setLayout(borderLayout1);
- jPanel2.setOpaque(false);
- jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
- jPanel2.setLayout(borderLayout3);
- jPanel3.setOpaque(false);
- jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
- jPanel3.setLayout(borderLayout2);
+
defaultButton.setFont(JvSwingUtils.getLabelFont());
defaultButton.setText(MessageManager.getString("label.set_as_default"));
defaultButton.addActionListener(new ActionListener()
defaultButton_actionPerformed(e);
}
});
+
smoothFont.setFont(JvSwingUtils.getLabelFont());
smoothFont.setOpaque(false);
smoothFont.setText(MessageManager.getString("label.anti_alias_fonts"));
- smoothFont.setBounds(new Rectangle(41, 65, 223, 23));
+ smoothFont.setBounds(new Rectangle(41, 65, 260, 23));
smoothFont.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
smoothFont_actionPerformed(e);
}
});
+
+ /*
+ * Scale protein as cDNA is only visible in SplitFrame protein alignment
+ */
+ scaleAsCdna.setVisible(false);
+ scaleAsCdna.setFont(JvSwingUtils.getLabelFont());
+ scaleAsCdna.setOpaque(false);
+ scaleAsCdna.setText(MessageManager.getString("label.scale_as_cdna"));
+ scaleAsCdna.setBounds(new Rectangle(41, 85, 260, 23));
+ scaleAsCdna.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleAsCdna_actionPerformed(e);
+ }
+ });
+
monospaced.setEnabled(false);
monospaced.setFont(JvSwingUtils.getLabelFont());
monospaced.setOpaque(false);
monospaced.setToolTipText(MessageManager
.getString("label.monospaced_fonts_faster_to_render"));
monospaced.setText(MessageManager.getString("label.monospaced_font"));
- jPanel4.setOpaque(false);
- jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
- jPanel1.add(jLabel1, BorderLayout.WEST);
+
+ /*
+ * jPanel1: Font dropdown, Monospaced checkbox
+ */
+ JPanel jPanel1 = new JPanel();
+ jPanel1.setOpaque(false);
+ jPanel1.setBounds(new Rectangle(5, 6, 308, 23));
+ jPanel1.setLayout(new BorderLayout());
+ jPanel1.add(fontLabel, BorderLayout.WEST);
jPanel1.add(fontName, BorderLayout.CENTER);
jPanel1.add(monospaced, java.awt.BorderLayout.EAST);
- this.add(jPanel3, null);
- this.add(jPanel2, null);
+
+ /*
+ * jPanel2: font size dropdown
+ */
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setOpaque(false);
+ jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
+ jPanel2.setLayout(new BorderLayout());
jPanel2.add(fontSize, java.awt.BorderLayout.CENTER);
- jPanel2.add(jLabel2, java.awt.BorderLayout.WEST);
+ jPanel2.add(sizeLabel, java.awt.BorderLayout.WEST);
+
+ /*
+ * jPanel3: font style dropdown
+ */
+ JPanel jPanel3 = new JPanel();
+ jPanel3.setOpaque(false);
+ jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
+ jPanel3.setLayout(new BorderLayout());
+ jPanel3.add(styleLabel, java.awt.BorderLayout.WEST);
+ jPanel3.add(fontStyle, java.awt.BorderLayout.CENTER);
+
+ /*
+ * jPanel4: Default and OK buttons
+ */
+ JPanel jPanel4 = new JPanel();
+ jPanel4.setOpaque(false);
+ jPanel4.setBounds(new Rectangle(24, 112, 300, 35));
jPanel4.add(defaultButton);
jPanel4.add(ok);
jPanel4.add(cancel);
+
this.add(smoothFont);
+ this.add(scaleAsCdna);
+ this.add(jPanel3, null);
+ this.add(jPanel2, null);
this.add(jPanel4);
- jPanel3.add(jLabel3, java.awt.BorderLayout.WEST);
- jPanel3.add(fontStyle, java.awt.BorderLayout.CENTER);
this.add(jPanel1, null);
}
+ protected void scaleAsCdna_actionPerformed(ActionEvent e)
+ {
+ }
+
/**
* DOCUMENT ME!
