Url links changes - incomplete checkin as battery low

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 117f103..718e14f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -31,6 +33,8 @@ import jalview.jbgui.GSequenceLink;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UrlProvider;
+import jalview.util.UrlProviderI;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.BorderLayout;
@@ -43,7 +47,6 @@ import java.awt.event.MouseEvent;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.StringTokenizer;
 import java.util.Vector;
 
 import javax.help.HelpSetException;
@@ -97,7 +100,8 @@ 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<String> sequenceURLLinks;
+  // public static Vector<String> sequenceURLLinks;
+  public static UrlProviderI sequenceUrlLinks;
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
@@ -110,44 +114,43 @@ public class Preferences extends GPreferences
   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 string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
+    sequenceUrlLinks = new UrlProvider(EMBLEBI_STRING.split("\\|")[0],
+            string); // TODO sort out the default string
+    // sequenceURLLinks = new Vector<String>();
 
-    try
-    {
-      StringTokenizer st = new StringTokenizer(string, "|");
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-        String url = st.nextToken();
-        // check for '|' within a regex
-        int rxstart = url.indexOf("$SEQUENCE_ID$");
-        while (rxstart == -1 && url.indexOf("/=$") == -1)
+    /*    try
+        {
+          StringTokenizer st = new StringTokenizer(string, "|");
+          while (st.hasMoreElements())
+          {
+            String name = st.nextToken();
+            String url = st.nextToken();
+            // check for '|' within a regex
+            int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
+            if (rxstart == -1)
+            {
+              rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+            }
+            while (rxstart == -1 && url.indexOf("/=$") == -1)
+            {
+              url = url + "|" + st.nextToken();
+            }
+            sequenceURLLinks.addElement(name + "|" + url);
+          }
+        } catch (Exception ex)
         {
-          url = url + "|" + st.nextToken();
+          System.out.println(ex + "\nError parsing sequence links");
         }
-        sequenceURLLinks.addElement(name + "|" + url);
-      }
-    } catch (Exception ex)
-    {
-      System.out.println(ex + "\nError parsing sequence links");
-    }
-    {
-      // 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");
-      if (srsPos > -1)
-      {
-        sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
-      }
-    }
-
+        {
+          // upgrade old SRS link
+          int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
+          if (srsPos > -1)
+          {
+            sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
+          }
+        }
+    */
     /**
      * TODO: reformulate groupURL encoding so two or more can be stored in the
      * .properties file as '|' separated strings
@@ -343,13 +346,14 @@ public class Preferences extends GPreferences
      */
     nameLinks = new Vector<String>();
     urlLinks = new Vector<String>();
-    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));
-    }
-
+    sequenceUrlLinks.getLinksForDisplay(nameLinks, urlLinks);
+    /*    for (HashMap.Entry<String, UrlLink> entry: sequenceUrlLinks.getUrlLinks())
+        {
+          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));
@@ -369,7 +373,6 @@ public class Preferences extends GPreferences
     /*
      * Set Output tab defaults
      */
-
     epsRendering.addItem(promptEachTimeOpt);
     epsRendering.addItem(lineArtOpt);
     epsRendering.addItem(textOpt);
@@ -385,8 +388,7 @@ public class Preferences extends GPreferences
     }
     else
     {
-      epsRendering.setSelectedItem(new OptionsParam(MessageManager
-              .getString("label.prompt_each_time"), "Prompt each time"));
+      epsRendering.setSelectedItem(promptEachTimeOpt);
     }
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
@@ -538,8 +540,8 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-      Cache.applicationProperties.setProperty("EPS_RENDERING",
-              ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+    Cache.applicationProperties.setProperty("EPS_RENDERING",
+            ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 
     /*
      * Save Connections settings
@@ -548,27 +550,39 @@ public class Preferences extends GPreferences
 
     jalview.util.BrowserLauncher.resetBrowser();
 
-    if (nameLinks.size() > 0)
+    String links = sequenceUrlLinks.writeUrlsAsString();
+    if (links.isEmpty())
     {
-      StringBuffer links = new StringBuffer();
-      sequenceURLLinks = new Vector<String>();
-      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());
+      Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
     else
     {
-      Cache.applicationProperties.remove("SEQUENCE_LINKS");
+      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+              links.toString());
     }
 
+    /*    if (nameLinks.size() > 0)
+        {
+          StringBuffer links = new StringBuffer();
+          sequenceURLLinks = new Vector<String>();
+          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");
+          sequenceURLLinks.clear();
+        }*/
+
     Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
 
@@ -1048,7 +1062,8 @@ public class Preferences extends GPreferences
     }
 
     @Override
-    public int hashCode(){
+    public int hashCode()
+    {
       return name.hashCode() + code.hashCode();
     }
   }