X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=58b171da24b96ef58fd6e1be6d2c4f9a676028f4;hb=d25ed8f9fb513fe5c33823afbeeb557c73a8c27b;hp=3b0dab41edeeb0b916f8920033dab51e5cb3baa7;hpb=6684899d56d5bfb61faf814560010d7cb7b8bd95;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 3b0dab4..58b171d 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -28,11 +28,13 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -41,11 +43,12 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.StringTokenizer;
+import java.util.Map.Entry;
 import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
@@ -74,23 +77,50 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class StockholmFile extends AlignFile
 {
-  private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+  private static final String ANNOTATION = "annotation";
 
-  private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+  private static final char UNDERSCORE = '_';
 
-  private static final Regex DETECT_BRACKETS = new Regex(
-          "(<|>|\\[|\\]|\\(|\\))");
+  // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+  // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
 
-  StringBuffer out; // output buffer
+  public static final Regex DETECT_BRACKETS = new Regex(
+          "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
 
-  AlignmentI al;
+  /*
+   * lookup table of Stockholm 'feature' (annotation) types
+   * see http://sonnhammer.sbc.su.se/Stockholm.html
+   */
+  private static Map<String, String> featureTypes = null;
+
+  static
+  {
+    featureTypes = new HashMap<>();
+    featureTypes.put("SS", "Secondary Structure");
+    featureTypes.put("SA", "Surface Accessibility");
+    featureTypes.put("TM", "transmembrane");
+    featureTypes.put("PP", "Posterior Probability");
+    featureTypes.put("LI", "ligand binding");
+    featureTypes.put("AS", "active site");
+    featureTypes.put("IN", "intron");
+    featureTypes.put("IR", "interacting residue");
+    featureTypes.put("AC", "accession");
+    featureTypes.put("OS", "organism");
+    featureTypes.put("CL", "class");
+    featureTypes.put("DE", "description");
+    featureTypes.put("DR", "reference");
+    featureTypes.put("LO", "look");
+    featureTypes.put("RF", "Reference Positions");
+  }
+
+  private AlignmentI al;
 
   public StockholmFile()
   {
   }
 
   /**
-   * Creates a new StockholmFile object for output.
+   * Creates a new StockholmFile object for output
    */
   public StockholmFile(AlignmentI al)
   {
@@ -108,6 +138,47 @@ public class StockholmFile extends AlignFile
     super(source);
   }
 
+  /**
+   * Answers the readable description for a (case-sensitive) annotation type
+   * code, for example "Reference Positions" for "RF". Returns the type code if
+   * no description is found.
+   * 
+   * @param id
+   * @return
+   */
+  public static String typeToDescription(String id)
+  {
+    if (featureTypes.containsKey(id))
+    {
+      return featureTypes.get(id);
+    }
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type code " + id);
+    return id;
+  }
+
+  /**
+   * Answers the annotation type code for a (non-case-sensitive) readable
+   * description, for example "RF" for "Reference Positions" (or null if not
+   * found)
+   * 
+   * @param description
+   * @return
+   */
+  public static String descriptionToType(String description)
+  {
+    for (Entry<String, String> entry : featureTypes.entrySet())
+    {
+      if (entry.getValue().equalsIgnoreCase(description))
+      {
+        return entry.getKey();
+      }
+    }
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type: " + description);
+    return null;
+  }
+
   @Override
   public void initData()
   {
@@ -163,8 +234,8 @@ public class StockholmFile extends AlignFile
 
       for (int k = 0; k < rna.length(); k++)
       {
-        ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
-                annot[k]).charAt(0), 0f);
+        ann[k] = new Annotation(annot[k], "",
+                Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
 
