X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=32aad84a7a2aad655b385849eb38ed3245f1b6b2;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=7e05eed270f42d60f017c66eb7bf039fbd55a43a;hpb=863f92d688429d50ac290e0f31639ed17d72390e;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7e05eed..32aad84 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,176 +1,430 @@
+/*
+ * 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.io.*;
+
 import jalview.jbgui.*;
+
 import jalview.schemes.*;
 
-import jalview.bin.Cache;
-import javax.swing.*;
-import java.awt.event.ActionEvent;
 import java.awt.*;
+import java.awt.event.*;
 
-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;
-  public static String fontSize;
-  public static String fontStyle;
-  public static char gapSymbol='-';
-  public static String defaultColour=null;
-
-  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("SHOW_FULL_ID");
-    if(string!=null)
-      showFullId = Boolean.valueOf(string).booleanValue();
-
-  fontName = Cache.getProperty("FONT_NAME");
-  fontStyle = Cache.getProperty("FONT_STYLE");
-  fontSize = Cache.getProperty("FONT_SIZE");
-
-  string = Cache.getProperty("DEFAULT_COLOUR");
-  if(string!=null)
-      defaultColour = string;
-
-
-      preferencesLoaded = true;
-  }
-
-  public Preferences()
-  {
-    if(!preferencesLoaded)
-      initPreferences();
-
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Preferences", 480,350 );
-
-    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+"");
+import javax.swing.*;
 
-   fontStyleCB.addItem("plain");
-   fontStyleCB.addItem("bold");
-   fontStyleCB.addItem("italic");
+import java.util.*;
 
-   fontNameCB.setSelectedItem(fontName);
-   fontSizeCB.setSelectedItem(fontSize);
-   fontStyleCB.setSelectedItem(fontStyle);
+import jalview.bin.Cache;
 
-   gapSymbolCB.addItem("-");
-   gapSymbolCB.addItem(".");
 
-   gapSymbolCB.setSelectedItem( gapSymbol+"" );
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+    /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
+    public static Vector sequenceURLLinks;
+    static
+    {
+      String string = Cache.getDefault("SEQUENCE_LINKS",
+                                       "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
+      sequenceURLLinks = new Vector();
+
+      try
+      {
+        StringTokenizer st = new StringTokenizer(string, "|");
+        while (st.hasMoreElements())
+        {
+          sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
+        }
+      }
+      catch (Exception ex)
+      {
+        System.out.println(ex + "\nError parsing sequence links");
+      }
+    }
+    Vector nameLinks, urlLinks;
+
+    JInternalFrame frame;
+
+
+    /**
+     * Creates a new Preferences object.
+     */
+    public Preferences()
+    {
+
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "Preferences", 480, 390);
+        frame.setMinimumSize(new Dimension(480,390));
+
+        fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));
+        fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
+        quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+        identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+        conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
+        quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
+        identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+
+        for (int i = 0; i < 13; i++)
+        {
+            colour.addItem(ColourSchemeProperty.getColourName(i));
+        }
+
+        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+
+        colour.setSelectedItem(string);
+
+        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(Cache.getDefault("FONT_NAME", "SansSerif"));
+        fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+        fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
+
+        gapSymbolCB.addItem("-");
+        gapSymbolCB.addItem(".");
+
+        gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
+
+        startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
+        startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+         "http://www.jalview.org/examples/exampleFile.jar"));
+
+        sortby.addItem("No sort");
+        sortby.addItem("Id");
+        sortby.addItem("Pairwise Identity");
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+
+        epsRendering.addItem("Prompt each time");
+        epsRendering.addItem("Lineart");
+        epsRendering.addItem("Text");
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
+
+  /****************************************************
+   * Set up Connections
+   */
+        nameLinks = new Vector();
+        urlLinks = new Vector();
+        for(int i=0; i<sequenceURLLinks.size(); i++)
+        {
+          String link = sequenceURLLinks.elementAt(i).toString();
+          nameLinks.addElement(link.substring(0, link.indexOf("|")) );
+          urlLinks.addElement(link.substring(link.indexOf("|")+1));
+        }
+
+        updateLinkData();
+
+        useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
+        proxyServerTB.setEnabled(useProxy.isSelected());
+        proxyPortTB.setEnabled(useProxy.isSelected());
+        proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
+        proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+        defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
   }
 
