Merge branch 'features/JAL-1641_JSON_' into develop

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 416773d..74410a1 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -38,6 +38,26 @@ import jalview.datamodel.SequenceI;
 public class FormatAdapter extends AppletFormatAdapter
 {
 
+  public FormatAdapter()
+  {
+    super();
+    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    {
+      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+              true);
+      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+            true);
+    serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+            true);
+    }
+    else
+    {
+      // disable all PDB annotation options
+      annotFromStructure = false;
+      localSecondaryStruct = false;
+      serviceSecondaryStruct = false;
+    }
+  }
   public String formatSequences(String format, SequenceI[] seqs,
           String[] omitHiddenColumns)
   {
@@ -239,17 +259,20 @@ public class FormatAdapter extends AppletFormatAdapter
           throws java.io.IOException
   {
     Alignment al;
-    if (format.equals("HTML"))
+    if (format.equals(JSONFile.FILE_DESC))
     {
-      afile = new HtmlFile(inFile, type);
+      afile = new JSONFile(inFile, type);
       al = new Alignment(afile.getSeqsAsArray());
       afile.addAnnotations(al);
+      for (SequenceGroup sg : afile.getSeqGroups())
+      {
+        al.addGroup(sg);
+      }
     }
     else
     {
       al = super.readFile(inFile, type, format);
     }
-
     return al;
   }
 
@@ -257,11 +280,12 @@ public class FormatAdapter extends AppletFormatAdapter
           throws java.io.IOException
   {
     Alignment al;
-    if (format.equals("HTML"))
+    if (format.equals(JSONFile.FILE_DESC))
     {
-      afile = new HtmlFile(source);
+      afile = new JSONFile(source);
       al = new Alignment(afile.getSeqsAsArray());
       afile.addAnnotations(al);
+      afile.addSeqGroups(al);
     }
     else
     {
@@ -303,4 +327,5 @@ public class FormatAdapter extends AppletFormatAdapter
     return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
   }
 
+
 }