       }
       AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
@@ -195,7 +266,7 @@ public class StockholmFile extends AlignFile
     String version;
     // String id;
     Hashtable seqAnn = new Hashtable(); // Sequence related annotations
-    LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+    LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
     Regex p, r, rend, s, x;
     // Temporary line for processing RNA annotation
     // String RNAannot = "";
@@ -207,9 +278,8 @@ public class StockholmFile extends AlignFile
     r = new Regex("# STOCKHOLM ([\\d\\.]+)");
     if (!r.search(nextLine()))
     {
-      throw new IOException(
-              MessageManager
-                      .getString("exception.stockholm_invalid_format"));
+      throw new IOException(MessageManager
+              .getString("exception.stockholm_invalid_format"));
     }
     else
     {
@@ -218,7 +288,7 @@ public class StockholmFile extends AlignFile
       // logger.debug("Stockholm version: " + version);
     }
 
-    // We define some Regexes here that will be used regularily later
+    // We define some Regexes here that will be used regularly later
     rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
     // id/from/to
@@ -231,7 +301,7 @@ public class StockholmFile extends AlignFile
     Regex closeparen = new Regex("(>|\\])", ")");
 
     // Detect if file is RNA by looking for bracket types
-    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+    // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 
     rend.optimize();
     p.optimize();
@@ -365,7 +435,12 @@ public class StockholmFile extends AlignFile
               Hashtable content = (Hashtable) features.remove(type);
 
               // add alignment annotation for this feature
-              String key = type2id(type);
+              String key = descriptionToType(type);
+
+              /*
+               * have we added annotation rows for this type ?
+               */
+              boolean annotsAdded = false;
               if (key != null)
               {
                 if (accAnnotations != null
@@ -374,6 +449,7 @@ public class StockholmFile extends AlignFile
                   Vector vv = (Vector) accAnnotations.get(key);
                   for (int ii = 0; ii < vv.size(); ii++)
                   {
+                    annotsAdded = true;
                     AlignmentAnnotation an = (AlignmentAnnotation) vv
                             .elementAt(ii);
                     seqO.addAlignmentAnnotation(an);
@@ -386,6 +462,11 @@ public class StockholmFile extends AlignFile
               while (j.hasMoreElements())
               {
                 String desc = j.nextElement().toString();
+                if (ANNOTATION.equals(desc) && annotsAdded)
+                {
+                  // don't add features if we already added an annotation row
+                  continue;
+                }
                 String ns = content.get(desc).toString();
                 char[] byChar = ns.toCharArray();
                 for (int k = 0; k < byChar.length; k++)
@@ -401,7 +482,7 @@ public class StockholmFile extends AlignFile
                     int new_pos = posmap[k]; // look up nearest seqeunce
                     // position to this column
                     SequenceFeature feat = new SequenceFeature(type, desc,
-                            new_pos, new_pos, 0f, null);
+                            new_pos, new_pos, null);
 
                     seqO.addSequenceFeature(feat);
                   }
@@ -428,8 +509,8 @@ 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)
@@ -572,22 +653,11 @@ public class StockholmFile extends AlignFile
           {
             String acc = s.stringMatched(1);
             String type = s.stringMatched(2);
-            String seq = new String(s.stringMatched(3));
-            String description = null;
-            // Check for additional information about the current annotation
-            // We use a simple string tokenizer here for speed
-            StringTokenizer sep = new StringTokenizer(seq, " \t");
-            description = sep.nextToken();
-            if (sep.hasMoreTokens())
-            {
-              seq = sep.nextToken();
-            }
-            else
-            {
-              seq = description;
-              description = new String();
-            }
-            // sequence id with from-to fields
+            String oseq = s.stringMatched(3);
+            /*
+             * copy of annotation field that may be processed into whitespace chunks
+             */
+            String seq = new String(oseq);
 
             Hashtable ann;
             // Get an object with all the annotations for this sequence
@@ -602,8 +672,12 @@ public class StockholmFile extends AlignFile
               ann = new Hashtable();
               seqAnn.put(acc, ann);
             }
+
+            // // start of block for appending annotation lines for wrapped
+            // stokchholm file
             // 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"))
@@ -619,27 +693,31 @@ public class StockholmFile extends AlignFile
             }
 
