X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=71891aaef54a0baa6017984a45d965aaaac084a6;hb=f85c8c88d6947b9f290409f1271429144df2c120;hp=d1005c2eb2a49a2b5cf1a555e11f0b03f8928586;hpb=e5c2e37b24f09c90f2f7c748f6be10ce025da261;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index d1005c2..71891aa 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -28,7 +28,12 @@ import java.awt.*;
 import java.awt.event.*;
 
 import java.util.*;
-import javax.swing.JOptionPane;
+import javax.swing.*;
+import java.io.FileOutputStream;
+import org.jibble.epsgraphics.EpsGraphics2D;
+import javax.imageio.ImageIO;
+import java.awt.image.BufferedImage;
+import java.awt.print.*;
 
 
 /**
@@ -51,38 +56,78 @@ 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();
+    }
+
+
 
 
     /**
@@ -140,6 +185,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
                                               , "Out of memory",
                                               JOptionPane.WARNING_MESSAGE);
         System.out.println("PCAPanel: "+er);
+        System.gc();
 
       }
 
@@ -201,4 +247,204 @@ 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)
+    {
+      boolean accurateText = true;
+
+      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+          "Prompt each time");
+
+  // If we need to prompt, and if the GUI is visible then
+  // Prompt for EPS rendering style
+      if (renderStyle.equalsIgnoreCase("Prompt each time")
+          && !
+          (System.getProperty("java.awt.headless") != null
+           && System.getProperty("java.awt.headless").equals("true")))
+      {
+        EPSOptions eps = new EPSOptions();
+        renderStyle = eps.getValue();
+
+        if (renderStyle == null || eps.cancelled)
+          return;
+
+      }
+
+      if (renderStyle.equalsIgnoreCase("text"))
+      {
+        accurateText = false;
+      }
+
+      int width = rc.getWidth();
+      int height = rc.getHeight();
+
+      try
+      {
+        jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+            jalview.bin.Cache.getProperty(
+                "LAST_DIRECTORY"), new String[]
+            {"eps"},
+            new String[]
+            {"Encapsulated Postscript"},
+            "Encapsulated Postscript");
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle("Create EPS file from PCA");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        {
+          return;
+        }
+
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                      chooser.getSelectedFile().getParent());
+
+        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+        EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width,
+                                             height);
+
+        pg.setAccurateTextMode(accurateText);
+
+        rc.drawBackground(pg, rc.bgColour);
+        rc.drawScene(pg);
+
+        if (rc.drawAxes == true)
+        {
+          rc.drawAxes(pg);
+        }
+
+
+        pg.flush();
+        pg.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void png_actionPerformed(ActionEvent e)
+    {
+      int width = rc.getWidth();
+      int height = rc.getHeight();
+
+      try
+      {
+        jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+            jalview.bin.Cache.getProperty(
+                "LAST_DIRECTORY"), new String[]
+            {"png"},
+            new String[]
+            {"Portable network graphics"},
+            "Portable network graphics");
+
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle("Create PNG image from PCA");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        {
+          return;
+        }
+
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                      chooser.getSelectedFile().getParent());
+
+        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+        BufferedImage bi = new BufferedImage(width, height,
+                                             BufferedImage.TYPE_INT_RGB);
+        Graphics big = bi.getGraphics();
+
+        big.drawImage(rc.img,0,0,this);
+
+        ImageIO.write(bi, "png", out);
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+
+  }