X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=8a3c372dcd2a7b615a883a1dc1c6e8dfc55a7aa6;hb=62737d15c0edb48128eb9ac6fe7fa419ab984125;hp=398c5bed6d1ee1201fcfae0b5e65bc2e9792f068;hpb=a33d19728e33ab67aacdb990e190cba2ef53e1af;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 398c5be..8a3c372 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,225 +1,375 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
+import jalview.bin.*;
+
+import jalview.io.*;
+
 import jalview.jbgui.*;
+
 import jalview.schemes.*;
-import jalview.io.*;
 
-import jalview.bin.Cache;
-import javax.swing.*;
-import java.awt.event.ActionEvent;
 import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
 
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class Preferences extends GPreferences
 {
-  static boolean preferencesLoaded=false;
-
-  public static boolean showFullscreen=false;
-  public static boolean showFullId=true;
-  public static boolean showAnnotation=true;
-  public static boolean showConservation=true;
-  public static boolean showQuality=true;
-  public static boolean showIdentity=true;
-  public static String fontName="SansSerif";
-  public static String fontSize="10";
-  public static String fontStyle=Font.PLAIN+"";
-  public static char gapSymbol='-';
-  public static String defaultColour=null;
-  public static boolean showStartupFile=true;
-  public static String startupFile = "http://www.compbio.dundee.ac.uk/~andrew/jalviewTEST/fasta";
-
-  JInternalFrame frame;
-
-  public static void initPreferences()
-  {
-  String string = Cache.getProperty("SHOW_FULL_ID");
-  if(string!=null)
-    showFullId = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_FULLSCREEN");
-  if(string!=null)
-    showFullscreen = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_ANNOTATIONS");
-      if(string!=null)
-    showAnnotation = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_CONSERVATION");
-      if(string!=null)
-    showConservation = Boolean.valueOf(string).booleanValue();
-  string = Cache.getProperty("SHOW_QUALITY");
-      if(string!=null)
-    showQuality = Boolean.valueOf(string).booleanValue();
-  string = Cache.getProperty("SHOW_IDENTITY");
-      if(string!=null)
-    showIdentity = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("GAP_SYMBOL");
-      if(string!=null)
-    gapSymbol = string.charAt(0);
-
-  string = Cache.getProperty("SHOW_FULL_ID");
-    if(string!=null)
-      showFullId = Boolean.valueOf(string).booleanValue();
-
-    string = Cache.getProperty("FONT_NAME");
-    if (string != null)
-      fontName = string;
-
-    string = Cache.getProperty("FONT_STYLE");
-    if (string != null)
-      fontStyle = string;
-
-    string = Cache.getProperty("FONT_SIZE");
-    if (string != null)
-      fontSize = string;
-
-
-  string = Cache.getProperty("DEFAULT_COLOUR");
-  if(string!=null)
-      defaultColour = string;
-
-  string = Cache.getProperty("STARTUP_FILE");
-    if(string!=null)
-      startupFile = string;
-
-  string = Cache.getProperty("SHOW_STARTUP_FILE");
-        if(string!=null)
-      showStartupFile = Boolean.valueOf(string).booleanValue();
-
-      preferencesLoaded = true;
-  }
-
-  public Preferences()
-  {
-    initPreferences();
-
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Preferences", 480,390 );
-
-    fullID.setSelected(showFullId);
-    String string = Cache.getProperty("SHOW_FULLSCREEN");
-    boolean value = false;
-    if(string!=null)
-      value =  Boolean.valueOf(string).booleanValue();
-
-    fullScreen.setSelected(value);
-    annotations.setSelected(showAnnotation);
-
-    conservation.setEnabled(showAnnotation);
-    quality.setEnabled(showAnnotation);
-    identity.setEnabled(showAnnotation);
-
-    conservation.setSelected(showConservation);
-    quality.setSelected(showQuality);
-    identity.setSelected(showIdentity);
-
-    for(int i=0; i<12; i++)
-      colour.addItem( ColourSchemeProperty.getColourName(i) );
-
-    string = Cache.getProperty("DEFAULT_COLOUR");
-    if(string!=null)
-      colour.setSelectedItem( string );
-    else
-      colour.setSelectedIndex( 11 );
-
