From f588f27a1c31799c9245950ba349c5197afc3f1f Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 17 Feb 2017 13:31:49 +0000 Subject: [PATCH] JAL-2416 SeqSpace PCA now provided as an alternative score matrix rather than an alternative method (+code tidying) --- resources/scoreModel/seqspace.scm | 31 ++++++++++ src/jalview/jbgui/GPCAPanel.java | 119 ++++++++++++++++++------------------- 2 files changed, 89 insertions(+), 61 deletions(-) create mode 100644 resources/scoreModel/seqspace.scm diff --git a/resources/scoreModel/seqspace.scm b/resources/scoreModel/seqspace.scm new file mode 100644 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 --- 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 xCombobox = new JComboBox(); - JLabel jLabel2 = new JLabel(); + protected JComboBox yCombobox = new JComboBox(); - 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 zCombobox = new JComboBox(); 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); -- 1.7.10.2