             Hashtable content;
-            if (features.containsKey(this.id2type(type)))
+            if (features.containsKey(StockholmFile.typeToDescription(type)))
             {
               // logger.debug("Found content for " + this.id2type(type));
-              content = (Hashtable) features.get(this.id2type(type));
+              content = (Hashtable) features
+                      .get(StockholmFile.typeToDescription(type));
             }
             else
             {
               // logger.debug("Creating new content holder for " +
               // this.id2type(type));
               content = new Hashtable();
-              features.put(this.id2type(type), content);
+              features.put(StockholmFile.typeToDescription(type), content);
             }
-            String ns = (String) content.get(description);
+            String ns = (String) content.get(ANNOTATION);
+
             if (ns == null)
             {
               ns = "";
             }
+            // finally, append the annotation line
             ns += seq;
-            content.put(description, ns);
+            content.put(ANNOTATION, ns);
+            // // end of wrapped annotation block.
+            // // Now a new row is created with the current set of data
 
-            // if(type.equals("SS")){
             Hashtable strucAnn;
             if (seqAnn.containsKey(acc))
             {
@@ -650,21 +728,22 @@ public class StockholmFile extends AlignFile
               strucAnn = new Hashtable();
             }
 
-            Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+            Vector<AlignmentAnnotation> newStruc = new Vector<>();
             parseAnnotationRow(newStruc, type, ns);
             for (AlignmentAnnotation alan : newStruc)
             {
               alan.visible = false;
             }
-            // annotations.addAll(newStruc);
+            // new annotation overwrites any existing annotation...
+
             strucAnn.put(type, newStruc);
             seqAnn.put(acc, strucAnn);
           }
           // }
           else
           {
-            System.err
-                    .println("Warning - couldn't parse sequence annotation row line:\n"
+            System.err.println(
+                    "Warning - couldn't parse sequence annotation row line:\n"
                             + line);
             // throw new IOException("Error parsing " + line);
           }
@@ -672,8 +751,8 @@ 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 }));
         }
       }
     }
@@ -701,7 +780,7 @@ public class StockholmFile extends AlignFile
   private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
   {
     DBRefEntry dbrf = null;
-    List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> dbrs = new ArrayList<>();
     String seqdb = "Unknown", sdbac = "" + dbr;
     int st = -1, en = -1, p;
     if ((st = sdbac.indexOf("/")) > -1)
@@ -786,8 +865,10 @@ 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);
       }
@@ -798,29 +879,36 @@ public class StockholmFile extends AlignFile
           Vector<AlignmentAnnotation> annotation, String label,
           String annots)
   {
-    String convert1, convert2 = null;
-
-    convert1 = OPEN_PAREN.replaceAll(annots);
-    convert2 = CLOSE_PAREN.replaceAll(convert1);
-    annots = convert2;
+    // String convert1 = OPEN_PAREN.replaceAll(annots);
+    // String convert2 = CLOSE_PAREN.replaceAll(convert1);
+    // annots = convert2;
 
     String type = label;
     if (label.contains("_cons"))
     {
-      type = (label.indexOf("_cons") == label.length() - 5) ? label
-              .substring(0, label.length() - 5) : label;
+      type = (label.indexOf("_cons") == label.length() - 5)
+              ? label.substring(0, label.length() - 5)
+              : label;
     }
-    boolean ss = false;
-    type = id2type(type);
-    if (type.equals("secondary structure"))
+    boolean ss = false, posterior = false;
+    type = typeToDescription(type);
+    if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
     }
+    if (type.equalsIgnoreCase("posterior probability"))
+    {
+      posterior = true;
+    }
     // decide on secondary structure or not.
     Annotation[] els = new Annotation[annots.length()];
     for (int i = 0; i < annots.length(); i++)
     {
       String pos = annots.substring(i, i + 1);
+      if (UNDERSCORE == pos.charAt(0))
+      {
+        pos = " ";
+      }
       Annotation ann;
       ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
       // be written out
@@ -831,23 +919,43 @@ public class StockholmFile extends AlignFile
           if (DETECT_BRACKETS.search(pos))
           {
             ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
+            ann.displayCharacter = "" + pos.charAt(0);
           }
           else
           {
             ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
                     .charAt(0);
-          }
 
