X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=a75de066eaee9a93d56416be9c563a12f32768d0;hb=59183747dbffe3ab6b141c5440d2f70799ae360b;hp=f470ffc445b9eacd95e80f774bdda7d5a05684eb;hpb=8c2ee75d86492f03e4c01404855f9ad2dd305719;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index f470ffc..a75de06 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, ActionListener, ItemListener
 {
   PCA pca;
   int top;
@@ -38,20 +38,34 @@ public class PCAPanel
   SequenceI [] seqs;
 
 
-  public PCAPanel(AlignViewport av, SequenceI[] s)
+  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().getSize() > 3)
+    if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() > 3)
     {
       seqs = new Sequence[av.getSelectionGroup().getSize()];
-      for (int i = 0; i < s.length; i++)
+      for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
       {
         seqs[i] = av.getSelectionGroup().getSequenceAt(i);
       }
     }
-
-    if (seqs == null)
+    else
     {
       seqs = new Sequence[av.getAlignment().getHeight()];
       for (int i = 0; i < av.getAlignment().getHeight(); i++)
@@ -59,8 +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();
   }
@@ -110,6 +130,7 @@ public class PCAPanel
               rc.setPoints(points, pca.getM().rows);
               rc.repaint();
               seqs = null;
+              this.repaint();
   }
 
   void doDimensionChange()
@@ -135,19 +156,103 @@ public class PCAPanel
     rc.paint(rc.getGraphics());
   }
 
-  protected void xCombobox_actionPerformed(ActionEvent e)
+  public void actionPerformed(ActionEvent evt)
+  {
+    values_actionPerformed();
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if(evt.getSource()==xCombobox)
+      xCombobox_actionPerformed();
+    else if(evt.getSource()==yCombobox)
+      yCombobox_actionPerformed();
+    else if(evt.getSource()==zCombobox)
+      zCombobox_actionPerformed();
+  }
+
+
+  protected void xCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
-  protected void yCombobox_actionPerformed(ActionEvent e)
+  protected void yCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
-  protected void zCombobox_actionPerformed(ActionEvent e)
+  protected void zCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
+  public void values_actionPerformed()
+  {
+
+    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(this);
+    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    yCombobox.addItemListener(this);
+    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    xCombobox.addItemListener(this);
+    this.setMenuBar(menuBar1);
+    menu1.setLabel("File");
+    menu2.setLabel("View");
+    labels.setLabel("Labels");
+    labels.addItemListener(this);
+    values.setLabel("Output Values...");
+    values.addActionListener(this);
+    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);
+  }
+
 }