GridLayout gridLayout2 = new GridLayout();
- JPanel jPanel3 = new JPanel();
+ JPanel annsettingsPanel = new JPanel();
JPanel autoAnnotSettings1 = new JPanel();
-
JPanel autoAnnotSettings2 = new JPanel();
+ JPanel autoAnnotSettings3 = new JPanel();
JPanel exportTab = new JPanel();
protected JCheckBox versioncheck = new JCheckBox();
protected JLabel showGroupbits = new JLabel();
protected JLabel showConsensbits = new JLabel();
- protected JCheckBox showConsensProfile = new JCheckBox();
+ protected JCheckBox showConsensLogo = new JCheckBox();
protected JCheckBox showConsensHistogram = new JCheckBox();
protected JCheckBox showGroupConsensus = new JCheckBox();
protected JCheckBox showGroupConservation = new JCheckBox();
+ protected JCheckBox shareSelections = new JCheckBox();
+ protected JCheckBox followHighlight = new JCheckBox();
+
/**
* Creates a new GPreferences object.
showGroupbits.setFont(verdana11);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText("Group:");
+ showGroupbits.setText("Show group:");
showConsensbits.setFont(verdana11);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
showConsensHistogram.setText("Histogram");
- showConsensProfile.setEnabled(false);
- showConsensProfile.setFont(verdana11);
- showConsensProfile.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensProfile.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensProfile.setSelected(true);
- showConsensProfile.setText("Profile");
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(verdana11);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText("Logo");
showGroupConsensus.setEnabled(false);
showGroupConsensus.setFont(verdana11);
showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setText("Conservation");
annotations.setFont(verdana11);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEADING);
annotations.setSelected(true);
annotations.setText("Show Annotations");
+ annotations.setBounds(new Rectangle(169, 16, 200, 23));
annotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
annotations_actionPerformed(e);
}
});
+ identity.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
showUnconserved.setFont(verdana11);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showunconserved_actionPerformed(e);
}
});
+ shareSelections.setFont(verdana11);
+ shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ shareSelections.setSelected(true);
+ shareSelections.setText("Share selection across views");
+ followHighlight.setFont(verdana11);
+ followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ followHighlight.setSelected(true);
+ followHighlight.setText("Scroll to highlighted regions");
gapLabel.setFont(verdana11);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
jPanel2.setLayout(gridLayout2);
gridLayout2.setRows(13);
- jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
- autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
- autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
+ // jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
+ //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
+ //jPanel3.setLayout(new GridLayout(3,3));
+// autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
+// autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
exportTab.setLayout(null);
epsLabel.setFont(verdana11);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
openoverv.setActionCommand("Open Overview");
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
- openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
- openoverv.setText("Open Overview Window");
- openoverv.setBounds(new Rectangle(169, 17, 200, 23));
+ openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
+ openoverv.setText("Open Overview");
jPanel2.add(fullScreen);
- jPanel2.add(annotations);
+ jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(rightAlign);
jPanel2.add(fontLabel);
jPanel2.add(colourLabel);
jPanel2.add(sortLabel);
jPanel2.add(startupCheckbox);
- visualTab.add(openoverv);
+ visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
visualTab.add(colour);
visualTab.add(gapSymbolCB);
- visualTab.add(jPanel3);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
- visualTab.add(autoAnnotSettings1);
- visualTab.add(autoAnnotSettings2);
- jPanel3.add(conservation);
- jPanel3.add(identity);
- jPanel3.add(quality);
- autoAnnotSettings1.setLayout(new FlowLayout());
- autoAnnotSettings2.setLayout(new FlowLayout());
- autoAnnotSettings1.add(showConsensbits);
- autoAnnotSettings1.add(showConsensHistogram);
- autoAnnotSettings1.add(showConsensProfile);
- autoAnnotSettings2.add(showGroupbits);
- autoAnnotSettings2.add(showGroupConsensus);
+ annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
+ annsettingsPanel.add(autoAnnotSettings1);
+ annsettingsPanel.add(autoAnnotSettings2);
+ annsettingsPanel.add(autoAnnotSettings3);
+ autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
+// autoAnnotSettings1.setPreferredSize(new Dimensions())
+ autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
+ autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
+ visualTab.add(annsettingsPanel);
+ //visualTab.add(autoAnnotSettings1);
+ //visualTab.add(autoAnnotSettings2);
+ Border jb = new EmptyBorder(1,1,4,5);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
+
+ autoAnnotSettings2.add(conservation);
+ autoAnnotSettings1.add(quality);
+ autoAnnotSettings3.add(identity);
+
+ /*FlowLayout fl = new FlowLayout();
+ fl.setAlignment(FlowLayout.LEFT);
+ autoAnnotSettings1.setLayout(fl);
+ fl = new FlowLayout();
+ fl.setAlignment(FlowLayout.LEFT);
+ autoAnnotSettings2.setLayout(fl); */
+ autoAnnotSettings1.add(showGroupbits);
+ autoAnnotSettings3.add(showGroupConsensus);
autoAnnotSettings2.add(showGroupConservation);
+ autoAnnotSettings1.add(showConsensbits);
+ autoAnnotSettings2.add(showConsensHistogram);
+ autoAnnotSettings3.add(showConsensLogo);
visualTab.add(jPanel2);
linkPanel.add(editLinkButtons, BorderLayout.EAST);