JAL-2326 updated references of JOptionPane to JvOptionPane

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c7e1332..b293e6f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,11 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -30,6 +35,7 @@ import jalview.jbgui.GPreferences;
 import jalview.jbgui.GSequenceLink;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.BorderLayout;
@@ -40,7 +46,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.io.File;
-import java.util.Collection;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -96,7 +102,7 @@ public class Preferences extends GPreferences
    * Holds name and link separated with | character. Sequence ID must be
    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
    */
-  public static Vector sequenceURLLinks;
+  public static Vector<String> sequenceURLLinks;
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
@@ -106,14 +112,11 @@ public class Preferences extends GPreferences
    * (TODO: proper escape for using | to separate ids or sequences
    */
 
-  public static Vector groupURLLinks;
+  public static List<String> groupURLLinks;
   static
   {
-    String string = Cache
-            .getDefault(
-                    "SEQUENCE_LINKS",
-                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
-    sequenceURLLinks = new Vector();
+    String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
+    sequenceURLLinks = new Vector<String>();
 
     try
     {
@@ -123,7 +126,11 @@ public class Preferences extends GPreferences
         String name = st.nextToken();
         String url = st.nextToken();
         // check for '|' within a regex
-        int rxstart = url.indexOf("$SEQUENCE_ID$");
+        int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
+        if (rxstart == -1)
+        {
+          rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+        }
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
@@ -136,14 +143,10 @@ public class Preferences extends GPreferences
     }
     {
       // upgrade old SRS link
-      int srsPos = sequenceURLLinks
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
       }
     }
 
@@ -152,10 +155,10 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new Vector();
+    groupURLLinks = new ArrayList<String>();
   }
 
-  Vector nameLinks, urlLinks;
+  Vector<String> nameLinks, urlLinks;
 
   JInternalFrame frame;
 
@@ -163,6 +166,16 @@ public class Preferences extends GPreferences
 
   private WsPreferences wsPrefs;
 
+  private OptionsParam promptEachTimeOpt = new OptionsParam(
+          MessageManager.getString("label.prompt_each_time"),
+          "Prompt each time");
+
+  private OptionsParam lineArtOpt = new OptionsParam(
+          MessageManager.getString("label.lineart"), "Lineart");
+
+  private OptionsParam textOpt = new OptionsParam(
+          MessageManager.getString("action.text"), "Text");
+
   /**
    * Creates a new Preferences object.
    */
@@ -176,7 +189,8 @@ public class Preferences extends GPreferences
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
-    if (new jalview.util.Platform().isAMac())
+    new jalview.util.Platform();
+    if (Platform.isAMac())
     {
       width = 570;
       height = 480;
@@ -329,8 +343,8 @@ public class Preferences extends GPreferences
     /*
      * Set Connections tab defaults
      */
-    nameLinks = new Vector();
-    urlLinks = new Vector();
+    nameLinks = new Vector<String>();
+    urlLinks = new Vector<String>();
     for (int i = 0; i < sequenceURLLinks.size(); i++)
     {
       String link = sequenceURLLinks.elementAt(i).toString();
@@ -357,12 +371,23 @@ public class Preferences extends GPreferences
     /*
      * Set Output tab defaults
      */
-    epsRendering
-            .addItem(MessageManager.getString("label.prompt_each_time"));
-    epsRendering.addItem(MessageManager.getString("label.lineart"));
-    epsRendering.addItem(MessageManager.getString("action.text"));
-    epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
-            "Prompt each time"));
+    epsRendering.addItem(promptEachTimeOpt);
+    epsRendering.addItem(lineArtOpt);
+    epsRendering.addItem(textOpt);
+    String defaultEPS = Cache.getDefault("EPS_RENDERING",
+            "Prompt each time");
+    if (defaultEPS.equalsIgnoreCase("Text"))
+    {
+      epsRendering.setSelectedItem(textOpt);
+    }
+    else if (defaultEPS.equalsIgnoreCase("Lineart"))
+    {
+      epsRendering.setSelectedItem(lineArtOpt);
+    }
+    else
+    {
+      epsRendering.setSelectedItem(promptEachTimeOpt);
+    }
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
@@ -513,15 +538,8 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-    if (epsRendering.getSelectedItem().equals("Prompt each time"))
-    {
-      Cache.applicationProperties.remove("EPS_RENDERING");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
-              .getSelectedItem().toString());
-    }
+    Cache.applicationProperties.setProperty("EPS_RENDERING",
+            ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 
     /*
      * Save Connections settings
@@ -533,7 +551,7 @@ public class Preferences extends GPreferences
     if (nameLinks.size() > 0)
     {
       StringBuffer links = new StringBuffer();
-      sequenceURLLinks = new Vector();
+      sequenceURLLinks = new Vector<String>();
       for (int i = 0; i < nameLinks.size(); i++)
       {
         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
@@ -549,6 +567,7 @@ public class Preferences extends GPreferences
     else
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
+      sequenceURLLinks.clear();
     }
 
     Cache.applicationProperties.setProperty("USE_PROXY",
@@ -735,9 +754,9 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -762,10 +781,10 @@ public class Preferences extends GPreferences
     int index = linkNameList.getSelectedIndex();
     if (index == -1)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.no_link_selected"),
               MessageManager.getString("label.no_link_selected"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       return;
     }
 
@@ -776,9 +795,9 @@ public class Preferences extends GPreferences
     while (!valid)
     {
 
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -802,10 +821,10 @@ public class Preferences extends GPreferences
     int index = linkNameList.getSelectedIndex();
     if (index == -1)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.no_link_selected"),
               MessageManager.getString("label.no_link_selected"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       return;
     }
     nameLinks.removeElementAt(index);
@@ -849,7 +868,7 @@ public class Preferences extends GPreferences
     super.showunconserved_actionPerformed(e);
   }
 
-  public static Collection getGroupURLLinks()
+  public static List<String> getGroupURLLinks()
   {
     return groupURLLinks;
   }
@@ -897,10 +916,10 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
     }
   }
@@ -923,10 +942,10 @@ public class Preferences extends GPreferences
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
-                JOptionPane.ERROR_MESSAGE);
+                JvOptionPane.ERROR_MESSAGE);
         return false;
       }
     }
@@ -962,13 +981,13 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JOptionPane.showInternalOptionDialog(
+      int showHelp = JvOptionPane.showInternalOptionDialog(
               Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
-              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
               null, options, options[0]);
-      if (showHelp == JOptionPane.NO_OPTION)
+      if (showHelp == JvOptionPane.NO_OPTION)
       {
         try
         {
@@ -981,4 +1000,58 @@ public class Preferences extends GPreferences
     }
   }
 
+  public class OptionsParam
+  {
+    private String name;
+
+    private String code;
+
+    public OptionsParam(String name, String code)
+    {
+      this.name = name;
+      this.code = code;
+    }
+
+    public String getName()
+    {
+      return name;
+    }
+
+    public void setName(String name)
+    {
+      this.name = name;
+    }
+
+    public String getCode()
+    {
+      return code;
+    }
+
+    public void setCode(String code)
+    {
+      this.code = code;
+    }
+
+    @Override
+    public String toString()
+    {
+      return name;
+    }
+
+    @Override
+    public boolean equals(Object that)
+    {
+      if (!(that instanceof OptionsParam))
+      {
+        return false;
+      }
+      return this.code.equalsIgnoreCase(((OptionsParam) that).code);
+    }
+
+    @Override
+    public int hashCode()
+    {
+      return name.hashCode() + code.hashCode();
+    }
+  }
 }