Feature Groups added

[jalview.git] / src / jalview / appletgui / PCAPanel.java

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index f470ffc..a75de06 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -26,10 +26,10 @@ import java.awt.event.*;
 \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
@@ -38,20 +38,34 @@ public class PCAPanel
   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() > 3)\r
     {\r
       seqs = new Sequence[av.getSelectionGroup().getSize()];\r
-      for (int i = 0; i < s.length; i++)\r
+      for (int i = 0; i < av.getSelectionGroup().getSize(); 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
@@ -59,8 +73,14 @@ public class PCAPanel
         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
@@ -110,6 +130,7 @@ public class PCAPanel
               rc.setPoints(points, pca.getM().rows);\r
               rc.repaint();\r
               seqs = null;\r
+              this.repaint();\r
   }\r
 \r
   void doDimensionChange()\r
@@ -135,19 +156,103 @@ public class PCAPanel
     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