From b4ae8736c4d0d6bcba332dc875dd5eabd8d4c851 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 8 Sep 2016 17:32:12 +0100
Subject: [PATCH] JAL-2164 renamed 'DEFAULT_STRUCTURE_FORMAT' property to
 'PDB_DOWNLOAD_FORMAT'

---
 help/html/features/viewingpdbs.html         |    2 +-
 src/jalview/bin/Cache.java                  |    4 ++--
 test/jalview/ws/PDBSequenceFetcherTest.java |    2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index d4819f1..61c13c4 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -127,7 +127,7 @@
     web-service. To enable mmCIF as the default format for 
     importing PBD sequences from the PDB sequence fetcher, add or modify the 
     property  
-    <code>DEFAULT_STRUCTURE_FORMAT=mmCIF</code> in Jalview properties file. 
+    <code>PDB_DOWNLOAD_FORMAT=mmCIF</code> in Jalview properties file. 
     Once this is done, the steps followed in retrieving PDB format files above can 
     be followed to obtain the same data with mmCIF. <em>mmCIF format file support was added in Jalview 2.9.1.</em></p>
     
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index df71ccc..508e8a7 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -232,7 +232,7 @@ public class Cache
   /**
    * Allowed values are PDB or mmCIF
    */
-  private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+  private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
           .toString();
 
   private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
@@ -445,7 +445,7 @@ public class Cache
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
             .getDefault(
-            "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+"PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
             .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
                     "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index fda0198..c1d1144 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -64,7 +64,7 @@ public class PDBSequenceFetcherTest
   {
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT",
             "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
-- 
1.7.10.2