From a7eff74f18498e209c422b7cd090e294b36806dc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 19 May 2005 17:59:20 +0000
Subject: [PATCH] A Flauss reccommends
---
src/jalview/jbgui/GAlignFrame.java | 77 ++++++-----
src/jalview/jbgui/GDesktop.java | 56 +++++++-
src/jalview/jbgui/GFinder.java | 244 +++++++++++++++++------------------
src/jalview/jbgui/GPreferences.java | 7 +-
src/jalview/jbgui/GTreePanel.java | 2 +-
5 files changed, 224 insertions(+), 162 deletions(-)
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 53c0bf6..7370995 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -14,6 +14,8 @@ import java.awt.*;
import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeProperty;
+import javax.swing.event.AncestorListener;
+import javax.swing.event.AncestorEvent;
public class GAlignFrame extends JInternalFrame
{
@@ -45,7 +47,7 @@ public class GAlignFrame extends JInternalFrame
protected JMenuItem clustalAlignMenuItem = new JMenuItem();
BorderLayout borderLayout1 = new BorderLayout();
public JLabel statusBar = new JLabel();
- protected JMenu saveAlignmentMenu = new JMenu();
+ protected JMenuItem saveAlignmentMenu = new JMenuItem();
protected JMenu outputTextboxMenu = new JMenu();
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
@@ -96,10 +98,10 @@ public class GAlignFrame extends JInternalFrame
JMenuItem modifyPID = new JMenuItem();
JMenuItem modifyConservation = new JMenuItem();
protected JMenu sortByTreeMenu = new JMenu();
- JMenu jMenu2 = new JMenu();
JMenu sort = new JMenu();
JMenu calculate = new JMenu();
JMenuItem msaAlignMenuItem = new JMenuItem();
+ JMenu jMenu2 = new JMenu();
public GAlignFrame()
{
ButtonGroup colours = new ButtonGroup();
@@ -148,16 +150,6 @@ public class GAlignFrame extends JInternalFrame
// dynamically fill save as menu with available formats
for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
- saveAlignmentMenu.add( item );
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- saveAs_actionPerformed(e);
- }
- });
-
- item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -181,7 +173,14 @@ public class GAlignFrame extends JInternalFrame
fileMenu.setMnemonic('F');
fileMenu.setText("File");
saveAlignmentMenu.setMnemonic('L');
- saveAlignmentMenu.setText("Save");
+ saveAlignmentMenu.setText("Save As");
+ saveAlignmentMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveAlignmentMenu_actionPerformed(e);
+ }
+ });
closeMenuItem.setMnemonic('C');
closeMenuItem.setText("Close");
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -275,7 +274,7 @@ public class GAlignFrame extends JInternalFrame
viewTextMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("Pairwise Identity");
+ sortPairwiseMenuItem.setText("By Pairwise Identity");
sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -283,7 +282,7 @@ public class GAlignFrame extends JInternalFrame
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("ID");
+ sortIDMenuItem.setText("By ID");
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -291,7 +290,7 @@ public class GAlignFrame extends JInternalFrame
sortIDMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("Group");
+ sortGroupMenuItem.setText("By Group");
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -349,6 +348,21 @@ public class GAlignFrame extends JInternalFrame
});
this.getContentPane().setLayout(borderLayout1);
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ alignFrameMenuBar.addAncestorListener(new AncestorListener()
+ {
+ public void ancestorAdded(AncestorEvent event)
+ {
+ alignFrameMenuBar_ancestorAdded(event);
+ }
+
+ public void ancestorRemoved(AncestorEvent event)
+ {
+ }
+
+ public void ancestorMoved(AncestorEvent event)
+ {
+ }
+ });
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
@@ -569,7 +583,7 @@ public class GAlignFrame extends JInternalFrame
});
searchMenu.setText("Search");
- abovePIDThreshold.setText("Above Identity threshold");
