From f7bce11fb6036cd7f94e17c9f136970984a9402a Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Fri, 22 Jul 2011 13:11:03 +0200
Subject: [PATCH] JAL-878; Additional structures with a 'GR' tag in
 StockholmFiles are associated their specific sequence.

Change-Id: I26913db05bef3983b63397304c97351f5361d61d
---
 src/jalview/gui/SeqPanel.java     |   13 +++----------
 src/jalview/io/StockholmFile.java |   39 +++++++++++++++++++++++++++++++++++--
 2 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 6a03b53..a57c2e4 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1303,7 +1303,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     else
     // ///Editing a single sequence///////////
     {
-      if (insertGap && !editSeq)
+      if (insertGap)
       {
         // dragging to the right
         if (fixedColumns && fixedRight != -1)
@@ -1312,17 +1312,13 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             insertChar(j, new SequenceI[]
             { seq }, fixedRight);
-    		System.out.println("InsertGap1");
-
           }
         }
         else
         {
           editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
           { seq }, lastres, startres - lastres, av.alignment, true);
-          System.out.println("InsertGap2 - lastres: "+lastres+" startres: "+startres);
-
-        }
+         }
       }
       else
       {
@@ -1368,14 +1364,11 @@ public class SeqPanel extends JPanel implements MouseListener,
                 insertChar(j, new SequenceI[]
                 { seq }, fixedRight);
               }
-      		System.out.println("EditSeq1");
-
-            }
+              }
             else
             {
               editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
               { seq }, lastres, startres - lastres, av.alignment, true);
-      		System.out.println("EditSeq2");
              }
     	}
       }
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 2e0fea7..8f6a12f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -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;
   }
-- 
1.7.10.2