JAL-2416 SeqSpace PCA now provided as an alternative score matrix rather

than an alternative method (+code tidying)

diff --git a/resources/scoreModel/seqspace.scm b/resources/scoreModel/seqspace.scm
new file mode 100644 (file)
index 0000000..a8bdc06
--- /dev/null
+++ b/resources/scoreModel/seqspace.scm
@@ -0,0 +1,31 @@
+ScoreMatrix Identity (SeqSpace)
+ARNDCQEGHILKMFPSTWYVBZX
+#
+# The identity substitution matrix, that gives the SeqSpace PCA calculation as in Jalview 2.10.1
+#
+# 
+#      A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X
+#
+A      1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+R      0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       
+N      0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+D      0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       
+C      0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+Q      0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+E      0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+G      0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+H      0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0       0
+I      0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0       0
+L      0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0       0
+K      0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0       0
+M      0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0       0
+F      0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0
+P      0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0
+S      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0
+T      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0
+W      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0       0
+Y      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0       0
+V      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0       0
+B      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0       0
+Z      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1       0
+X      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       1

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 0bc6cac..774641c 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -25,6 +25,7 @@ import jalview.util.MessageManager;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.FlowLayout;
+import java.awt.Font;
 import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -43,54 +44,20 @@ import javax.swing.event.MenuListener;
 
 public class GPCAPanel extends JInternalFrame
 {
-  JPanel jPanel2 = new JPanel();
+  private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
 
-  JLabel jLabel1 = new JLabel();
+  protected JComboBox<String> xCombobox = new JComboBox<String>();
 
-  JLabel jLabel2 = new JLabel();
+  protected JComboBox<String> yCombobox = new JComboBox<String>();
 
-  JLabel jLabel3 = new JLabel();
-
-  protected JComboBox xCombobox = new JComboBox();
-
-  protected JComboBox yCombobox = new JComboBox();
-
-  protected JComboBox zCombobox = new JComboBox();
-
-  protected JButton resetButton = new JButton();
-
-  FlowLayout flowLayout1 = new FlowLayout();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  JMenuBar jMenuBar1 = new JMenuBar();
-
-  JMenu fileMenu = new JMenu();
-
-  JMenu saveMenu = new JMenu();
+  protected JComboBox<String> zCombobox = new JComboBox<String>();
 
   protected JMenu scoreMatrixMenu = new JMenu();
 
-  JMenuItem eps = new JMenuItem();
-
-  JMenuItem png = new JMenuItem();
-
-  JMenuItem print = new JMenuItem();
-
-  JMenuItem outputValues = new JMenuItem();
-
-  JMenuItem outputPoints = new JMenuItem();
-
-  JMenuItem outputProjPoints = new JMenuItem();
-
   protected JMenu viewMenu = new JMenu();
 
   protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
 
-  JMenuItem bgcolour = new JMenuItem();
-
-  JMenuItem originalSeqData = new JMenuItem();
-
   protected JMenu associateViewsMenu = new JMenu();
 
   protected JMenu calcSettings = new JMenu();
@@ -103,8 +70,6 @@ public class GPCAPanel extends JInternalFrame
 
   protected JLabel statusBar = new JLabel();
 
-  protected GridLayout statusPanelLayout = new GridLayout();
-
   protected JPanel statusPanel = new JPanel();
 
   public GPCAPanel()
@@ -123,49 +88,55 @@ public class GPCAPanel extends JInternalFrame
       yCombobox.addItem("dim " + i);
       zCombobox.addItem("dim " + i);
     }
-
-    setJMenuBar(jMenuBar1);
   }
 
