X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=3a7a739858b90919e2690eddd3dd20def6bbe4d8;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=2e0fea70b8b375b2ae1c74651f012cba8c097ccb;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 2e0fea7..3a7a739 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -149,12 +149,16 @@ public class StockholmFile extends AlignFile
           int start = 1;
           int end = -1;
           String sid = acc;
-          // Retrieve hash of annotations for this accession
+          /*
+           * Retrieve hash of annotations for this accession
+           * Associate Annotation with accession
+           */
           Hashtable accAnnotations = null;
 
           if (seqAnn != null && seqAnn.containsKey(acc))
           {
             accAnnotations = (Hashtable) seqAnn.remove(acc);
+            //TODO: add structures to sequence
           }
 
           // Split accession in id and from/to
@@ -184,7 +188,19 @@ public class StockholmFile extends AlignFile
               jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
               // seqO.addDBRef(dbref);
             }
+          }        
+          if (accAnnotations != null && accAnnotations.containsKey("SS"))
+          {
+        	  Vector v = (Vector) accAnnotations.get("SS");
+        	  
+        	  for (int i = 0; i < v.size(); i++)
+        	    {
+        		  AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);
+        		  seqO.addAlignmentAnnotation(an);
+        		  //annotations.add(an);
+        	    }
           }
+        
           Hashtable features = null;
           // We need to adjust the positions of all features to account for gaps
           try
@@ -426,7 +442,7 @@ public class StockholmFile extends AlignFile
               ann = new Hashtable();
               seqAnn.put(acc, ann);
             }
-
+            //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence
             Hashtable features;
             // Get an object with all the content for an annotation
             if (ann.containsKey("features"))
@@ -461,6 +477,24 @@ public class StockholmFile extends AlignFile
             }
             ns += seq;
             content.put(description, ns);
+
+            if(type.equals("SS")){
+                Hashtable strucAnn;
+                if (seqAnn.containsKey(acc))
+                {
+                  strucAnn = (Hashtable) seqAnn.get(acc);
+                }
+                else
+                {
+                  strucAnn = new Hashtable();
+                }
+                
+                Vector newStruc=new Vector();
+                parseAnnotationRow(newStruc, type,ns);
+                
+                strucAnn.put(type, newStruc);
+                seqAnn.put(acc, strucAnn);
+             }
           }
           else
           {
@@ -566,6 +600,7 @@ public class StockholmFile extends AlignFile
               annot.annotations.length);
       System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
       annot.annotations = anns;
+      //System.out.println("else: ");
     }
     return annot;
   }