-  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();
-
-    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);
-
-    try    {
-      frame.setClosed(true);
-    }    catch (Exception ex)  {}
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
+    {
+
+      Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
+
+      Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
+
+      Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
+
+      Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
+
+      Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
+      Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
+
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
+
+      if(epsRendering.getSelectedItem().equals("Prompt each time"))
+        Cache.applicationProperties.remove("EPS_RENDERING");
+      else
+        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
+
+      if(defaultBrowser.getText().trim().length()<1)
+        Cache.applicationProperties.remove("DEFAULT_BROWSER");
+      else
+        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+                                                defaultBrowser.getText());
+
+        jalview.util.BrowserLauncher.resetBrowser();
+
+        if(nameLinks.size()>0)
+        {
+          StringBuffer links = new StringBuffer();
+          sequenceURLLinks = new Vector();
+          for (int i = 0; i < nameLinks.size(); i++)
+          {
+            sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
+            links.append(sequenceURLLinks.elementAt(i).toString());
+            links.append("|");
+          }
+          // remove last "|"
+          links.setLength( links.length()-1 );
+          Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
+        }
+        else
+          Cache.applicationProperties.remove("SEQUENCE_LINKS");
+
+
+        Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
+
+        if (proxyServerTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_SERVER");
+        else
+          Cache.applicationProperties.setProperty("PROXY_SERVER",
+                                                  proxyServerTB.getText());
+
+        if (proxyPortTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_PORT");
+        else
+          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+
+        if(useProxy.isSelected())
+        {
+          System.setProperty("http.proxyHost", proxyServerTB.getText());
+          System.setProperty("http.proxyPort", proxyPortTB.getText());
+        }
+        else
+        {
+          System.setProperty("http.proxyHost","");
+          System.setProperty("http.proxyPort","");
+        }
+
+
+
+        Cache.saveProperties();
+        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.applicationProperties.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());
+    }
+
+
+    public void newLink_actionPerformed(ActionEvent e) {
+
+      GSequenceLink link = new GSequenceLink();
+      boolean valid = false;
+      while( !valid )
+      {
+        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                  "New sequence URL link",
+                                                  JOptionPane.OK_CANCEL_OPTION
+                                                  ,-1, null)
+            == JOptionPane.OK_OPTION)
+        {
+          if (link.checkValid())
+          {
+            nameLinks.addElement(link.getName());
+            urlLinks.addElement(link.getURL());
+            updateLinkData();
+            valid = true;
+          }
+        }
+        else
+          break;
+      }
+    }
+
+    public void editLink_actionPerformed(ActionEvent e) {
+      GSequenceLink link = new GSequenceLink();
+
+      int index = linkNameList.getSelectedIndex();
+      if(index==-1)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
+            ,"No link selected", JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      link.setName( nameLinks.elementAt(index).toString() );
+      link.setURL( urlLinks.elementAt(index).toString() );
+
+      boolean valid = false;
+      while (!valid)
+      {
+
+        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                  "New sequence URL link",
+                                                  JOptionPane.OK_CANCEL_OPTION
+                                                  ,-1, null)
+            == JOptionPane.OK_OPTION)
+        {
+          if (link.checkValid())
+          {
+            nameLinks.setElementAt(link.getName(), index);
+            urlLinks.setElementAt(link.getURL(), index);
+            updateLinkData();
+            valid = true;
+          }
+        }
+
+        else
+          break;
+      }
+    }
+
+    public void deleteLink_actionPerformed(ActionEvent e) {
+      int index = linkNameList.getSelectedIndex();
+      if(index==-1)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
+            ,"No link selected", JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+      nameLinks.removeElementAt(index);
+      urlLinks.removeElementAt(index);
+      updateLinkData();
+    }
+
+    void updateLinkData()
+    {
+      linkNameList.setListData(nameLinks);
+      linkURLList.setListData(urlLinks);
+    }
+
+    public void defaultBrowser_mouseClicked(MouseEvent e)
+    {
+      JFileChooser chooser = new JFileChooser(".");
+      chooser.setDialogTitle("Select default web browser");
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JFileChooser.APPROVE_OPTION)
+      {
+        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+      }
 
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
   }
 
-  public void annotations_actionPerformed(ActionEvent e)
+  private void jbInit()
+      throws Exception
   {
-    conservation.setEnabled(annotations.isSelected());
-    quality.setEnabled(annotations.isSelected());
-    identity.setEnabled(annotations.isSelected());
   }
-
 }