   private void jbInit() throws Exception
   {
-    this.getContentPane().setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    this.getContentPane().setLayout(new BorderLayout());
+    JPanel jPanel2 = new JPanel();
+    jPanel2.setLayout(new FlowLayout());
+    JLabel jLabel1 = new JLabel();
+    jLabel1.setFont(VERDANA_12);
     jLabel1.setText("x=");
-    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+    JLabel jLabel2 = new JLabel();
+    jLabel2.setFont(VERDANA_12);
     jLabel2.setText("y=");
-    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+    JLabel jLabel3 = new JLabel();
+    jLabel3.setFont(VERDANA_12);
     jLabel3.setText("z=");
     jPanel2.setBackground(Color.white);
     jPanel2.setBorder(null);
-    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    zCombobox.addActionListener(new java.awt.event.ActionListener()
+    zCombobox.setFont(VERDANA_12);
+    zCombobox.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         zCombobox_actionPerformed(e);
       }
     });
-    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    yCombobox.addActionListener(new java.awt.event.ActionListener()
+    yCombobox.setFont(VERDANA_12);
+    yCombobox.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         yCombobox_actionPerformed(e);
       }
     });
-    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    xCombobox.addActionListener(new java.awt.event.ActionListener()
+    xCombobox.setFont(VERDANA_12);
+    xCombobox.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         xCombobox_actionPerformed(e);
       }
     });
-    resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
+    JButton resetButton = new JButton();
+    resetButton.setFont(VERDANA_12);
     resetButton.setText(MessageManager.getString("action.reset"));
-    resetButton.addActionListener(new java.awt.event.ActionListener()
+    resetButton.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -173,51 +144,64 @@ public class GPCAPanel extends JInternalFrame
         resetButton_actionPerformed(e);
       }
     });
+    JMenu fileMenu = new JMenu();
     fileMenu.setText(MessageManager.getString("action.file"));
+    JMenu saveMenu = new JMenu();
     saveMenu.setText(MessageManager.getString("action.save_as"));
-    eps.setText("EPS");
+    JMenuItem eps = new JMenuItem("EPS");
     eps.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         eps_actionPerformed(e);
       }
     });
-    png.setText("PNG");
+    JMenuItem png = new JMenuItem("PNG");
     png.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         png_actionPerformed(e);
       }
     });
+    JMenuItem outputValues = new JMenuItem();
     outputValues.setText(MessageManager.getString("label.output_values"));
     outputValues.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         outputValues_actionPerformed(e);
       }
     });
+    JMenuItem outputPoints = new JMenuItem();
     outputPoints.setText(MessageManager.getString("label.output_points"));
     outputPoints.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         outputPoints_actionPerformed(e);
       }
     });
+    JMenuItem outputProjPoints = new JMenuItem();
     outputProjPoints.setText(MessageManager
             .getString("label.output_transformed_points"));
     outputProjPoints.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         outputProjPoints_actionPerformed(e);
       }
     });
+    JMenuItem print = new JMenuItem();
+    print.setText(MessageManager.getString("action.print"));
     print.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         print_actionPerformed(e);
@@ -226,15 +210,18 @@ public class GPCAPanel extends JInternalFrame
     viewMenu.setText(MessageManager.getString("action.view"));
     viewMenu.addMenuListener(new MenuListener()
     {
+      @Override
       public void menuSelected(MenuEvent e)
       {
         viewMenu_menuSelected();
       }
 
+      @Override
       public void menuDeselected(MenuEvent e)
       {
       }
 
+      @Override
       public void menuCanceled(MenuEvent e)
       {
       }
@@ -243,15 +230,18 @@ public class GPCAPanel extends JInternalFrame
             .getString("label.select_score_model"));
     scoreMatrixMenu.addMenuListener(new MenuListener()
     {
+      @Override
       public void menuSelected(MenuEvent e)
       {
         scoreMatrix_menuSelected();
       }
 
+      @Override
       public void menuDeselected(MenuEvent e)
       {
       }
 
+      @Override
       public void menuCanceled(MenuEvent e)
       {
       }
@@ -259,23 +249,27 @@ public class GPCAPanel extends JInternalFrame
     showLabels.setText(MessageManager.getString("label.show_labels"));
     showLabels.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showLabels_actionPerformed(e);
       }
     });
-    print.setText(MessageManager.getString("action.print"));
+    JMenuItem bgcolour = new JMenuItem();
     bgcolour.setText(MessageManager.getString("action.background_colour"));
     bgcolour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         bgcolour_actionPerformed(e);
       }
     });
+    JMenuItem originalSeqData = new JMenuItem();
     originalSeqData.setText(MessageManager.getString("label.input_data"));
     originalSeqData.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         originalSeqData_actionPerformed(e);
@@ -315,12 +309,12 @@ public class GPCAPanel extends JInternalFrame
         jvVersionSetting_actionPerfomed(arg0);
       }
     });
-    calcSettings.add(jvVersionSetting);
+    // calcSettings.add(jvVersionSetting); // todo remove? JAL-2416
     calcSettings.add(nuclSetting);
     calcSettings.add(protSetting);
     calcSettings.add(scoreMatrixMenu);
-    statusPanel.setLayout(statusPanelLayout);
-    statusBar.setFont(new java.awt.Font("Verdana", 0, 12));
+    statusPanel.setLayout(new GridLayout());
+    statusBar.setFont(VERDANA_12);
     // statusPanel.setBackground(Color.lightGray);
     // statusBar.setBackground(Color.lightGray);
     // statusPanel.add(statusBar, null);
@@ -335,9 +329,12 @@ public class GPCAPanel extends JInternalFrame
     jPanel2.add(jLabel3, null);
     jPanel2.add(zCombobox, null);
     jPanel2.add(resetButton, null);
+
+    JMenuBar jMenuBar1 = new JMenuBar();
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(viewMenu);
     jMenuBar1.add(calcSettings);
+    setJMenuBar(jMenuBar1);
     fileMenu.add(saveMenu);
     fileMenu.add(outputValues);
     fileMenu.add(print);