-          if (ann.secondaryStructure == pos.charAt(0))
-          {
-            ann.displayCharacter = ""; // null; // " ";
+            if (ann.secondaryStructure == pos.charAt(0))
+            {
+              ann.displayCharacter = ""; // null; // " ";
+            }
+            else
+            {
+              ann.displayCharacter = " " + ann.displayCharacter;
+            }
           }
-          else
+        }
+
+      }
+      if (posterior && !ann.isWhitespace()
+              && !Comparison.isGap(pos.charAt(0)))
+      {
+        float val = 0;
+        // symbol encodes values - 0..*==0..10
+        if (pos.charAt(0) == '*')
+        {
+          val = 10;
+        }
+        else
+        {
+          val = pos.charAt(0) - '0';
+          if (val > 9)
           {
-            ann.displayCharacter = " " + ann.displayCharacter;
+            val = 10;
           }
         }
-
+        ann.value = val;
       }
 
       els[i] = ann;
@@ -882,153 +990,123 @@ public class StockholmFile extends AlignFile
   }
 
   @Override
-  public String print(SequenceI[] s, boolean jvSuffix)
+  public String print(final SequenceI[] sequences, boolean jvSuffix)
   {
-    out = new StringBuffer();
+    StringBuilder out = new StringBuilder();
     out.append("# STOCKHOLM 1.0");
     out.append(newline);
 
-    // find max length of id
-    int max = 0;
-    int maxid = 0;
-    int in = 0;
-    Hashtable dataRef = null;
-    while ((in < s.length) && (s[in] != null))
+    int maxIdWidth = 0;
+    for (SequenceI seq : sequences)
     {
-      String tmp = printId(s[in], jvSuffix);
-      if (s[in].getSequence().length > max)
+      if (seq != null)
       {
-        max = s[in].getSequence().length;
-      }
-
-      if (tmp.length() > maxid)
-      {
-        maxid = tmp.length();
-      }
-      if (s[in].getDBRefs() != null)
-      {
-        for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
-        {
-          if (dataRef == null)
-          {
-            dataRef = new Hashtable();
-          }
-
-          String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
-                  + " ; "
-                  + s[in].getDBRefs()[idb].getAccessionId().toString();
-          dataRef.put(tmp, datAs1);
-        }
+        String formattedId = printId(seq, jvSuffix);
+        maxIdWidth = Math.max(maxIdWidth, formattedId.length());
       }
-      in++;
     }
-    maxid += 9;
-    int i = 0;
+    maxIdWidth += 9;
 
-    // output database type
-    if (al.getProperties() != null)
+    /*
+     * generic alignment properties
+     */
+    Hashtable props = al.getProperties();
+    if (props != null)
     {
-      if (!al.getProperties().isEmpty())
+      for (Object key : props.keySet())
       {
-        Enumeration key = al.getProperties().keys();
-        Enumeration val = al.getProperties().elements();
-        while (key.hasMoreElements())
-        {
-          out.append("#=GF " + key.nextElement() + " " + val.nextElement());
-          out.append(newline);
-        }
+        out.append(String.format("#=GF %s %s", key.toString(),
+                props.get(key).toString()));
+        out.append(newline);
       }
     }
 
-    // output database accessions
-    if (dataRef != null)
+    /*
+     * output database accessions as #=GS (per sequence annotation)
+     * PFAM or RFAM are output as AC <accession number>
+     * others are output as DR <dbname> ; <accession>
+     */
+    Format formatter = new Format("%-" + (maxIdWidth - 2) + "s");
+    for (SequenceI seq : sequences)
     {
-      Enumeration en = dataRef.keys();
-      while (en.hasMoreElements())
+      if (seq != null)
       {
-        Object idd = en.nextElement();
-        String type = (String) dataRef.remove(idd);
-        out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS "
-                + idd.toString() + " "));
-        if (type.contains("PFAM") || type.contains("RFAM"))
-        {
-
-          out.append(" AC " + type.substring(type.indexOf(";") + 1));
-        }
-        else
+        DBRefEntry[] dbRefs = seq.getDBRefs();
+        if (dbRefs != null)
         {
-          out.append(" DR " + type + " ");
+          String idField = formatter
+                  .form("#=GS " + printId(seq, jvSuffix) + " ");
+          for (DBRefEntry dbRef : dbRefs)
+          {
+            out.append(idField);
+            printDbRef(out, dbRef);
+          }
         }
-        out.append(newline);
       }
     }
 
