X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=23c4d2179e8d2934e20a9c3f8291e6a400a26759;hb=df7802fdd54e7d3b12bda12ac55e6057c985bdf2;hp=96c462c11e9b5c24ff1c62affbd68ab833080840;hpb=0dc330c0d829ac668fbc8a323f5ad3e6d60c28f9;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 96c462c..23c4d21 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 2.8.2)
- * 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.
  * 
@@ -420,8 +420,8 @@ 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 +533,9 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            throw new IOException(MessageManager.formatMessage(
-                    "exception.error_parsing_line", new String[]
-                    { line }));
+            // throw new IOException(MessageManager.formatMessage(
+            // "exception.error_parsing_line", new String[] { line }));
+            System.err.println(">> missing annotation: " + line);
           }
         }
         else if (annType.equals("GC"))
@@ -665,8 +665,8 @@ 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 +779,8 @@ 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 +825,7 @@ public class StockholmFile extends AlignFile
       // be written out
       if (ss)
       {
-        //if (" .-_".indexOf(pos) == -1)
+        // if (" .-_".indexOf(pos) == -1)
         {
           if (detectbrackets.search(pos))
           {
@@ -848,7 +847,7 @@ public class StockholmFile extends AlignFile
             ann.displayCharacter = " " + ann.displayCharacter;
           }
         }
-        
+
       }
 
       els[i] = ann;
@@ -901,18 +900,18 @@ 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);
         }
       }
@@ -978,6 +977,7 @@ public class StockholmFile extends AlignFile
             {
               feature = ds.getSequenceFeatures()[0].type;
             }
+            // ?bug - feature may still have previous loop value
             String key = type2id(feature);
 
             if (key == null)
@@ -1027,13 +1027,21 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          label = (key = type2id(aa.label.toLowerCase())) + "_cons";
+          key = type2id(aa.label.toLowerCase());
+          if (key == null)
+          {
+            label = aa.label;
+          }
+          else
+          {
+            label = key + "_cons";
+          }
         }
-
         if (label == null)
         {
           label = aa.label;
         }
+        label = label.replace(" ", "_");
 
         out.append(new Format("%-" + maxid + "s").form("#=GC " + label
                 + " "));
@@ -1059,21 +1067,19 @@ 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;
-    if (key.equals("SS"))
+            .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
       {