X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=e680ddeab3fcb15970cd0817878fad8521c221a2;hb=refs%2Fheads%2FvamsasDemo;hp=7e893eb785d3015c5730ce73f5e155803484eed6;hpb=98eb909d0a4fe04ff6ad93f71086f1127fe4a530;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 7e893eb..e680dde 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -28,7 +28,8 @@ import java.awt.*;
 import java.awt.event.*;
 
 import java.util.*;
-import javax.swing.JOptionPane;
+import javax.swing.*;
+import java.awt.print.*;
 
 
 /**
@@ -51,38 +52,78 @@ public class PCAPanel extends GPCAPanel implements Runnable
      * @param av DOCUMENT ME!
      * @param s DOCUMENT ME!
      */
-    public PCAPanel(AlignViewport av, SequenceI[] s)
+    public PCAPanel(AlignViewport av)
     {
         this.av = av;
 
+        boolean sameLength = true;
+
         if ((av.getSelectionGroup() != null) &&
                 (av.getSelectionGroup().getSize() > 3))
         {
             seqs = new Sequence[av.getSelectionGroup().getSize()];
-
-            for (int i = 0; i < s.length; i++)
+            int length = av.getSelectionGroup().getSequenceAt(0).getLength();
+            for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
             {
                 seqs[i] = av.getSelectionGroup().getSequenceAt(i);
+                if(seqs[i].getLength()!=length)
+                {
+                  sameLength = false;
+                  break;
+                }
             }
         }
-
-        if (s == null)
+        else
         {
             seqs = new Sequence[av.getAlignment().getHeight()];
+            int length = av.alignment.getSequenceAt(0).getLength();
 
             for (int i = 0; i < av.getAlignment().getHeight(); i++)
             {
                 seqs[i] = av.getAlignment().getSequenceAt(i);
+                if(seqs[i].getLength()!=length)
+               {
+                 sameLength = false;
+                 break;
+               }
+
             }
         }
 
+        if (!sameLength)
+        {
+          JOptionPane.showMessageDialog(Desktop.desktop,
+                                        "The sequences must be aligned before calculating PCA.\n" +
+                                        "Try using the Pad function in the edit menu,\n" +
+                                        "or one of the multiple sequence alignment web services.",
+                                        "Sequences not aligned",
+                                        JOptionPane.WARNING_MESSAGE);
+
+          return;
+        }
+
+
+        Desktop.addInternalFrame(this, "Principal component analysis",
+                               400, 400);
+
 
         rc = new RotatableCanvas(av);
-        add(rc, BorderLayout.CENTER);
+        this.getContentPane().add(rc, BorderLayout.CENTER);
         Thread worker = new Thread(this);
         worker.start();
     }
 
+    public void bgcolour_actionPerformed(ActionEvent e)
+    {
+      Color col = JColorChooser.showDialog(this, "Select Background Colour",
+                rc.bgColour);
+
+      if(col!=null)
+        rc.bgColour = col;
+      rc.repaint();
+    }
+
+
 
 
     /**
@@ -202,4 +243,121 @@ public class PCAPanel extends GPCAPanel implements Runnable
     {
         doDimensionChange();
     }
-}
+
+
+    public void outputValues_actionPerformed(ActionEvent e)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      Desktop.addInternalFrame(cap, "PCA details", 500,
+                500);
+
+      cap.setText(pca.getDetails());
+     }
+
+    public void showLabels_actionPerformed(ActionEvent e)
+    {
+      rc.showLabels(showLabels.getState());
+    }
+
+    public void print_actionPerformed(ActionEvent e)
+    {
+      PCAPrinter printer = new PCAPrinter();
+      printer.start();
+    }
+
+
+    class PCAPrinter extends Thread implements Printable
+    {
+      public void run()
+      {
+        PrinterJob printJob = PrinterJob.getPrinterJob();
+        PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+
+        printJob.setPrintable(this, pf);
+
+        if (printJob.printDialog())
+        {
+          try
+          {
+            printJob.print();
+          }
+          catch (Exception PrintException)
+          {
+            PrintException.printStackTrace();
+          }
+        }
+      }
+
+      public int print(Graphics pg, PageFormat pf, int pi)
+          throws PrinterException
+      {
+        pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+
+        rc.drawBackground(pg, rc.bgColour);
+        rc.drawScene(pg);
+        if (rc.drawAxes == true)
+        {
+          rc.drawAxes(pg);
+        }
+
+        if (pi == 0)
+          return Printable.PAGE_EXISTS;
+        else
+          return Printable.NO_SUCH_PAGE;
+      }
+    }
+
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void eps_actionPerformed(ActionEvent e)
+    {
+      makePCAImage(jalview.util.ImageMaker.EPS);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void png_actionPerformed(ActionEvent e)
+    {
+       makePCAImage(jalview.util.ImageMaker.PNG);
+    }
+
+    void makePCAImage(int type)
+    {
+      int width = rc.getWidth();
+      int height = rc.getHeight();
+
+      jalview.util.ImageMaker im;
+
+      if(type == jalview.util.ImageMaker.PNG)
+        im = new jalview.util.ImageMaker(this,
+                                         jalview.util.ImageMaker.PNG,
+                                         "Make PNG image from PCA",
+                                         width, height,
+                                         null, null);
+        else
+          im = new jalview.util.ImageMaker(this,
+                                 jalview.util.ImageMaker.EPS,
+                                 "Make EPS file from PCA",
+                                 width, height,
+                                 null, this.getTitle());
+
+      if(im.getGraphics()!=null)
+       {
+         rc.drawBackground(im.getGraphics(), Color.black);
+         rc.drawScene(im.getGraphics());
+         if (rc.drawAxes == true)
+         {
+           rc.drawAxes(im.getGraphics());
+         }
+         im.writeImage();
+       }
+    }
+  }