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-    for(int i=0; i<fonts.length; i++)
-      fontNameCB.addItem(fonts[i]);
-
-    for(int i=1; i<31; i++)
-      fontSizeCB.addItem(i+"");
-
-   fontStyleCB.addItem("plain");
-   fontStyleCB.addItem("bold");
-   fontStyleCB.addItem("italic");
-
-   fontNameCB.setSelectedItem(fontName);
-   fontSizeCB.setSelectedItem(fontSize);
-   fontStyleCB.setSelectedItem(fontStyle);
-
-   gapSymbolCB.addItem("-");
-   gapSymbolCB.addItem(".");
-
-   gapSymbolCB.setSelectedItem( gapSymbol+"" );
-
-   startupCheckbox.setSelected(showStartupFile);
-   startupFileTextfield.setText(startupFile);
-
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    showFullId =  fullID.isSelected() ;
-    showFullscreen = fullScreen.isSelected();
-    showAnnotation = annotations.isSelected();
-    showConservation = conservation.isSelected();
-    showQuality = quality.isSelected();
-    showIdentity = identity.isSelected();
-    defaultColour = colour.getSelectedItem().toString();
-    gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);
-    fontName = fontNameCB.getSelectedItem().toString();
-    fontSize = fontSizeCB.getSelectedItem().toString();
-    fontStyle = fontStyleCB.getSelectedItem().toString();
-    startupFile = startupFileTextfield.getText();
-    showStartupFile = startupCheckbox.isSelected();
-
-    Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
-    Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( showFullscreen ) );
-
-    Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( showAnnotation  ));
-    Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( showConservation ));
-    Cache.setProperty("SHOW_QUALITY", Boolean.toString( showQuality ));
-    Cache.setProperty("SHOW_IDENTITY", Boolean.toString( showIdentity ));
-
-    Cache.setProperty("DEFAULT_COLOUR", defaultColour);
-    Cache.setProperty("GAP_SYMBOL", gapSymbol+"");
-
-    Cache.setProperty("FONT_NAME", fontName);
-    Cache.setProperty("FONT_STYLE", fontStyle);
-    Cache.setProperty("FONT_SIZE", fontSize);
-
-    Cache.setProperty("STARTUP_FILE", startupFile);
-    Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
-
-
-
-    try    {
-      frame.setClosed(true);
-    }    catch (Exception ex)  {}
-
-  }
-
-  public void startupFileTextfield_mouseClicked()
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-        new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
-        new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}
-       ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Select startup file");
-   int value = chooser.showOpenDialog(this);
-   if(value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
-     startupFileTextfield.setText( chooser.getSelectedFile().getAbsolutePath() );
-   }
-  }
-
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    conservation.setEnabled(annotations.isSelected());
-    quality.setEnabled(annotations.isSelected());
-    identity.setEnabled(annotations.isSelected());
-  }
+    static boolean preferencesLoaded = false;
+
+    /** DOCUMENT ME!! */
+    public static boolean showFullscreen = false;
+
+    /** DOCUMENT ME!! */
+    public static boolean showFullId = true;
+
+    /** DOCUMENT ME!! */
+    public static boolean showAnnotation = true;
+
+    /** DOCUMENT ME!! */
+    public static boolean showConservation = true;
+
+    /** DOCUMENT ME!! */
+    public static boolean showQuality = true;
+
+    /** DOCUMENT ME!! */
+    public static boolean showIdentity = true;
+
+    /** DOCUMENT ME!! */
+    public static String fontName = "SansSerif";
+
+    /** DOCUMENT ME!! */
+    public static String fontSize = "10";
+
+    /** DOCUMENT ME!! */
+    public static String fontStyle = Font.PLAIN + "";
+
+    /** DOCUMENT ME!! */
+    public static char gapSymbol = '-';
+
+    /** DOCUMENT ME!! */
+    public static String defaultColour = null;
+
+    /** DOCUMENT ME!! */
+    public static boolean showStartupFile = true;
+
+    /** DOCUMENT ME!! */
+    public static String startupFile = "http://www.jalview.org/examples/exampleFile.jar";
+    JInternalFrame frame;
+
+    /**
+     * Creates a new Preferences object.