+ abovePIDThreshold.setText("Above Identity Threshold");
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
abovePIDThreshold_actionPerformed(e);
@@ -666,7 +680,7 @@ public class GAlignFrame extends JInternalFrame
createPNG_actionPerformed(e);
}
});
- createPNG.setActionCommand("Save as PNG Image");
+ createPNG.setActionCommand("Save As PNG Image");
createPNG.setText("PNG");
font.setText("Font...");
font.addActionListener(new java.awt.event.ActionListener()
@@ -753,8 +767,7 @@ public class GAlignFrame extends JInternalFrame
modifyConservation_actionPerformed(e);
}
});
- sortByTreeMenu.setText("Tree Order");
- jMenu2.setText("Save as");
+ sortByTreeMenu.setText("By Tree Order");
sort.setText("Sort");
calculate.setText("Calculate Tree");
msaAlignMenuItem.setText("Muscle Alignment...");
@@ -763,6 +776,7 @@ public class GAlignFrame extends JInternalFrame
msaAlignMenuItem_actionPerformed(e);
}
});
+ jMenu2.setText("Export");
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(searchMenu);
@@ -844,22 +858,17 @@ public class GAlignFrame extends JInternalFrame
this.getContentPane().add(statusBar, BorderLayout.SOUTH);
jMenu1.add(pasteNew);
jMenu1.add(pasteThis);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
sort.add(sortIDMenuItem);
- sort.add(sortGroupMenuItem);
sort.add(sortByTreeMenu);
+ sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
calculate.add(averageDistanceTreeMenuItem);
calculate.add(neighbourTreeMenuItem);
calculate.add(avDistanceTreeBlosumMenuItem);
calculate.add(njTreeBlosumMenuItem);
- }
-
- protected void saveAs_actionPerformed(ActionEvent e)
- {
-
+ jMenu2.add(htmlMenuItem);
+ jMenu2.add(epsFile);
+ jMenu2.add(createPNG);
}
protected void outputText_actionPerformed(ActionEvent e)
@@ -1218,4 +1227,14 @@ public class GAlignFrame extends JInternalFrame
}
+ public void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+ {
+
+ }
+
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ {
+
+ }
+
}
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index c0b247b..1be96fb 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -28,6 +28,9 @@ public class GDesktop extends JFrame
protected static JMenu windowMenu = new JMenu();
JMenu toolsMenu = new JMenu();
JMenuItem preferences = new JMenuItem();
+ JMenuItem saveState = new JMenuItem();
+ JMenuItem loadState = new JMenuItem();
+ JMenu jMenu1 = new JMenu();
public GDesktop()
{
try
@@ -47,7 +50,7 @@ public class GDesktop extends JFrame
FileMenu.setText("File");
HelpMenu.setText("Help");
inputLocalFileMenuItem.setMnemonic('L');
- inputLocalFileMenuItem.setText("Input Alignment From Local File");
+ inputLocalFileMenuItem.setText("Local File");
inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -56,7 +59,7 @@ public class GDesktop extends JFrame
}
});
inputURLMenuItem.setMnemonic('U');
- inputURLMenuItem.setText("Input Alignment From URL");
+ inputURLMenuItem.setText("From URL");
inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -64,8 +67,8 @@ public class GDesktop extends JFrame
inputURLMenuItem_actionPerformed(e);
}
});
- inputTextboxMenuItem.setMnemonic('T');
- inputTextboxMenuItem.setText("Input Alignment via Textbox");
+ inputTextboxMenuItem.setMnemonic('C');
+ inputTextboxMenuItem.setText("Cut & Paste Textbox");
inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -110,19 +113,43 @@ public class GDesktop extends JFrame
}
});
toolsMenu.setText("Tools");
+ saveState.setMnemonic('S');
+ saveState.setText("Save Project");
+ saveState.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(e);
+ }
+ });
+ loadState.setMnemonic('L');
+ loadState.setText("Load Project");
+ loadState.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ loadState_actionPerformed(e);
+ }
+ });
+ jMenu1.setMnemonic('I');
+ jMenu1.setText("Input Alignment");
DesktopMenubar.add(FileMenu);
DesktopMenubar.add(toolsMenu);
DesktopMenubar.add(HelpMenu);
