X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=344c4e1e940f9c295bf35b4f8ef6f34a26b179b6;hb=3609d4b908fa64cab35f2348401baab3347188fc;hp=8d340f2fe7eec06b31ed717e19c17688a1b495b0;hpb=d2e495268df6f50286b972f1145f302ad181da00;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 8d340f2..344c4e1 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -28,12 +28,14 @@ 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.DBRefUtils;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -74,23 +76,38 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class StockholmFile extends AlignFile
 {
+  private static final String ANNOTATION = "annotation";
+
+  private static final char UNDERSCORE = '_';
+  
   private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
 
   private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
 
+  // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+  // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+
   public static final Regex DETECT_BRACKETS = new Regex(
           "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
 
+  // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+  public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+
+  // use the following regex to decide an annotations (whole) line is NOT an RNA
+  // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
+  private static final Regex NOT_RNASS = new Regex(
+          "^[^<>[\\](){}A-DF-Za-df-z]*$");
+
   StringBuffer out; // output buffer
 
-  AlignmentI al;
+  private AlignmentI al;
 
   public StockholmFile()
   {
   }
 
   /**
-   * Creates a new StockholmFile object for output.
+   * Creates a new StockholmFile object for output
    */
   public StockholmFile(AlignmentI al)
   {
@@ -163,8 +180,8 @@ 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.",
@@ -207,9 +224,8 @@ 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 +234,7 @@ 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
@@ -323,17 +339,14 @@ public class StockholmFile extends AlignFile
 
           if (accAnnotations != null && accAnnotations.containsKey("AC"))
           {
-            if (dbsource != null)
+            String dbr = (String) accAnnotations.get("AC");
+            if (dbr != null)
             {
-              String dbr = (String) accAnnotations.get("AC");
-              if (dbr != null)
-              {
-                // we could get very clever here - but for now - just try to
-                // guess accession type from source of alignment plus structure
-                // of accession
-                guessDatabaseFor(seqO, dbr, dbsource);
-
-              }
+              // we could get very clever here - but for now - just try to
+              // guess accession type from type of sequence, source of alignment plus
+              // structure
+              // of accession
+              guessDatabaseFor(seqO, dbr, dbsource);
             }
             // else - do what ? add the data anyway and prompt the user to
             // specify what references these are ?
@@ -392,7 +405,7 @@ public class StockholmFile extends AlignFile
               while (j.hasMoreElements())
               {
                 String desc = j.nextElement().toString();
-                if ("annotations".equals(desc) && annotsAdded)
+                if (ANNOTATION.equals(desc) && annotsAdded)
                 {
                   // don't add features if we already added an annotation row
                   continue;
@@ -412,7 +425,7 @@ 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);
                   }
@@ -439,8 +452,8 @@ 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)
@@ -518,6 +531,9 @@ public class StockholmFile extends AlignFile
               treeName = an.stringMatched(2);
               treeString = new StringBuffer();
             }
+            // TODO: JAL-3532 - this is where GF comments and database references are lost
+            // suggest overriding this method for Stockholm files to catch and properly
+            // process CC, DR etc into multivalued properties
             setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
           }
         }
@@ -626,16 +642,17 @@ public class StockholmFile extends AlignFile
             if (features.containsKey(this.id2type(type)))
             {
               // logger.debug("Found content for " + this.id2type(type));
-              content = (Hashtable) features.get(this.id2type(type));
+              content = (Hashtable) features
+                      .get(this.id2type(type));
             }
             else
             {
               // logger.debug("Creating new content holder for " +
               // this.id2type(type));
               content = new Hashtable();
-              features.put(this.id2type(type), content);
+              features.put(id2type(type), content);
             }
-            String ns = (String) content.get("annotation");
+            String ns = (String) content.get(ANNOTATION);
 
             if (ns == null)
             {
@@ -643,7 +660,7 @@ public class StockholmFile extends AlignFile
             }
             // finally, append the annotation line
             ns += seq;
-            content.put("annotation", ns);
+            content.put(ANNOTATION, ns);
             // // end of wrapped annotation block.
             // // Now a new row is created with the current set of data
 
@@ -671,8 +688,8 @@ public class StockholmFile extends AlignFile
           // }
           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);
           }
@@ -680,8 +697,8 @@ 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 }));
         }
       }
     }
@@ -746,6 +763,12 @@ public class StockholmFile extends AlignFile
         st = -1;
       }
     }
+    if (dbsource == null)
+    {
+      // make up an origin based on whether the sequence looks like it is nucleotide
+      // or protein
+      dbsource = (seqO.isProtein()) ? "PFAM" : "RFAM";
+    }
     if (dbsource.equals("PFAM"))
     {
       seqdb = "UNIPROT";
@@ -794,8 +817,10 @@ 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);
       }
@@ -806,23 +831,29 @@ 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);
+	  String convert1, convert2 = null;
+    // 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, posterior = false;
     type = id2type(type);
+
+    boolean isrnass = false;
+
     if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
+      isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+                                           // here (it's easier for dealing with
+                                           // other non-alpha-non-brace chars)
     }
     if (type.equalsIgnoreCase("posterior probability"))
     {
@@ -833,6 +864,10 @@ public class StockholmFile extends AlignFile
     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
@@ -840,7 +875,7 @@ public class StockholmFile extends AlignFile
       {
         // if (" .-_".indexOf(pos) == -1)
         {
-          if (DETECT_BRACKETS.search(pos))
+          if (isrnass && RNASS_BRACKETS.indexOf(pos) >= 0)
           {
             ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
             ann.displayCharacter = "" + pos.charAt(0);
@@ -850,14 +885,14 @@ public class StockholmFile extends AlignFile
             ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
                     .charAt(0);
 