+     */
+    public Preferences()
+    {
+        initPreferences();
+
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "Preferences", 480, 390);
+
+        fullID.setSelected(showFullId);
+
+        String string = Cache.getProperty("SHOW_FULLSCREEN");
+        boolean value = false;
+
+        if (string != null)
+        {
+            value = Boolean.valueOf(string).booleanValue();
+        }
+
+        fullScreen.setSelected(value);
+        annotations.setSelected(showAnnotation);
+
+        conservation.setEnabled(showAnnotation);
+        quality.setEnabled(showAnnotation);
+        identity.setEnabled(showAnnotation);
+
+        conservation.setSelected(showConservation);
+        quality.setSelected(showQuality);
+        identity.setSelected(showIdentity);
+
+        for (int i = 0; i < 12; i++)
+        {
+            colour.addItem(ColourSchemeProperty.getColourName(i));
+        }
+
+        string = Cache.getProperty("DEFAULT_COLOUR");
+
+        if (string != null)
+        {
+            colour.setSelectedItem(string);
+        }
+        else
+        {
+            colour.setSelectedIndex(11);
+        }
+
+        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+                                                     .getAvailableFontFamilyNames();
+
+        for (int i = 0; i < fonts.length; i++)
+        {
+            fontNameCB.addItem(fonts[i]);
+        }
+
+        for (int i = 1; i < 31; i++)
+        {
+            fontSizeCB.addItem(i + "");
+        }
+
+        fontStyleCB.addItem("plain");
+        fontStyleCB.addItem("bold");
+        fontStyleCB.addItem("italic");
+
+        fontNameCB.setSelectedItem(fontName);
+        fontSizeCB.setSelectedItem(fontSize);
+        fontStyleCB.setSelectedItem(fontStyle);
+
+        gapSymbolCB.addItem("-");
+        gapSymbolCB.addItem(".");
+
+        gapSymbolCB.setSelectedItem(gapSymbol + "");
+
+        startupCheckbox.setSelected(showStartupFile);
+        startupFileTextfield.setText(startupFile);
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public static void initPreferences()
+    {
+        String string = Cache.getProperty("SHOW_FULL_ID");
+
+        if (string != null)
+        {
+            showFullId = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("SHOW_FULLSCREEN");
 
+        if (string != null)
+        {
+            showFullscreen = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("SHOW_ANNOTATIONS");
+
+        if (string != null)
+        {
+            showAnnotation = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("SHOW_CONSERVATION");
+
+        if (string != null)
+        {
+            showConservation = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("SHOW_QUALITY");
+
+        if (string != null)
+        {
+            showQuality = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("SHOW_IDENTITY");
+
+        if (string != null)
+        {
+            showIdentity = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("GAP_SYMBOL");
+
+        if (string != null)
+        {
+            gapSymbol = string.charAt(0);
+        }
+
+        string = Cache.getProperty("SHOW_FULL_ID");
+
+        if (string != null)
+        {
+            showFullId = Boolean.valueOf(string).booleanValue();
+        }
+
+        string = Cache.getProperty("FONT_NAME");
+
+        if (string != null)
+        {
+            fontName = string;
+        }
+
+        string = Cache.getProperty("FONT_STYLE");
+
+        if (string != null)
+        {
+            fontStyle = string;
+        }
+
+        string = Cache.getProperty("FONT_SIZE");
+
+        if (string != null)
+        {
+            fontSize = string;
+        }
+
+        string = Cache.getProperty("DEFAULT_COLOUR");
+
+        if (string != null)
+        {
+            defaultColour = string;
+        }
+
+        string = Cache.getProperty("STARTUP_FILE");
+
+        if (string != null)
+        {
+            startupFile = string;
+        }
+
+        string = Cache.getProperty("SHOW_STARTUP_FILE");
+
+        if (string != null)
+        {
+            showStartupFile = Boolean.valueOf(string).booleanValue();
+        }
+
+        preferencesLoaded = true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
+    {
+        showFullId = fullID.isSelected();
+        showFullscreen = fullScreen.isSelected();
+        showAnnotation = annotations.isSelected();
+        showConservation = conservation.isSelected();
+        showQuality = quality.isSelected();
+        showIdentity = identity.isSelected();
+        defaultColour = colour.getSelectedItem().toString();
+        gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);
+        fontName = fontNameCB.getSelectedItem().toString();
+        fontSize = fontSizeCB.getSelectedItem().toString();
+        fontStyle = fontStyleCB.getSelectedItem().toString();
+        startupFile = startupFileTextfield.getText();
+        showStartupFile = startupCheckbox.isSelected();
+
+        Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
+        Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen));
+
+        Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation));
+        Cache.setProperty("SHOW_CONSERVATION",
+            Boolean.toString(showConservation));
+        Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality));
+        Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity));
+
+        Cache.setProperty("DEFAULT_COLOUR", defaultColour);
+        Cache.setProperty("GAP_SYMBOL", gapSymbol + "");
+
+        Cache.setProperty("FONT_NAME", fontName);
+        Cache.setProperty("FONT_STYLE", fontStyle);
+        Cache.setProperty("FONT_SIZE", fontSize);
+
+        Cache.setProperty("STARTUP_FILE", startupFile);
+        Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
+
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void startupFileTextfield_mouseClicked()
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"),
+                new String[]
+                {
+                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+                    "jar"
+                },
+                new String[]
+                {
+                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+                }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Select startup file");
+
+        int value = chooser.showOpenDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                chooser.getSelectedFormat());
+            startupFileTextfield.setText(chooser.getSelectedFile()
+                                                .getAbsolutePath());
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
+    {
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void annotations_actionPerformed(ActionEvent e)
+    {
+        conservation.setEnabled(annotations.isSelected());
+        quality.setEnabled(annotations.isSelected());
+        identity.setEnabled(annotations.isSelected());
+    }
 }