X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=ab80ffa8f3bf15678a792de78abac19567b50861;hb=d63bbc2d56c86d7dca68e76104a8682b5e38c763;hp=6490d28ab1c28329b28314c350be798632002e81;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 6490d28..ab80ffa 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -101,6 +101,7 @@ public class StockholmFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
@@ -178,6 +179,7 @@ public class StockholmFile extends AlignFile
    * @throws IOException
    *           If there is an error with the input file
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer treeString = new StringBuffer();
@@ -420,8 +422,8 @@ public class StockholmFile extends AlignFile
         {
           // logger.error("Could not parse sequence line: " + line);
           throw new IOException(MessageManager.formatMessage(
-                  "exception.couldnt_parse_sequence_line", new String[]
-                  { line }));
+                  "exception.couldnt_parse_sequence_line",
+                  new String[] { line }));
         }
         String ns = seqs.get(x.stringMatched(1));
         if (ns == null)
@@ -533,9 +535,8 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            throw new IOException(MessageManager.formatMessage(
-                    "exception.error_parsing_line", new String[]
-                    { line }));
+            // throw new IOException("Error parsing " + line);
+            System.err.println(">> missing annotation: " + line);
           }
         }
         else if (annType.equals("GC"))
@@ -665,8 +666,8 @@ public class StockholmFile extends AlignFile
         else
         {
           throw new IOException(MessageManager.formatMessage(
-                  "exception.unknown_annotation_detected", new String[]
-                  { annType, annContent }));
+                  "exception.unknown_annotation_detected", new String[] {
+                      annType, annContent }));
         }
       }
     }
@@ -779,9 +780,8 @@ public class StockholmFile extends AlignFile
     {
       for (DBRefEntry d : dbrs)
       {
-        jalview.util.MapList mp = new jalview.util.MapList(new int[]
-        { seqO.getStart(), seqO.getEnd() }, new int[]
-        { st, en }, 1, 1);
+        jalview.util.MapList mp = new jalview.util.MapList(new int[] {
+            seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
         jalview.datamodel.Mapping mping = new Mapping(mp);
         d.setMap(mping);
       }
@@ -826,7 +826,7 @@ public class StockholmFile extends AlignFile
       // be written out
       if (ss)
       {
-        //if (" .-_".indexOf(pos) == -1)
+        // if (" .-_".indexOf(pos) == -1)
         {
           if (detectbrackets.search(pos))
           {
@@ -848,7 +848,7 @@ public class StockholmFile extends AlignFile
             ann.displayCharacter = " " + ann.displayCharacter;
           }
         }
-        
+
       }
 
       els[i] = ann;
@@ -901,18 +901,18 @@ public class StockholmFile extends AlignFile
       {
         maxid = tmp.length();
       }
-      if (s[in].getDBRef() != null)
+      if (s[in].getDBRefs() != null)
       {
-        for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+        for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
         {
           if (dataRef == null)
           {
             dataRef = new Hashtable();
           }
 
-          String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+          String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
                   + " ; "
-                  + s[in].getDBRef()[idb].getAccessionId().toString();
+                  + s[in].getDBRefs()[idb].getAccessionId().toString();
           dataRef.put(tmp, datAs1);
         }
       }
@@ -1068,21 +1068,19 @@ public class StockholmFile extends AlignFile
    * @param ann
    * @param sequenceI
    */
-  private char outputCharacter(String key, int k,
-          boolean isrna, Annotation[] ann, SequenceI sequenceI)
+  private char outputCharacter(String key, int k, boolean isrna,
+          Annotation[] ann, SequenceI sequenceI)
   {
     char seq = ' ';
     Annotation annot = ann[k];
     String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
-            .toString(sequenceI.getCharAt(k)))
-            : annot.displayCharacter;
+            .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
     if (key != null && key.equals("SS"))
     {
       if (annot == null)
       {
         // sensible gap character if one is available or make one up
-        return sequenceI == null ? '-' : sequenceI
-                .getCharAt(k);
+        return sequenceI == null ? '-' : sequenceI.getCharAt(k);
       }
       else
       {
@@ -1109,6 +1107,7 @@ public class StockholmFile extends AlignFile
     return seq;
   }
 
+  @Override
   public String print()
   {
     out = new StringBuffer();