*
*/
package jalview.jbgui;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.SwingConstants;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
import javax.swing.border.TitledBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
+import jalview.util.MessageManager;
+
/**
* Base class for the Preferences panel.
*
*/
public class GPreferences extends JPanel
{
- private static final Font verdana11 = JvSwingUtils.getLabelFont();
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
+
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils
+ .getLabelFont(false, true);
/*
* Visual tab components
protected JCheckBox smoothFont = new JCheckBox();
+ protected JCheckBox scaleProteinToCdna = new JCheckBox();
+
protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
protected JCheckBox wrap = new JCheckBox();
{
JPanel editingTab = new JPanel();
editingTab.setLayout(null);
- autoCalculateConsCheck.setFont(verdana11);
+ autoCalculateConsCheck.setFont(LABEL_FONT);
autoCalculateConsCheck.setText(MessageManager
.getString("label.autocalculate_consensus"));
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(verdana11);
+ padGaps.setFont(LABEL_FONT);
padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(verdana11);
+ sortByTree.setFont(LABEL_FONT);
sortByTree
.setText(MessageManager.getString("label.sort_with_new_tree"));
sortByTree
JPanel outputTab = new JPanel();
outputTab.setLayout(null);
JLabel epsLabel = new JLabel();
- epsLabel.setFont(verdana11);
+ epsLabel.setFont(LABEL_FONT);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
- epsRendering.setFont(verdana11);
+ epsRendering.setFont(LABEL_FONT);
epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
JLabel jLabel1 = new JLabel();
- jLabel1.setFont(verdana11);
+ jLabel1.setFont(LABEL_FONT);
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
jLabel1.setText(MessageManager.getString("label.append_start_end"));
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
+ jLabel1.setFont(LABEL_FONT);
+ fastajv.setFont(LABEL_FONT);
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
clustaljv.setText(MessageManager.getString("label.clustal") + " ");
blcjv.setText(MessageManager.getString("label.blc") + " ");
msfjv.setText(MessageManager.getString("label.msf") + " ");
pfamjv.setText(MessageManager.getString("label.pfam") + " ");
pileupjv.setText(MessageManager.getString("label.pileup") + " ");
- msfjv.setFont(verdana11);
+ msfjv.setFont(LABEL_FONT);
msfjv.setHorizontalAlignment(SwingConstants.LEFT);
pirjv.setText(MessageManager.getString("label.pir") + " ");
JPanel jPanel11 = new JPanel();
- jPanel11.setFont(verdana11);
+ jPanel11.setFont(LABEL_FONT);
TitledBorder titledBorder2 = new TitledBorder(
MessageManager.getString("label.file_output"));
jPanel11.setBorder(titledBorder2);
GridLayout gridLayout3 = new GridLayout();
jPanel11.setLayout(gridLayout3);
gridLayout3.setRows(8);
- blcjv.setFont(verdana11);
+ blcjv.setFont(LABEL_FONT);
blcjv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setFont(verdana11);
+ clustaljv.setFont(LABEL_FONT);
clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
- pfamjv.setFont(verdana11);
+ pfamjv.setFont(LABEL_FONT);
pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
- pileupjv.setFont(verdana11);
+ pileupjv.setFont(LABEL_FONT);
pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setFont(verdana11);
+ pirjv.setFont(LABEL_FONT);
pirjv.setHorizontalAlignment(SwingConstants.LEFT);
- autoIdWidth.setFont(verdana11);
+ autoIdWidth.setFont(LABEL_FONT);
autoIdWidth.setText(MessageManager
.getString("label.automatically_set_id_width"));
autoIdWidth
autoIdWidth_actionPerformed();
}
});
- userIdWidthlabel.setFont(verdana11);
+ userIdWidthlabel.setFont(LABEL_FONT);
userIdWidthlabel.setText(MessageManager
.getString("label.figure_id_column_width"));
userIdWidth
outputTab.add(epsLabel);
outputTab.add(epsRendering);
outputTab.add(jPanel11);
- modellerOutput.setFont(verdana11);
+ modellerOutput.setFont(LABEL_FONT);
modellerOutput.setText(MessageManager
.getString("label.use_modeller_output"));
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
JLabel serverLabel = new JLabel();
serverLabel.setText(MessageManager.getString("label.address"));
