From: hansonr <hansonr@stolaf.edu>
Date: Mon, 2 Jul 2018 15:37:26 +0000 (+0100)
Subject: JAL-3026 GD#75 Stockholm file load fails
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~610
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=98fdba84857a44ec1ace01181c9a00dd84509ac6;p=jalview.git

JAL-3026 GD#75 Stockholm file load fails

Transpiler and runtime fixes for enhanced for syntax with implicit
variable type changing, boxing, and unboxing.

JavaScript alternative to using reflection method getClass().getFields()
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 7a30141..47d1082 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -25,6 +25,9 @@ import java.util.ArrayList;
 import java.util.List;
 
 /**
+ * BH 2018 SwingJS note: If additional final static Strings are added to this
+ * file, they should be added to public static final String[] allTypes.
+ * 
  * Defines internal constants for unambiguous annotation of DbRefEntry source
  * strings and describing the data retrieved from external database sources (see
  * jalview.ws.DbSourcProxy) <br/>
@@ -32,11 +35,16 @@ import java.util.List;
  * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
  * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
  * 
+ * 
+ * 
  * @author JimP
  * 
  */
 public class DBRefSource
 {
+  
+  
+  
   /**
    * UNIPROT Accession Number
    */
@@ -52,9 +60,9 @@ public class DBRefSource
    */
   public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
 
-  public static final String EMBLCDSProduct = "EMBLCDSProtein"
-          .toUpperCase();
+  public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
 
+  
   /**
    * PDB Entry Code
    */
@@ -70,6 +78,7 @@ public class DBRefSource
    */
   public static final String EMBLCDS = "EMBLCDS";
 
+  
   /**
    * PFAM ID
    */
@@ -85,6 +94,7 @@ public class DBRefSource
    */
   public static final String GENEDB = "GeneDB".toUpperCase();
 
+  
   /**
    * Ensembl
    */
@@ -92,7 +102,8 @@ public class DBRefSource
 
   public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
 
-  /**
+  
+   /**
    * List of databases whose sequences might have coding regions annotated
    */
   public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
@@ -103,22 +114,49 @@ public class DBRefSource
   public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
       EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 
+  
+  public static final String[] allTypes = new String[] {
+      UNIPROT, UP_NAME, UNIPROTKB, 
+      EMBLCDSProduct, PDB, EMBL, 
+      EMBLCDS, PFAM, RFAM, 
+      GENEDB, ENSEMBL, ENSEMBLGENOMES 
+      };
+
+
+  public static String[] allSourcesFromReflection;
+
   public static String[] allSources()
+
   {
-    List<String> src = new ArrayList<>();
-    for (Field f : DBRefSource.class.getFields())
+    /**
+     * @j2sNative
+     * 
+     *            return C$.allTypes;
+     * 
+     */
+
     {
-      if (String.class.equals(f.getType()))
+      if (allSourcesFromReflection == null)
       {
-        try
-        {
-          src.add((String) f.get(null));
-        } catch (Exception x)
+        List<String> src = new ArrayList<>();
+        for (Field f : DBRefSource.class.getFields())
         {
-          x.printStackTrace();
+          if (String.class.equals(f.getType()))
+          {
+            try
+            {
+              src.add((String) f.get(null));
+            } catch (Exception x)
+            {
+              x.printStackTrace();
+            }
+          }
         }
+        allSourcesFromReflection = src.toArray(new String[0]);
       }
+      return allSourcesFromReflection;
     }
-    return src.toArray(new String[0]);
   }
+  
+  
 }
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 11f9d44..988e63d 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/net.sf.j2s.core.jar b/swingjs/net.sf.j2s.core.jar
index 950a40e..0aa84ff 100644
Binary files a/swingjs/net.sf.j2s.core.jar and b/swingjs/net.sf.j2s.core.jar differ