-    // output annotations
-    while (i < s.length && s[i] != null)
+    /*
+     * output annotations
+     */
+    for (SequenceI seq : sequences)
     {
-      if (s[i].getDatasetSequence() != null)
+      if (seq != null)
       {
-        SequenceI ds = s[i].getDatasetSequence();
-        AlignmentAnnotation[] alAnot;
-        Annotation[] ann;
-        Annotation annot;
-        alAnot = s[i].getAnnotation();
-        String feature = "";
+        AlignmentAnnotation[] alAnot = seq.getAnnotation();
         if (alAnot != null)
         {
           for (int j = 0; j < alAnot.length; j++)
           {
-
-            String key = type2id(alAnot[j].label);
-            boolean isrna = alAnot[j].isValidStruc();
-
+            AlignmentAnnotation ann = alAnot[j];
+            String key = descriptionToType(ann.label);
+            boolean isrna = ann.isValidStruc();
             if (isrna)
             {
-              // hardwire to secondary structure if there is RNA secondary
-              // structure on the annotation
+              /*
+               * output as secondary structure if there is 
+               * RNA secondary structure on the annotation
+               */
               key = "SS";
             }
             if (key == null)
             {
-
               continue;
             }
 
-            // out.append("#=GR ");
-            out.append(new Format("%-" + maxid + "s").form("#=GR "
-                    + printId(s[i], jvSuffix) + " " + key + " "));
-            ann = alAnot[j].annotations;
-            String seq = "";
-            for (int k = 0; k < ann.length; k++)
+            out.append(new Format("%-" + maxIdWidth + "s").form(
+                    "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
+            Annotation[] anns = ann.annotations;
+            StringBuilder seqString = new StringBuilder();
+            for (int k = 0; k < anns.length; k++)
             {
-              seq += outputCharacter(key, k, isrna, ann, s[i]);
+              seqString
+                      .append(getAnnotationCharacter(key, k, anns[k], seq));
             }
-            out.append(seq);
+            out.append(seqString.toString());
             out.append(newline);
           }
         }
-      }
 
-      out.append(new Format("%-" + maxid + "s")
-              .form(printId(s[i], jvSuffix) + " "));
-      out.append(s[i].getSequenceAsString());
-      out.append(newline);
-      i++;
+        out.append(new Format("%-" + maxIdWidth + "s")
+                .form(printId(seq, jvSuffix) + " "));
+        out.append(seq.getSequenceAsString());
+        out.append(newline);
+      }
     }
 
-    // alignment annotation
-    AlignmentAnnotation aa;
+    /*
+     * output alignment annotation (but not auto-calculated or sequence-related)
+     */
     if (al.getAlignmentAnnotation() != null)
     {
       for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
       {
-        aa = al.getAlignmentAnnotation()[ia];
+        AlignmentAnnotation aa = al.getAlignmentAnnotation()[ia];
         if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
         {
           continue;
         }
-        String seq = "";
-        String label;
+        String label = aa.label;
         String key = "";
         if (aa.label.equals("seq"))
         {
@@ -1036,30 +1114,28 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          key = type2id(aa.label.toLowerCase());
-          if (key == null)
+          key = descriptionToType(aa.label);
+          if ("RF".equals(key))
           {
-            label = aa.label;
+            label = key;
           }
-          else
+          else if (key != null)
           {
             label = key + "_cons";
           }
         }
-        if (label == null)
-        {
-          label = aa.label;
-        }
         label = label.replace(" ", "_");
 