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- serverLabel.setFont(verdana11);
- proxyServerTB.setFont(verdana11);
- proxyPortTB.setFont(verdana11);
+ serverLabel.setFont(LABEL_FONT);
+ proxyServerTB.setFont(LABEL_FONT);
+ proxyPortTB.setFont(LABEL_FONT);
JLabel portLabel = new JLabel();
- portLabel.setFont(verdana11);
+ portLabel.setFont(LABEL_FONT);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
portLabel.setText(MessageManager.getString("label.port"));
JLabel browserLabel = new JLabel();
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
browserLabel.setText(MessageManager
.getString("label.default_browser_unix"));
- defaultBrowser.setFont(verdana11);
+ defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
usagestats.setText(MessageManager
.getString("label.send_usage_statistics"));
- usagestats.setFont(verdana11);
+ usagestats.setFont(LABEL_FONT);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
questionnaire.setText(MessageManager
.getString("label.check_for_questionnaires"));
- questionnaire.setFont(verdana11);
+ questionnaire.setFont(LABEL_FONT);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
versioncheck.setText(MessageManager
.getString("label.check_for_latest_version"));
- versioncheck.setFont(verdana11);
+ versioncheck.setFont(LABEL_FONT);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
JButton newLink = new JButton();
JPanel editLinkButtons = new JPanel();
editLinkButtons.setLayout(gridLayout1);
gridLayout1.setRows(3);
- linkNameList.setFont(verdana11);
+ linkNameList.setFont(LABEL_FONT);
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
BorderLayout borderLayout3 = new BorderLayout();
JPanel linkPanel2 = new JPanel();
linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(verdana11);
+ linkURLList.setFont(LABEL_FONT);
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
defaultBrowser.addMouseListener(new MouseAdapter()
}
}
});
- useProxy.setFont(verdana11);
+ useProxy.setFont(LABEL_FONT);
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
useProxy.setText(MessageManager.getString("label.use_proxy_server"));
.getString("action.open_new_alignment")));
coloursTab.setLayout(new FlowLayout());
JLabel mincolourLabel = new JLabel();
- mincolourLabel.setFont(verdana11);
+ mincolourLabel.setFont(LABEL_FONT);
mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
mincolourLabel.setText(MessageManager.getString("label.min_colour"));
- minColour.setFont(verdana11);
+ minColour.setFont(LABEL_FONT);
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
minColour.addMouseListener(new MouseAdapter()
}
});
JLabel maxcolourLabel = new JLabel();
- maxcolourLabel.setFont(verdana11);
+ maxcolourLabel.setFont(LABEL_FONT);
maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
- maxColour.setFont(verdana11);
+ maxColour.setFont(LABEL_FONT);
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
maxColour.addMouseListener(new MouseAdapter()
}
});
- protColour.setFont(verdana11);
+ protColour.setFont(LABEL_FONT);
protColour.setBounds(new Rectangle(172, 225, 155, 21));
JLabel protColourLabel = new JLabel();
- protColourLabel.setFont(verdana11);
+ protColourLabel.setFont(LABEL_FONT);
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
protColourLabel.setText(MessageManager
.getString("label.prot_alignment_colour") + " ");
.getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
- nucColour.setFont(verdana11);
+ nucColour.setFont(LABEL_FONT);
nucColour.setBounds(new Rectangle(172, 240, 155, 21));
JLabel nucColourLabel = new JLabel();
- nucColourLabel.setFont(verdana11);
+ nucColourLabel.setFont(LABEL_FONT);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(MessageManager
.getString("label.nuc_alignment_colour")
final int lineSpacing = 25;
int ypos = 30;
- structFromPdb.setFont(verdana11);
+ structFromPdb.setFont(LABEL_FONT);
structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
structFromPdb.addActionListener(new ActionListener()
// indent checkboxes that are conditional on the first one
ypos += lineSpacing;
- useRnaView.setFont(verdana11);
+ useRnaView.setFont(LABEL_FONT);
useRnaView.setText(MessageManager.getString("label.use_rnaview"));
