Merge develop to Release_2_8_3_Branch

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 3483cc4..2674617 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,19 +20,40 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
 import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.PCAModel;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+import java.util.Hashtable;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+
 /**
  * DOCUMENT ME!
  * 
@@ -47,7 +68,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   AlignmentPanel ap;
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   PCAModel pcaModel;
 
@@ -135,9 +156,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              if (!pcaModel.getScore_matrix().equals((String) sm))
+              if (!pcaModel.getScore_matrix().equals(sm))
               {
-                pcaModel.setScore_matrix((String) sm);
+                pcaModel.setScore_matrix(sm);
                 Thread worker = new Thread(us);
                 worker.start();
               }
@@ -445,7 +466,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public void eps_actionPerformed(ActionEvent e)
   {
-    makePCAImage(jalview.util.ImageMaker.EPS);
+    makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
   }
 
   /**
@@ -456,27 +477,36 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public void png_actionPerformed(ActionEvent e)
   {
-    makePCAImage(jalview.util.ImageMaker.PNG);
+    makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
   }
 
-  void makePCAImage(int type)
+  void makePCAImage(jalview.util.ImageMaker.TYPE type)
   {
     int width = rc.getWidth();
     int height = rc.getHeight();
 
     jalview.util.ImageMaker im;
 
-    if (type == jalview.util.ImageMaker.PNG)
+    if (type == jalview.util.ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.PNG,
               "Make PNG image from PCA", width, height, null, null);
     }
-    else
+    else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.EPS,
               "Make EPS file from PCA", width, height, null,
               this.getTitle());
     }
+    else
+    {
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+              width, height, null, this.getTitle());
+
+    }
 
     if (im.getGraphics() != null)
     {