-        out.append(new Format("%-" + maxid + "s").form("#=GC " + label
-                + " "));
-        boolean isrna = aa.isValidStruc();
+        out.append(
+                new Format("%-" + maxIdWidth + "s")
+                        .form("#=GC " + label + " "));
+        StringBuilder sb = new StringBuilder(aa.annotations.length);
         for (int j = 0; j < aa.annotations.length; j++)
         {
-          seq += outputCharacter(key, j, isrna, aa.annotations, null);
+          sb.append(
+                  getAnnotationCharacter(key, j, aa.annotations[j], null));
         }
-        out.append(seq);
+        out.append(sb.toString());
         out.append(newline);
       }
     }
@@ -1071,28 +1147,50 @@ public class StockholmFile extends AlignFile
   }
 
   /**
-   * add an annotation character to the output row
+   * A helper method that appends a formatted dbref to the output buffer
+   * 
+   * @param out
+   * @param dbRef
+   */
+  protected void printDbRef(StringBuilder out, DBRefEntry dbRef)
+  {
+    String db = dbRef.getSource();
+    String acc = dbRef.getAccessionId();
+    if (DBRefSource.PFAM.equalsIgnoreCase(db)
+            || DBRefSource.RFAM.equalsIgnoreCase(db))
+    {
+      out.append(" AC " + acc);
+    }
+    else
+    {
+      out.append(" DR " + db + " ; " + acc);
+    }
+    out.append(newline);
+  }
+
+  /**
+   * Returns an annotation character to add to the output row
    * 
    * @param seq
    * @param key
    * @param k
-   * @param isrna
    * @param ann
    * @param sequenceI
    */
-  private char outputCharacter(String key, int k, boolean isrna,
-          Annotation[] ann, SequenceI sequenceI)
+  static char getAnnotationCharacter(String key, int k, Annotation annot,
+          SequenceI sequenceI)
   {
     char seq = ' ';
-    Annotation annot = ann[k];
-    String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
-            .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
+    String ch = (annot == null)
+            ? ((sequenceI == null) ? "-"
+                    : Character.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);
+        // Stockholm format requires underscore, not space
+        return UNDERSCORE;
       }
       else
       {
@@ -1119,77 +1217,6 @@ public class StockholmFile extends AlignFile
     return seq;
   }
 
-  public String print()
-  {
-    out = new StringBuffer();
-    out.append("# STOCKHOLM 1.0");
-    out.append(newline);
-    print(getSeqsAsArray(), false);
-
-    out.append("//");
-    out.append(newline);
-    return out.toString();
-  }
-
-  private static Hashtable typeIds = null;
-
-  static
-  {
-    if (typeIds == null)
-    {
-      typeIds = new Hashtable();
-      typeIds.put("SS", "secondary structure");
-      typeIds.put("SA", "surface accessibility");
-      typeIds.put("TM", "transmembrane");
-      typeIds.put("PP", "posterior probability");
-      typeIds.put("LI", "ligand binding");
-      typeIds.put("AS", "active site");
-      typeIds.put("IN", "intron");
-      typeIds.put("IR", "interacting residue");
-      typeIds.put("AC", "accession");
-      typeIds.put("OS", "organism");
-      typeIds.put("CL", "class");
-      typeIds.put("DE", "description");
-      typeIds.put("DR", "reference");
-      typeIds.put("LO", "look");
-      typeIds.put("RF", "reference positions");
-
-    }
-  }
-
-  protected static String id2type(String id)
-  {
-    if (typeIds.containsKey(id))
-    {
-      return (String) typeIds.get(id);
-    }
-    System.err.println("Warning : Unknown Stockholm annotation type code "
-            + id);
-    return id;
-  }
-
-  protected static String type2id(String type)
-  {
-    String key = null;
-    Enumeration e = typeIds.keys();
-    while (e.hasMoreElements())
-    {
-      Object ll = e.nextElement();
-      if (typeIds.get(ll).toString().equals(type))
-      {
-        key = (String) ll;
-        break;
-      }
-    }
-    if (key != null)
-    {
-      return key;
-    }
-    System.err.println("Warning : Unknown Stockholm annotation type: "
-            + type);
-    return key;
-  }
-
   /**
    * make a friendly ID string.
    *