useRnaView.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(useRnaView);
ypos += lineSpacing;
- addSecondaryStructure.setFont(verdana11);
+ addSecondaryStructure.setFont(LABEL_FONT);
addSecondaryStructure.setText(MessageManager
.getString("label.autoadd_secstr"));
addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(addSecondaryStructure);
ypos += lineSpacing;
- addTempFactor.setFont(verdana11);
+ addTempFactor.setFont(LABEL_FONT);
addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(addTempFactor);
ypos += lineSpacing;
JLabel viewerLabel = new JLabel();
- viewerLabel.setFont(verdana11);
+ viewerLabel.setFont(LABEL_FONT);
viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
structureTab.add(viewerLabel);
- structViewer.setFont(verdana11);
+ structViewer.setFont(LABEL_FONT);
structViewer.setBounds(new Rectangle(160, ypos, 120, height));
structViewer.addItem(ViewerType.JMOL.name());
structViewer.addItem(ViewerType.CHIMERA.name());
pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
structureTab.add(pathLabel);
- chimeraPath.setFont(verdana11);
+ chimeraPath.setFont(LABEL_FONT);
chimeraPath.setText("");
chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
chimeraPath.addMouseListener(new MouseAdapter()
visualTab.setBorder(new TitledBorder(MessageManager
.getString("action.open_new_alignment")));
visualTab.setLayout(null);
- fullScreen.setFont(verdana11);
+ fullScreen.setFont(LABEL_FONT);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
fullScreen.setText(MessageManager.getString("label.maximize_window"));
quality.setEnabled(false);
- quality.setFont(verdana11);
+ quality.setFont(LABEL_FONT);
quality.setHorizontalAlignment(SwingConstants.RIGHT);
quality.setHorizontalTextPosition(SwingConstants.LEFT);
quality.setSelected(true);
quality.setText(MessageManager.getString("label.quality"));
conservation.setEnabled(false);
- conservation.setFont(verdana11);
+ conservation.setFont(LABEL_FONT);
conservation.setHorizontalAlignment(SwingConstants.RIGHT);
conservation.setHorizontalTextPosition(SwingConstants.LEFT);
conservation.setSelected(true);
conservation.setText(MessageManager.getString("label.conservation"));
identity.setEnabled(false);
- identity.setFont(verdana11);
+ identity.setFont(LABEL_FONT);
identity.setHorizontalAlignment(SwingConstants.RIGHT);
identity.setHorizontalTextPosition(SwingConstants.LEFT);
identity.setSelected(true);
identity.setText(MessageManager.getString("label.consensus"));
JLabel showGroupbits = new JLabel();
- showGroupbits.setFont(verdana11);
+ showGroupbits.setFont(LABEL_FONT);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupbits.setText(MessageManager.getString("action.show_group")
+ ":");
JLabel showConsensbits = new JLabel();
- showConsensbits.setFont(verdana11);
+ showConsensbits.setFont(LABEL_FONT);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensbits.setText(MessageManager.getString("label.consensus")
+ ":");
showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
+ showConsensHistogram.setFont(LABEL_FONT);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
showConsensHistogram.setText(MessageManager
.getString("label.histogram"));
showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
+ showConsensLogo.setFont(LABEL_FONT);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensLogo.setSelected(true);
showConsensLogo.setText(MessageManager.getString("label.logo"));
showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
+ showGroupConsensus.setFont(LABEL_FONT);
showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConsensus.setSelected(true);
showGroupConsensus.setText(MessageManager.getString("label.consensus"));
showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
+ showGroupConservation.setFont(LABEL_FONT);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
showGroupConservation.setText(MessageManager
.getString("label.conservation"));
showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
+ showNpTooltip.setFont(LABEL_FONT);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
showNpTooltip.setText(MessageManager
.getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
- showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setFont(LABEL_FONT);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
