JAL-2344 test fix and code tidy for review comments

diff --git a/src/jalview/io/FileFormats.java b/src/jalview/io/FileFormats.java
index 158489e..19a61cf 100644 (file)
--- a/src/jalview/io/FileFormats.java
+++ b/src/jalview/io/FileFormats.java
@@ -74,7 +74,9 @@ public class FileFormats
    */
   public void registerFileFormat(FileFormatI format)
   {
-    registerFileFormat(format, false);
+    boolean isIdentifiable = format instanceof FileFormat
+            && ((FileFormat) format).isIdentifiable();
+    registerFileFormat(format, isIdentifiable);
   }
 
   protected void registerFileFormat(FileFormatI format,

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index a8258e2..b85073f 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -108,8 +108,8 @@ public class Alignment extends InputType
   @Override
   public List<String> getURLEncodedParameter()
   {
-    ArrayList<String> prms = new ArrayList<String>();
-    prms.add("format='" + format + "'");
+    List<String> prms = new ArrayList<String>();
+    prms.add("format='" + format.getName() + "'");
     if (type != null)
     {
       prms.add("type='" + type.toString() + "'");

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 8df228f..ffc844c 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -21,17 +21,21 @@ public class FileFormatsTest
   }
 
   @Test(groups = "Functional")
-  public void testIsDynamic()
+  public void testIsIdentifiable()
   {
     FileFormats formats = FileFormats.getInstance();
-    for (FileFormatI ff : FileFormat.values())
-    {
-      assertFalse(formats.isIdentifiable(ff));
-    }
-    assertTrue(formats.isIdentifiable(null));
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
+            .getName())));
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
+            .getName())));
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
+            .getName())));
+    assertFalse(formats.isIdentifiable(formats.forName(FileFormat.Jalview
+            .getName())));
+    assertFalse(formats.isIdentifiable(null));
 
     /*
-     * remove and re-add a format: it is now considered 'dynamically added'
+     * remove and re-add a format: it is still 'identifiable'
      */
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
     assertNull(formats.forName(FileFormat.Fasta.getName()));
@@ -104,7 +108,7 @@ public class FileFormatsTest
     FileFormats formats = FileFormats.getInstance();
     assertSame(FileFormat.MMCif,
             formats.forName(FileFormat.MMCif.getName()));
-    assertFalse(formats.isIdentifiable(FileFormat.MMCif));
+    assertTrue(formats.isIdentifiable(FileFormat.MMCif));
 
     /*
      * deregister mmCIF format
@@ -114,7 +118,7 @@ public class FileFormatsTest
 
     /*
      * re-register mmCIF format
-     * it is reinstated (but now classed as 'dynamic')
+     * it is reinstated (still 'identifiable')
      */
     formats.registerFileFormat(FileFormat.MMCif);
     assertSame(FileFormat.MMCif,