DesktopMenubar.add(windowMenu);
FileMenu.addSeparator();
- FileMenu.add(inputLocalFileMenuItem);
- FileMenu.add(inputURLMenuItem);
- FileMenu.add(inputTextboxMenuItem);
+ FileMenu.add(jMenu1);
+ FileMenu.addSeparator();
+ FileMenu.add(saveState);
+ FileMenu.add(loadState);
FileMenu.addSeparator();
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
HelpMenu.add(documentationMenuItem);
toolsMenu.add(preferences);
+ jMenu1.add(inputLocalFileMenuItem);
+ jMenu1.add(inputURLMenuItem);
+ jMenu1.add(inputTextboxMenuItem);
}
@@ -153,4 +180,19 @@ public class GDesktop extends JFrame
{
}
+
+ public void saveState_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void loadState_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void loadJalviewAlign_actionPerformed(ActionEvent e)
+ {
+
+ }
}
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index cc202bc..3720d67 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,122 +1,122 @@
-package jalview.jbgui;
-
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-
-
-public class GFinder extends JPanel
-{
- JLabel jLabel1 = new JLabel();
- protected JTextField textfield = new JTextField();
- protected JButton findAll = new JButton();
- protected JButton findNext = new JButton();
- JPanel jPanel1 = new JPanel();
- GridLayout gridLayout1 = new GridLayout();
- protected JButton createNewGroup = new JButton();
-
- public GFinder()
- {
- try
- {
- jbInit();
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- }
- private void jbInit() throws Exception
- {
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText("Find");
- jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
- this.setLayout(null);
- textfield.setFont(new java.awt.Font("Verdana", 0, 12));
- textfield.setText("");
- textfield.setBounds(new Rectangle(40, 27, 133, 21));
- textfield.addKeyListener(new java.awt.event.KeyAdapter()
- {
- public void keyTyped(KeyEvent e)
- {
- textfield_keyTyped(e);
- }
- });
- textfield.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- textfield_actionPerformed(e);
- }
- });
- findAll.setFont(new java.awt.Font("Verdana", 0, 12));
- findAll.setText("Find all");
- findAll.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- findAll_actionPerformed(e);
- }
- });
- findNext.setEnabled(false);
- findNext.setFont(new java.awt.Font("Verdana", 0, 12));
- findNext.setText("Find Next");
- findNext.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- findNext_actionPerformed(e);
- }
- });
- jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
- jPanel1.setLayout(gridLayout1);
- gridLayout1.setHgap(0);
- gridLayout1.setRows(3);
- gridLayout1.setVgap(2);
- createNewGroup.setEnabled(false);
- createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
- createNewGroup.setToolTipText("");
- createNewGroup.setMargin(new Insets(0, 0, 0, 0));
- createNewGroup.setText("Create new group");
- createNewGroup.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- createNewGroup_actionPerformed(e);
- }
- });
- jPanel1.add(findNext, null);
- jPanel1.add(findAll, null);
- jPanel1.add(createNewGroup, null);
- this.add(textfield, null);
- this.add(jLabel1, null);
- this.add(jPanel1, null);
- }
-
- protected void findNext_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void findAll_actionPerformed(ActionEvent e)
- {
-
- }
-
-
- protected void textfield_actionPerformed(ActionEvent e)
- {
-
- }
-
- void textfield_keyTyped(KeyEvent e)
- {
- findNext.setEnabled(true);
- }
-
- public void createNewGroup_actionPerformed(ActionEvent e)
- {
-
- }
-
-}
+package jalview.jbgui;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.*;
+
+
+public class GFinder extends JPanel
+{
+ JLabel jLabel1 = new JLabel();
+ protected JTextField textfield = new JTextField();
+ protected JButton findAll = new JButton();
+ protected JButton findNext = new JButton();
+ JPanel jPanel1 = new JPanel();
+ GridLayout gridLayout1 = new GridLayout();