showDbRefTooltip.setText(MessageManager
.getString("label.database_references"));
- annotations.setFont(verdana11);
+ annotations.setFont(LABEL_FONT);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEADING);
annotations.setSelected(true);
annotations_actionPerformed(e);
}
});
- showUnconserved.setFont(verdana11);
+ showUnconserved.setFont(LABEL_FONT);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
// followHighlight.setText(MessageManager
// .getString("label.scroll_highlighted_regions"));
- seqLimit.setFont(verdana11);
+ seqLimit.setFont(LABEL_FONT);
seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
- smoothFont.setFont(verdana11);
+ smoothFont.setFont(LABEL_FONT);
smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ scaleProteinToCdna.setFont(LABEL_FONT);
+ scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
+ scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
+ scaleProteinToCdna.setText(MessageManager
+ .getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(MessageManager
+ .getString("label.scale_protein_to_cdna_tip"));
JLabel gapLabel = new JLabel();
- gapLabel.setFont(verdana11);
+ gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
JLabel fontLabel = new JLabel();
- fontLabel.setFont(verdana11);
+ fontLabel.setFont(LABEL_FONT);
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
fontLabel.setText(MessageManager.getString("label.font"));
- fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
- fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
- fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
- gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
+ fontSizeCB.setFont(LABEL_FONT);
+ fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
+ fontStyleCB.setFont(LABEL_FONT);
+ fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
+ fontNameCB.setFont(LABEL_FONT);
+ fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
+ gapSymbolCB.setFont(LABEL_FONT);
+ gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
gapSymbolCB.setRenderer(dlcr);
startupCheckbox.setText(MessageManager.getString("action.open_file"));
- startupCheckbox.setFont(verdana11);
+ startupCheckbox.setFont(LABEL_FONT);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
- startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
+ startupFileTextfield.setFont(LABEL_FONT);
+ startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
startupFileTextfield.addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
}
});
- sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 240, 155, 21));
+ sortby.setFont(LABEL_FONT);
+ sortby.setBounds(new Rectangle(172, 260, 155, 21));
JLabel sortLabel = new JLabel();
- sortLabel.setFont(verdana11);
+ sortLabel.setFont(LABEL_FONT);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText(MessageManager.getString("label.sort_by"));
- sortAnnBy.setFont(verdana11);
- sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
+ sortAnnBy.setFont(LABEL_FONT);
+ sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
JLabel sortAnnLabel = new JLabel();
- sortAnnLabel.setFont(verdana11);
+ sortAnnLabel.setFont(LABEL_FONT);
sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
- sortAutocalc.setFont(verdana11);
- sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
+ sortAutocalc.setFont(LABEL_FONT);
+ sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
+
JPanel annsettingsPanel = new JPanel();
- annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
+ annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
- JPanel autoAnnotSettings1 = new JPanel();
- autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
- annsettingsPanel.add(autoAnnotSettings1);
- JPanel autoAnnotSettings2 = new JPanel();
- autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
- annsettingsPanel.add(autoAnnotSettings2);
- JPanel autoAnnotSettings3 = new JPanel();
- autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
- annsettingsPanel.add(autoAnnotSettings3);
+ annsettingsPanel.setBorder(new EtchedBorder());
visualTab.add(annsettingsPanel);
Border jb = new EmptyBorder(1, 1, 4, 5);
quality.setBorder(jb);
showConsensHistogram.setBorder(jb);
showConsensLogo.setBorder(jb);
