X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=a9124d9325173203481ecd58129d230cd9b5d5f0;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=6b60cd528e264978d6970521fea9b525e93a2695;hpb=c24d7fddcbce270e9d766872238e3f14b6bf6719;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 6b60cd5..a9124d9 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -150,15 +150,15 @@ public class StockholmFile extends AlignFile
           int end = -1;
           String sid = acc;
           /*
-           * Retrieve hash of annotations for this accession
-           * Associate Annotation with 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
+            // TODO: add structures to sequence
           }
 
           // Split accession in id and from/to
@@ -188,19 +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);
-        	    }
+            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
@@ -442,7 +442,8 @@ public class StockholmFile extends AlignFile
               ann = new Hashtable();
               seqAnn.put(acc, ann);
             }
-            //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence
+            // 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"))
@@ -477,24 +478,25 @@ 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);
-             }
+
+            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
           {
@@ -521,8 +523,8 @@ public class StockholmFile extends AlignFile
     }
   }
 
-  protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,
-          String label, String annots)
+  protected static AlignmentAnnotation parseAnnotationRow(
+          Vector annotation, String label, String annots)
   {
     String convert1, convert2 = null;
 
@@ -600,7 +602,7 @@ 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: ");
+      // System.out.println("else: ");
     }
     return annot;
   }