X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=dfbdf86f14dc01f4460b06cb3ce7d6cfcc38b04b;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=c2a317a01ffaea4da6cb5bb5b943f324bbc96fea;hpb=4b8e37b39d6599396ea8538e1737b65eb869aa21;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index c2a317a..dfbdf86 100755
--- 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.
  * 
@@ -21,7 +21,13 @@
 package jalview.io;
 
 import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -32,6 +38,26 @@ import jalview.datamodel.*;
 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)
   {
@@ -154,8 +180,10 @@ public class FormatAdapter extends AppletFormatAdapter
   public boolean getCacheSuffixDefault(String format)
   {
     if (isValidFormat(format))
+    {
       return jalview.bin.Cache.getDefault(format.toUpperCase()
               + "_JVSUFFIX", true);
+    }
     return false;
   }
 
@@ -227,6 +255,41 @@ 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("HTML"))
+    {
+      afile = new HtmlFile(inFile, type);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(al);
+    }
+    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("HTML"))
+    {
+      afile = new HtmlFile(source);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(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