- autoAnnotSettings2.add(conservation);
- autoAnnotSettings1.add(quality);
- autoAnnotSettings3.add(identity);
- autoAnnotSettings1.add(showGroupbits);
- autoAnnotSettings3.add(showGroupConsensus);
- autoAnnotSettings2.add(showGroupConservation);
- autoAnnotSettings1.add(showConsensbits);
- autoAnnotSettings2.add(showConsensHistogram);
- autoAnnotSettings3.add(showConsensLogo);
+ JPanel autoAnnotSettings = new JPanel();
+ autoAnnotSettings.setLayout(new GridLayout(3, 3));
+ annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.add(quality);
+ autoAnnotSettings.add(conservation);
+ autoAnnotSettings.add(identity);
+ autoAnnotSettings.add(showGroupbits);
+ autoAnnotSettings.add(showGroupConservation);
+ autoAnnotSettings.add(showGroupConsensus);
+ autoAnnotSettings.add(showConsensbits);
+ autoAnnotSettings.add(showConsensHistogram);
+ autoAnnotSettings.add(showConsensLogo);
JPanel tooltipSettings = new JPanel();
tooltipSettings.setBorder(new TitledBorder(MessageManager
.getString("label.sequence_id_tooltip")));
- tooltipSettings.setBounds(173, 130, 200, 62);
+ tooltipSettings.setBounds(173, 140, 220, 62);
tooltipSettings.setLayout(new GridLayout(2, 1));
tooltipSettings.add(showDbRefTooltip);
tooltipSettings.add(showNpTooltip);
visualTab.add(tooltipSettings);
- wrap.setFont(verdana11);
+ wrap.setFont(LABEL_FONT);
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
- rightAlign.setFont(verdana11);
+ rightAlign.setFont(LABEL_FONT);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
rightAlign.setText(MessageManager.getString("label.right_align_ids"));
- idItalics.setFont(verdana11);
+ idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
idItalics.setText(MessageManager
.getString("label.sequence_name_italics"));
- openoverv.setFont(verdana11);
+ openoverv.setFont(LABEL_FONT);
openoverv.setActionCommand(MessageManager
.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString(("label.open_overview")));
JPanel jPanel2 = new JPanel();
- jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
- GridLayout gridLayout2 = new GridLayout();
- jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(13);
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
+ jPanel2.setLayout(new GridLayout(14, 1));
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(showUnconserved);
jPanel2.add(idItalics);
jPanel2.add(smoothFont);
+ jPanel2.add(scaleProteinToCdna);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
jPanel2.add(sortLabel);
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
+
+ @Override
+ public boolean isScaleProteinAsCdna()
+ {
+ return viewStyle.isScaleProteinAsCdna();
+ }
+
+ @Override
+ public void setScaleProteinAsCdna(boolean b)
+ {
+ viewStyle.setScaleProteinAsCdna(b);
+ }
}
package jalview.viewmodel.styles;
-import jalview.api.ViewStyleI;
-
import java.awt.Color;
import java.lang.reflect.Method;
import java.util.HashMap;
+import jalview.api.ViewStyleI;
+
/**
* A container for holding alignment view properties. View properties are
* data-independent, which means they can be safely copied between views
* name of base font for view
*/
private String fontName;
+
/**
* size for base font
*/
private int fontSize;
-
+
+ /*
+ * If true, scale protein residues to 3 times width of cDNA bases (in
+ * SplitFrame views only)
+ */
+ private boolean scaleProteinAsCdna = false;
+
public ViewStyle(ViewStyleI viewStyle)
{
ViewStyle.configureFrom(this, viewStyle);
{
this.shownpfeats = shownpfeats;
}
+
+ @Override
+ public boolean isScaleProteinAsCdna()
+ {
+ return this.scaleProteinAsCdna;
+ }
+
+ @Override
+ public void setScaleProteinAsCdna(boolean b)
+ {
+ this.scaleProteinAsCdna = b;
+ }
}
orig.setCharHeight(23);
orig.setWrappedWidth(253);
orig.setWrapAlignment(true);
+ orig.setScaleProteinAsCdna(true);
+
ViewStyle copy = new ViewStyle(orig);
orig.setWrapAlignment(false);
Assert.assertEquals(copy.getCharHeight(), orig.getCharHeight());
Assert.assertEquals(copy.getWrappedWidth(), orig.getWrappedWidth());
Assert.assertEquals(copy.getWrapAlignment(), !orig.getWrapAlignment());
+ Assert.assertEquals(copy.isScaleProteinAsCdna(),
+ orig.isScaleProteinAsCdna());
}
}
git://source.jalview.org / jalview.git / commitdiff