JAL-1641 cherry-picked changes into develop compatible branch

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index ccabbb3..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 2.8.2b1)
- * 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.
  * 
@@ -255,6 +255,45 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
+  public Alignment readFile(String inFile, String type, String format)
+          throws java.io.IOException
+  {
+    Alignment al;
+    if (format.equals(JSONFile.FILE_DESC))
+    {
+      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;
+  }
+
+  public AlignmentI readFromFile(FileParse source, String format)
+          throws java.io.IOException
+  {
+    Alignment al;
+    if (format.equals(JSONFile.FILE_DESC))
+    {
+      afile = new JSONFile(source);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(al);
+      afile.addSeqGroups(al);
+    }
+    else
+    {
+      al = (Alignment) super.readFromFile(source, format);
+    }
+    return al;
+  }
+
   /**
    * validate format is valid for IO in Application. This is basically the
    * AppletFormatAdapter.isValidFormat call with additional checks for
@@ -288,4 +327,5 @@ public class FormatAdapter extends AppletFormatAdapter
     return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
   }
 
+
 }