\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
+\r
\r
public class PCAPanel\r
- extends GPCAPanel implements Runnable\r
+ extends Frame implements Runnable, ActionListener, ItemListener\r
{\r
PCA pca;\r
int top;\r
SequenceI [] seqs;\r
\r
\r
- public PCAPanel(AlignViewport av, SequenceI[] s)\r
+ public PCAPanel(AlignViewport av)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ for (int i = 1; i < 8; i++)\r
+ {\r
+ xCombobox.addItem("dim " + i);\r
+ yCombobox.addItem("dim " + i);\r
+ zCombobox.addItem("dim " + i);\r
+ }\r
\r
this.av = av;\r
- if (av.getSelectionGroup().getSize() > 3)\r
+ if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize(false) > 3)\r
{\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
- for (int i = 0; i < s.length; i++)\r
+ seqs = new Sequence[av.getSelectionGroup().getSize(false)];\r
+ for (int i = 0; i < av.getSelectionGroup().getSize(false); i++)\r
{\r
seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
}\r
}\r
-\r
- if (seqs == null)\r
+ else\r
{\r
seqs = new Sequence[av.getAlignment().getHeight()];\r
for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
seqs[i] = av.getAlignment().getSequenceAt(i);\r
}\r
}\r
+\r
rc = new RotatableCanvas(av);\r
add(rc, BorderLayout.CENTER);\r
+\r
+ jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",\r
+ 400, 400);\r
+\r
+\r
Thread worker = new Thread(this);\r
worker.start();\r
}\r
rc.setPoints(points, pca.getM().rows);\r
rc.repaint();\r
seqs = null;\r
+ this.repaint();\r
}\r
\r
void doDimensionChange()\r
rc.paint(rc.getGraphics());\r
}\r
\r
- protected void xCombobox_actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ values_actionPerformed();\r
+ }\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==xCombobox)\r
+ xCombobox_actionPerformed();\r
+ else if(evt.getSource()==yCombobox)\r
+ yCombobox_actionPerformed();\r
+ else if(evt.getSource()==zCombobox)\r
+ zCombobox_actionPerformed();\r
+ }\r
+\r
+\r
+ protected void xCombobox_actionPerformed()\r
{\r
doDimensionChange();\r
}\r
\r
- protected void yCombobox_actionPerformed(ActionEvent e)\r
+ protected void yCombobox_actionPerformed()\r
{\r
doDimensionChange();\r
}\r
\r
- protected void zCombobox_actionPerformed(ActionEvent e)\r
+ protected void zCombobox_actionPerformed()\r
{\r
doDimensionChange();\r
}\r
\r
+ public void values_actionPerformed()\r
+ {\r
+\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);\r
+\r
+ cap.setText(pca.getDetails());\r
+ }\r
+\r
+ public void labels_itemStateChanged(ItemEvent itemEvent)\r
+ {\r
+ rc.showLabels( labels.getState() );\r
+ }\r
+ Panel jPanel2 = new Panel();\r
+ Label jLabel1 = new Label();\r
+ Label jLabel2 = new Label();\r
+ Label jLabel3 = new Label();\r
+ protected Choice xCombobox = new Choice();\r
+ protected Choice yCombobox = new Choice();\r
+ protected Choice zCombobox = new Choice();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ MenuBar menuBar1 = new MenuBar();\r
+ Menu menu1 = new Menu();\r
+ Menu menu2 = new Menu();\r
+ protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
+ MenuItem values = new MenuItem();\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ this.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("x=");\r
+ jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel2.setText("y=");\r
+ jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel3.setText("z=");\r
+ jPanel2.setBackground(Color.white);\r
+ zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ zCombobox.addItemListener(this);\r
+ yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ yCombobox.addItemListener(this);\r
+ xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ xCombobox.addItemListener(this);\r
+ this.setMenuBar(menuBar1);\r
+ menu1.setLabel("File");\r
+ menu2.setLabel("View");\r
+ labels.setLabel("Labels");\r
+ labels.addItemListener(this);\r
+ values.setLabel("Output Values...");\r
+ values.addActionListener(this);\r
+ this.add(jPanel2, BorderLayout.SOUTH);\r
+ jPanel2.add(jLabel1, null);\r
+ jPanel2.add(xCombobox, null);\r
+ jPanel2.add(jLabel2, null);\r
+ jPanel2.add(yCombobox, null);\r
+ jPanel2.add(jLabel3, null);\r
+ jPanel2.add(zCombobox, null);\r
+ menuBar1.add(menu1);\r
+ menuBar1.add(menu2);\r
+ menu2.add(labels);\r
+ menu1.add(values);\r
+ }\r
+\r
}\r