X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=0368d2a8770e934428a251144fefee9fff219c06;hb=08044f16da407871ea84ccbfbc09e34cceb74080;hp=399fce8a68d719972e58ea4a825e6c1f6c9ad945;hpb=e808c2394befe0655fc9dbd9928160cf4c3b1aa3;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 399fce8..0368d2a 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -26,10 +26,10 @@ import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
+
 
 public class PCAPanel
-    extends GPCAPanel implements Runnable
+    extends Frame implements Runnable
 {
   PCA pca;
   int top;
@@ -40,6 +40,21 @@ public class PCAPanel
 
   public PCAPanel(AlignViewport av)
   {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    for (int i = 1; i < 8; i++)
+    {
+      xCombobox.addItem("dim " + i);
+      yCombobox.addItem("dim " + i);
+      zCombobox.addItem("dim " + i);
+    }
 
     this.av = av;
     if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() > 3)
@@ -58,8 +73,14 @@ public class PCAPanel
         seqs[i] = av.getAlignment().getSequenceAt(i);
       }
     }
+
     rc = new RotatableCanvas(av);
     add(rc, BorderLayout.CENTER);
+
+    jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
+                                       400, 400);
+
+
     Thread worker = new Thread(this);
     worker.start();
   }
@@ -109,6 +130,7 @@ public class PCAPanel
               rc.setPoints(points, pca.getM().rows);
               rc.repaint();
               seqs = null;
+              this.repaint();
   }
 
   void doDimensionChange()
@@ -149,4 +171,102 @@ public class PCAPanel
     doDimensionChange();
   }
 
+  public void values_actionPerformed(ActionEvent actionEvent)
+  {
+
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
+
+      cap.setText(pca.getDetails());
+  }
+
+  public void labels_itemStateChanged(ItemEvent itemEvent)
+  {
+    rc.showLabels( labels.getState() );
+  }
+  Panel jPanel2 = new Panel();
+  Label jLabel1 = new Label();
+  Label jLabel2 = new Label();
+  Label jLabel3 = new Label();
+  protected Choice xCombobox = new Choice();
+  protected Choice yCombobox = new Choice();
+  protected Choice zCombobox = new Choice();
+  FlowLayout flowLayout1 = new FlowLayout();
+  BorderLayout borderLayout1 = new BorderLayout();
+  MenuBar menuBar1 = new MenuBar();
+  Menu menu1 = new Menu();
+  Menu menu2 = new Menu();
+  protected CheckboxMenuItem labels = new CheckboxMenuItem();
+  MenuItem values = new MenuItem();
+
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("x=");
+    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel2.setText("y=");
+    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel3.setText("z=");
+    jPanel2.setBackground(Color.white);
+    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    zCombobox.addItemListener(new java.awt.event.ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        zCombobox_actionPerformed(null);
+      }
+    });
+    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    yCombobox.addItemListener(new java.awt.event.ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        yCombobox_actionPerformed(null);
+      }
+    });
+    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    xCombobox.addItemListener(new java.awt.event.ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        xCombobox_actionPerformed(null);
+      }
+    });
+    this.setMenuBar(menuBar1);
+    menu1.setLabel("File");
+    menu2.setLabel("View");
+    labels.setLabel("Labels");
+    labels.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent itemEvent)
+      {
+        labels_itemStateChanged(itemEvent);
+      }
+    });
+    values.setLabel("Output Values...");
+    values.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        values_actionPerformed(actionEvent);
+      }
+    });
+    this.add(jPanel2, BorderLayout.SOUTH);
+    jPanel2.add(jLabel1, null);
+    jPanel2.add(xCombobox, null);
+    jPanel2.add(jLabel2, null);
+    jPanel2.add(yCombobox, null);
+    jPanel2.add(jLabel3, null);
+    jPanel2.add(zCombobox, null);
+    menuBar1.add(menu1);
+    menuBar1.add(menu2);
+    menu2.add(labels);
+    menu1.add(values);
+  }
+
 }