+ protected JButton createNewGroup = new JButton();
+
+ public GFinder()
+ {
+ try
+ {
+ jbInit();
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ private void jbInit() throws Exception
+ {
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+ jLabel1.setText("Find");
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
+ this.setLayout(null);
+ textfield.setFont(new java.awt.Font("Verdana", 0, 12));
+ textfield.setText("");
+ textfield.setBounds(new Rectangle(40, 27, 133, 21));
+ textfield.addKeyListener(new java.awt.event.KeyAdapter()
+ {
+ public void keyTyped(KeyEvent e)
+ {
+ textfield_keyTyped(e);
+ }
+ });
+ textfield.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textfield_actionPerformed(e);
+ }
+ });
+ findAll.setFont(new java.awt.Font("Verdana", 0, 12));
+ findAll.setText("Find all");
+ findAll.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ findAll_actionPerformed(e);
+ }
+ });
+ findNext.setEnabled(false);
+ findNext.setFont(new java.awt.Font("Verdana", 0, 12));
+ findNext.setText("Find Next");
+ findNext.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ findNext_actionPerformed(e);
+ }
+ });
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+ jPanel1.setLayout(gridLayout1);
+ gridLayout1.setHgap(0);
+ gridLayout1.setRows(3);
+ gridLayout1.setVgap(2);
+ createNewGroup.setEnabled(false);
+ createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
+ createNewGroup.setToolTipText("");
+ createNewGroup.setMargin(new Insets(0, 0, 0, 0));
+ createNewGroup.setText("Create new group");
+ createNewGroup.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createNewGroup_actionPerformed(e);
+ }
+ });
+ jPanel1.add(findNext, null);
+ jPanel1.add(findAll, null);
+ jPanel1.add(createNewGroup, null);
+ this.add(textfield, null);
+ this.add(jLabel1, null);
+ this.add(jPanel1, null);
+ }
+
+ protected void findNext_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void findAll_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void textfield_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ void textfield_keyTyped(KeyEvent e)
+ {
+ findNext.setEnabled(true);
+ }
+
+ public void createNewGroup_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+}
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 8f30fb3..a3091e4 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -57,10 +57,11 @@ public class GPreferences
fullID.setHorizontalTextPosition(SwingConstants.LEFT);
fullID.setText("Full Sequence ID");
fullID.setBounds(new Rectangle(9, 78, 129, 23));
+ fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText("Full Screen");
- fullScreen.setBounds(new Rectangle(31, 28, 107, 23));
+ fullScreen.setText("Maximise Window");
+ fullScreen.setBounds(new Rectangle(5, 29, 132, 23));
conservation.setEnabled(false);
conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
conservation.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -111,7 +112,6 @@ public class GPreferences
gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
gapSymbolCB.setBounds(new Rectangle(121, 140, 67, 21));
jPanel2.add(annotations);
- jPanel2.add(fullScreen);
jPanel2.add(conservation);
jPanel2.add(quality);
jPanel2.add(fullID);
@@ -124,6 +124,7 @@ public class GPreferences
jPanel2.add(fontSizeCB);
jPanel2.add(fontStyleCB);
jPanel2.add(identity);
+ jPanel2.add(fullScreen);
jPanel1.add(ok);
jPanel1.add(cancel);
this.add(visaulTab, java.awt.BorderLayout.CENTER);
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index fe1fe81..27b5c5c 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -41,7 +41,7 @@ public class GTreePanel extends JInternalFrame
this.setFont(new java.awt.Font("Verdana", 0, 12));
scrollPane.setOpaque(false);
jMenu1.setText("File");
- saveAsNewick.setText("Newick format");
+ saveAsNewick.setText("Newick Format");
saveAsNewick.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
--
1.7.10.2