X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=ec9ea342e4745436c4de25a1643ea944a7a32ace;hb=3bff9f93376444b36ca6b69d30193e10ea3c07ab;hp=8a3c372dcd2a7b615a883a1dc1c6e8dfc55a7aa6;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8a3c372..ec9ea34 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.*;
-
 import jalview.io.*;
 
 import jalview.jbgui.*;
@@ -31,6 +29,10 @@ import java.awt.event.*;
 
 import javax.swing.*;
 
+import java.util.*;
+
+import jalview.bin.Cache;
+
 
 /**
  * DOCUMENT ME!
@@ -40,95 +42,75 @@ import javax.swing.*;
  */
 public class Preferences extends GPreferences
 {
-    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 = '-';
+    /** 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;
 
-    /** DOCUMENT ME!! */
-    public static String defaultColour = null;
+    JInternalFrame frame;
 
-    /** DOCUMENT ME!! */
-    public static boolean showStartupFile = true;
+    DasSourceBrowser dasSource;
 
-    /** 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;
+        dasSource = new DasSourceBrowser();
+        dasPanel.add(dasSource, BorderLayout.CENTER);
 
-        if (string != null)
+        int width = 500, height = 420;
+        if(System.getProperty("os.name").startsWith("Mac"))
         {
-            value = Boolean.valueOf(string).booleanValue();
+          width = 570;
+          height = 460;
         }
 
-        fullScreen.setSelected(value);
-        annotations.setSelected(showAnnotation);
+        Desktop.addInternalFrame(frame, "Preferences", width, height);
+        frame.setMinimumSize(new Dimension(width, height));
 
-        conservation.setEnabled(showAnnotation);
-        quality.setEnabled(showAnnotation);
-        identity.setEnabled(showAnnotation);
+        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
+        fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-        conservation.setSelected(showConservation);
-        quality.setSelected(showQuality);
-        identity.setSelected(showIdentity);
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
+        quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+        identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-        for (int i = 0; i < 12; i++)
+        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 = Cache.getProperty("DEFAULT_COLOUR");
+        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 
-        if (string != null)
-        {
-            colour.setSelectedItem(string);
-        }
-        else
-        {
-            colour.setSelectedIndex(11);
-        }
+        colour.setSelectedItem(string);
 
         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
                                                      .getAvailableFontFamilyNames();
@@ -147,165 +129,185 @@ public class Preferences extends GPreferences
         fontStyleCB.addItem("bold");
         fontStyleCB.addItem("italic");
 
-        fontNameCB.setSelectedItem(fontName);
-        fontSizeCB.setSelectedItem(fontSize);
-        fontStyleCB.setSelectedItem(fontStyle);
+        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(".");
+        smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
-        gapSymbolCB.setSelectedItem(gapSymbol + "");
-
-        startupCheckbox.setSelected(showStartupFile);
-        startupFileTextfield.setText(startupFile);
-    }
+        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 
-    /**
-     * DOCUMENT ME!
-     */
-    public static void initPreferences()
-    {
-        String string = Cache.getProperty("SHOW_FULL_ID");
+        gapSymbolCB.addItem("-");
+        gapSymbolCB.addItem(".");
 
-        if (string != null)
+        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"));
+
+        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
+        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
+        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
+        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
+        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
+        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
+        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
+
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
+        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+
+  /****************************************************
+   * Set up Connections
+   */
+        nameLinks = new Vector();
+        urlLinks = new Vector();
+        for(int i=0; i<sequenceURLLinks.size(); i++)
         {
-            showFullId = Boolean.valueOf(string).booleanValue();
+          String link = sequenceURLLinks.elementAt(i).toString();
+          nameLinks.addElement(link.substring(0, link.indexOf("|")) );
+          urlLinks.addElement(link.substring(link.indexOf("|")+1));
         }
 
-        string = Cache.getProperty("SHOW_FULLSCREEN");
+        updateLinkData();
 
-        if (string != null)
-        {
-            showFullscreen = Boolean.valueOf(string).booleanValue();
-        }
+        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", ""));
 
