*/
package jalview.jbgui;
+import jalview.gui.JvSwingUtils;
+
import java.awt.*;
import java.awt.event.*;
protected JCheckBox quality = new JCheckBox();
JPanel visualTab = new JPanel();
+ JPanel visual2Tab = new JPanel();
protected JCheckBox fullScreen = new JCheckBox();
protected JCheckBox annotations = new JCheckBox();
+ protected JPanel minColour = new JPanel();
+ JLabel mincolourLabel = new JLabel();
+
+ protected JPanel maxColour = new JPanel();
+ JLabel maxcolourLabel = new JLabel();
+
JLabel gapLabel = new JLabel();
protected JComboBox colour = new JComboBox();
JLabel sortLabel = new JLabel();
JPanel jPanel2 = new JPanel();
+ JPanel visual2panel = new JPanel();
GridLayout gridLayout2 = new GridLayout();
+ GridLayout gridLayout4 = new GridLayout();
+
JPanel annsettingsPanel = new JPanel();
JPanel autoAnnotSettings1 = new JPanel();
JPanel jPanel11 = new JPanel();
- Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
+ Font verdana11 = JvSwingUtils.getLabelFont();
protected JCheckBox seqLimit = new JCheckBox();
protected JCheckBox modellerOutput = new JCheckBox();
protected JPanel dasPanel = new JPanel();
-
+
BorderLayout borderLayout4 = new BorderLayout();
protected JPanel wsPanel = new JPanel();
protected JCheckBox shareSelections = new JCheckBox();
protected JCheckBox followHighlight = new JCheckBox();
-
-
+ protected JCheckBox sortByTree= new JCheckBox();
/**
* Creates a new GPreferences object.
quality.setText("Quality");
visualTab.setBorder(new TitledBorder("Open new alignment"));
visualTab.setLayout(null);
+ visual2Tab.setBorder(new TitledBorder("Open new alignment"));
+ visual2Tab.setLayout(new FlowLayout());
fullScreen.setFont(verdana11);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
colour.setBounds(new Rectangle(172, 225, 155, 21));
colourLabel.setFont(verdana11);
colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText("Colour ");
+ colourLabel.setText("Alignment Colour ");
fontLabel.setFont(verdana11);
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
fontLabel.setText("Font ");
fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
gapSymbolCB.setFont(verdana11);
gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
+ mincolourLabel.setFont(verdana11);
+ mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ mincolourLabel.setText("Minimum Colour");
+ minColour.setFont(verdana11);
+ minColour.setBorder(BorderFactory.createEtchedBorder());
+ minColour.setPreferredSize(new Dimension(40, 20));
+ minColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ minColour_actionPerformed();
+ }
+ });
+ maxcolourLabel.setFont(verdana11);
+ maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ maxcolourLabel.setText("Maximum Colour ");
+ maxColour.setFont(verdana11);
+ maxColour.setBorder(BorderFactory.createEtchedBorder());
+ maxColour.setPreferredSize(new Dimension(40, 20));
+ maxColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ maxColour_actionPerformed();
+ }
+ });
+
startupCheckbox.setText("Open file");
startupCheckbox.setFont(verdana11);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText("Sort by ");
jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(13);
+ gridLayout2.setRows(12);
exportTab.setLayout(null);
epsLabel.setFont(verdana11);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
smoothFont.setText("Smooth Font");
calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
- 11));
+ autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
autoCalculateConsCheck.setText("AutoCalculate Consensus");
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- padGaps.setText("Pad gaps when editing");
+ padGaps.setFont(JvSwingUtils.getLabelFont());
+ padGaps.setText("Pad Gaps When Editing");
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ sortByTree.setFont(JvSwingUtils.getLabelFont());
+ sortByTree.setText("Sort With New Tree");
+ sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ modellerOutput.setFont(JvSwingUtils.getLabelFont());
modellerOutput.setText("Use Modeller Output");
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
dasPanel.setLayout(borderLayout4);
wsPanel.setLayout(borderLayout5);
- wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ wrap.setFont(JvSwingUtils.getLabelFont());
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText("Wrap Alignment");
- rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ rightAlign.setFont(JvSwingUtils.getLabelFont());
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
rightAlign.setText("Right Align Ids");
- idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ idItalics.setFont(JvSwingUtils.getLabelFont());
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
idItalics.setText("Sequence Name Italics");
- openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ openoverv.setFont(JvSwingUtils.getLabelFont());
openoverv.setActionCommand("Open Overview");
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
jPanel2.add(showUnconserved);
jPanel2.add(idItalics);
jPanel2.add(smoothFont);
- jPanel2.add(wrap);
jPanel2.add(gapLabel);
- jPanel2.add(colourLabel);
+ jPanel2.add(wrap);
jPanel2.add(sortLabel);
jPanel2.add(startupCheckbox);
visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
- visualTab.add(colour);
visualTab.add(gapSymbolCB);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
tooltipSettings.add(showNpTooltip);
visualTab.add(tooltipSettings);
visualTab.add(jPanel2);
+ JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
+ JPanel annotationShding=new JPanel();
+ annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
+ annotationShding.setLayout(new GridLayout(1,2));
+ JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
+ JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
+ visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
+
+// visual2panel.add(minColour);
+// visual2panel.add(maxColour);
+// visual2Tab.add(visual2panel);
linkPanel.add(editLinkButtons, BorderLayout.EAST);
editLinkButtons.add(newLink, null);
gapSymbolCB.setRenderer(dlcr);
tabbedPane.add(visualTab, "Visual");
+ tabbedPane.add(visual2Tab,"Colours");
tabbedPane.add(connectTab, "Connections");
tabbedPane.add(exportTab, "Output");
jPanel11.add(jLabel1);
tabbedPane.add(calcTab, "Editing");
calcTab.add(autoCalculateConsCheck);
calcTab.add(padGaps);
+ calcTab.add(sortByTree);
+
tabbedPane.add(dasPanel, "DAS Settings");
tabbedPane.add(wsPanel, "Web Services");
exportTab.add(jPanel11);
}
+ protected void maxColour_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void minColour_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void showunconserved_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub