JAL-653 GFF attributes parsing mechanism, with first attempt at processing exonerate...

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8ca0c35..7c117b9 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.
  * 
@@ -37,10 +37,20 @@ import jalview.datamodel.SequenceI;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
+  public FormatAdapter(AlignViewportI viewport)
+  {
+    super(viewport);
+    init();
+  }
 
   public FormatAdapter()
   {
     super();
+    init();
+  }
+
+  private void init()
+  {
     if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
     {
       annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
@@ -58,6 +68,7 @@ public class FormatAdapter extends AppletFormatAdapter
       serviceSecondaryStruct = false;
     }
   }
+
   public String formatSequences(String format, SequenceI[] seqs,
           String[] omitHiddenColumns)
   {
@@ -255,6 +266,20 @@ 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 = super.readFile(inFile, type, format);
+    return al;
+  }
+
+  public AlignmentI readFromFile(FileParse source, String format)
+          throws java.io.IOException
+  {
+    Alignment 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 +313,5 @@ public class FormatAdapter extends AppletFormatAdapter
     return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
   }
 
+
 }