-        string = Cache.getProperty("SHOW_ANNOTATIONS");
+        defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
-        if (string != null)
-        {
-            showAnnotation = Boolean.valueOf(string).booleanValue();
-        }
+  }
 
-        string = Cache.getProperty("SHOW_CONSERVATION");
 
-        if (string != null)
-        {
-            showConservation = Boolean.valueOf(string).booleanValue();
-        }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
+    {
 
-        string = Cache.getProperty("SHOW_QUALITY");
+      Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
 
-        if (string != null)
-        {
-            showQuality = Boolean.valueOf(string).booleanValue();
-        }
+      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()));
 
-        string = Cache.getProperty("SHOW_IDENTITY");
+      Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
 
-        if (string != null)
-        {
-            showIdentity = Boolean.valueOf(string).booleanValue();
-        }
+      Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
 
-        string = Cache.getProperty("GAP_SYMBOL");
+      Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
 
-        if (string != null)
-        {
-            gapSymbol = string.charAt(0);
-        }
+      Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));
 
-        string = Cache.getProperty("SHOW_FULL_ID");
+      Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
+      Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
 
-        if (string != null)
-        {
-            showFullId = Boolean.valueOf(string).booleanValue();
-        }
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
 
-        string = Cache.getProperty("FONT_NAME");
+      if(epsRendering.getSelectedItem().equals("Prompt each time"))
+        Cache.applicationProperties.remove("EPS_RENDERING");
+      else
+        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
 
-        if (string != null)
-        {
-            fontName = string;
-        }
+      if(defaultBrowser.getText().trim().length()<1)
+        Cache.applicationProperties.remove("DEFAULT_BROWSER");
+      else
+        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+                                                defaultBrowser.getText());
 
-        string = Cache.getProperty("FONT_STYLE");
+        jalview.util.BrowserLauncher.resetBrowser();
 
-        if (string != null)
+        if(nameLinks.size()>0)
         {
-            fontStyle = string;
+          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");
 
-        string = Cache.getProperty("FONT_SIZE");
 
-        if (string != null)
-        {
-            fontSize = string;
-        }
+        Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
 
-        string = Cache.getProperty("DEFAULT_COLOUR");
+        if (proxyServerTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_SERVER");
+        else
+          Cache.applicationProperties.setProperty("PROXY_SERVER",
+                                                  proxyServerTB.getText());
 
-        if (string != null)
+        if (proxyPortTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_PORT");
+        else
+          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+
+        if(useProxy.isSelected())
         {
-            defaultColour = string;
+          System.setProperty("http.proxyHost", proxyServerTB.getText());
+          System.setProperty("http.proxyPort", proxyPortTB.getText());
         }
-
-        string = Cache.getProperty("STARTUP_FILE");
-
-        if (string != null)
+        else
         {
-            startupFile = string;
+          System.setProperty("http.proxyHost","");
+          System.setProperty("http.proxyPort","");
         }
 
-        string = Cache.getProperty("SHOW_STARTUP_FILE");
 
-        if (string != null)
-        {
-            showStartupFile = Boolean.valueOf(string).booleanValue();
-        }
+        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
+        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
+        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
+        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
-        preferencesLoaded = true;
-    }
+        Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+                                                Boolean.toString(autoCalculateConsCheck.isSelected()));
+        Cache.applicationProperties.setProperty("PAD_GAPS",
+                                                Boolean.toString(padGaps.isSelected()));
 
-    /**
-     * 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));
+        dasSource.saveProperties(Cache.applicationProperties);
 
+        Cache.saveProperties();
         try
         {
             frame.setClosed(true);
@@ -338,7 +340,7 @@ public class Preferences extends GPreferences
 
         if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+            jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
                 chooser.getSelectedFormat());
             startupFileTextfield.setText(chooser.getSelectedFile()
                                                 .getAbsolutePath());
@@ -372,4 +374,106 @@ public class Preferences extends GPreferences
         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());
+      }
+
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+  }
 }