\r
import java.util.Vector;\r
import jalview.io.FormatAdapter;\r
+import javax.swing.event.ChangeListener;\r
+import javax.swing.event.ChangeEvent;\r
\r
\r
/**\r
JMenuItem discoverPDB = new JMenuItem();\r
JMenu outputMenu = new JMenu();\r
JMenuItem sequenceFeature = new JMenuItem();\r
+ JMenuItem textColour = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
\r
/**\r
* Creates a new PopupMenu object.\r
\r
if (seq != null)\r
{\r
- int start = Math.max(sequence.getName().length()-15, 0);\r
- sequenceMenu.setText(sequence.getName().substring(start));\r
+ sequenceMenu.setText(sequence.getName());\r
\r
JMenuItem menuItem;\r
if( seq.getDatasetSequence().getPDBId() != null)\r
sequenceFeature_actionPerformed(e);\r
}\r
});\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setText("Group");\r
add(groupMenu);\r
\r
add(sequenceMenu);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputMenu);\r
- groupMenu.addSeparator();\r
groupMenu.add(sequenceFeature);\r
- groupMenu.addSeparator();\r
- groupMenu.add(groupName);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
- groupMenu.add(outline);\r
+ groupMenu.add(jMenu1);\r
sequenceMenu.add(sequenceName);\r
sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(textColour);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
pdbMenu.add(pdbFromFile);\r
pdbMenu.add(enterPDB);\r
pdbMenu.add(discoverPDB);\r
+ jMenu1.add(groupName);\r
+ jMenu1.add(unGroupMenuItem);\r
+ jMenu1.add(colourMenu);\r
+ jMenu1.add(showBoxes);\r
+ jMenu1.add(showText);\r
+ jMenu1.add(showColourText);\r
+ jMenu1.add(outline);\r
noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
\r
if (abovePIDColour.isSelected())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
refresh();\r
}\r
\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
refresh();\r
}\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth());\r
+ sg.getSequences(true),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
groupName.setText(reply);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
-\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
- sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
}\r
\r
s = s.replace(' ', '_');\r
- sequence.getDatasetSequence().setName(s);\r
sequence.setName(s);\r
ap.repaint();\r
}\r
\r
- sequence.getDatasetSequence().setDescription(description.getText());\r
sequence.setDescription(description.getText());\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
\r
/**\r
ap.av.firePropertyChange("alignment", null,\r
ap.av.getAlignment().getSequences());\r
\r
-\r
- // PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
}\r
}\r
\r
public void outputText_actionPerformed(ActionEvent e)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(null);\r
Desktop.addInternalFrame(cap,\r
"Alignment output - " + e.getActionCommand(), 600,\r
500);\r
ap.highlightSearchResults(null);\r
}\r
}\r
+\r
+ public void textColour_actionPerformed(ActionEvent e)\r
+ {\r
+ final SequenceGroup sg = getGroup();\r
+\r
+ int original1 = sg.textColour.getRGB();\r
+ int original2 = sg.textColour2.getRGB();\r
+ int thresh = sg.thresholdTextColour;\r
+ final JSlider slider = new JSlider(0, 750,sg.thresholdTextColour);\r
+ final JButton col1 = new JButton("DARK");\r
+ col1.setBackground(sg.textColour);\r
+ col1.setForeground(sg.textColour);\r
+ final JButton col2 = new JButton("LIGHT");\r
+ col2.setBackground(sg.textColour2);\r
+ col2.setForeground(sg.textColour2);\r
+ final JPanel bigpanel = new JPanel(new BorderLayout());\r
+ JPanel panel = new JPanel();\r
+ bigpanel.add(panel, BorderLayout.CENTER);\r
+ bigpanel.add(new JLabel(\r
+ "<html><i>Select a dark and light text colour, then set the threshold to"\r
+ +"<br>switch between colours, based on background colour</i></html>"),\r
+ BorderLayout.NORTH);\r
+ panel.add(col1);\r
+ panel.add(slider);\r
+ panel.add(col2);\r
+\r
+ col1.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ Color col = JColorChooser.showDialog(bigpanel,\r
+ "Select Colour for Text",\r
+ sg.textColour);\r
+ if (col != null)\r
+ {\r
+ sg.textColour = col;\r
+ col1.setBackground(col);\r
+ col1.setForeground(col);\r
+ }\r
+ ap.repaint();\r
+ }\r
+ });\r
+\r
+ col2.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ Color col = JColorChooser.showDialog(bigpanel,\r
+ "Select Colour for Text",\r
+ sg.textColour);\r
+ if (col != null)\r
+ {\r
+ sg.textColour2 = col;\r
+ col2.setBackground(col);\r
+ col2.setForeground(col);\r
+ }\r
+ ap.repaint();\r
+ }\r
+ });\r
+\r
+\r
+ slider.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ sg.thresholdTextColour = slider.getValue();\r
+ ap.repaint();\r
+ }\r
+ });\r
+\r
+ int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
+ bigpanel,\r
+ "Adjust Foreground Text Colour Threshold",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null, null);\r
+\r
+ if(reply==JOptionPane.CANCEL_OPTION)\r
+ {\r
+ sg.textColour = new Color(original1);\r
+ sg.textColour2 = new Color(original2);\r
+ sg.thresholdTextColour = thresh;\r
+ }\r
+ }\r
}\r