-          if (ann.secondaryStructure == pos.charAt(0))
-          {
-            ann.displayCharacter = ""; // null; // " ";
-          }
-          else
-          {
-            ann.displayCharacter = " " + ann.displayCharacter;
-          }
+            if (ann.secondaryStructure == pos.charAt(0))
+            {
+              ann.displayCharacter = ""; // null; // " ";
+            }
+            else
+            {
+              ann.displayCharacter = " " + ann.displayCharacter;
+            }
           }
         }
 
@@ -913,15 +948,13 @@ public class StockholmFile extends AlignFile
     return annot;
   }
 
-  @Override
-  public String print(SequenceI[] s, boolean jvSuffix)
+  private String dbref_to_ac_record(DBRefEntry ref)
   {
-    String string = print(s, jvSuffix, false);
-    return string;
+    return ref.getSource().toString() + " ; "
+            + ref.getAccessionId().toString();
   }
-
-  public String print(SequenceI[] s, boolean jvSuffix,
-          boolean removeAnnotations)
+  @Override
+  public String print(SequenceI[] s, boolean jvSuffix)
   {
     out = new StringBuffer();
     out.append("# STOCKHOLM 1.0");
@@ -932,13 +965,12 @@ public class StockholmFile extends AlignFile
     int maxid = 0;
     int in = 0;
     Hashtable dataRef = null;
+    boolean isAA = s[in].isProtein();
     while ((in < s.length) && (s[in] != null))
     {
+
       String tmp = printId(s[in], jvSuffix);
-      if (s[in].getSequence().length > max)
-      {
-        max = s[in].getSequence().length;
-      }
+      max = Math.max(max, s[in].getLength());
 
       if (tmp.length() > maxid)
       {
@@ -946,17 +978,33 @@ public class StockholmFile extends AlignFile
       }
       if (s[in].getDBRefs() != null)
       {
-        for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
+        if (dataRef == null)
+        {
+          dataRef = new Hashtable();
+        }
+        List<DBRefEntry> primrefs = s[in].getPrimaryDBRefs();
+        if (primrefs.size() >= 1)
         {
-          if (dataRef == null)
+          dataRef.put(tmp, dbref_to_ac_record(primrefs.get(0)));
+        }
+        else
+        {
+          for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
           {
-            dataRef = new Hashtable();
+            DBRefEntry dbref = s[in].getDBRefs()[idb];
+            dataRef.put(tmp, dbref_to_ac_record(dbref));
+            // if we put in a uniprot or EMBL record then we're done:
+            if (isAA && DBRefSource.UNIPROT
+                    .equals(DBRefUtils.getCanonicalName(dbref.getSource())))
+            {
+              break;
+            }
+            if (!isAA && DBRefSource.EMBL
+                    .equals(DBRefUtils.getCanonicalName(dbref.getSource())))
+            {
+              break;
+            }
           }
-
-          String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
-                  + " ; "
-                  + s[in].getDBRefs()[idb].getAccessionId().toString();
-          dataRef.put(tmp, datAs1);
         }
       }
       in++;
@@ -987,9 +1035,10 @@ public class StockholmFile extends AlignFile
       {
         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(new Format("%-" + (maxid - 2) + "s")
+                .form("#=GS " + idd.toString() + " "));
+        if (isAA && type.contains("UNIPROT")
+                || (!isAA && type.contains("EMBL")))
         {
 
           out.append(" AC " + type.substring(type.indexOf(";") + 1));
@@ -1002,17 +1051,18 @@ public class StockholmFile extends AlignFile
       }
     }
 
-
-      // output annotations
-      while (i < s.length && s[i] != null)
+    // output annotations
+    while (i < s.length && s[i] != null)
+    {
+      AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+      if (alAnot != null)
       {
-        AlignmentAnnotation[] alAnot = s[i].getAnnotation();
-      if (alAnot != null && !removeAnnotations)
+        Annotation[] ann;
+
+        for (int j = 0; j < alAnot.length; j++)
         {
-          Annotation[] ann;
-          for (int j = 0; j < alAnot.length; j++)
+          if (alAnot[j].annotations != null)
           {
-
             String key = type2id(alAnot[j].label);
             boolean isrna = alAnot[j].isValidStruc();
 
@@ -1042,61 +1092,60 @@ public class StockholmFile extends AlignFile
           }
         }
 
-        out.append(new Format("%-" + maxid + "s")
-                .form(printId(s[i], jvSuffix) + " "));
-        out.append(s[i].getSequenceAsString());
-        out.append(newline);
-        i++;
       }
 
-    if (!removeAnnotations)
+      out.append(new Format("%-" + maxid + "s")
+              .form(printId(s[i], jvSuffix) + " "));
+      out.append(s[i].getSequenceAsString());
+      out.append(newline);
+      i++;
+    }
+
+    // alignment annotation
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
     {
-      // alignment annotation
-      AlignmentAnnotation aa;
-      if (al.getAlignmentAnnotation() != null)
+      for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
       {
-        for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
+        aa = al.getAlignmentAnnotation()[ia];
+        if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
         {
-          aa = al.getAlignmentAnnotation()[ia];
-          if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
-          {
-            continue;
-          }
-          String seq = "";
-          String label;
-          String key = "";
-          if (aa.label.equals("seq"))
+          continue;
+        }
+        String seq = "";
+        String label;
+        String key = "";
+        if (aa.label.equals("seq"))
+        {
+          label = "seq_cons";
+        }
+        else
+        {
+          key = type2id(aa.label.toLowerCase());
+          if (key == null)
           {
-            label = "seq_cons";
+            label = aa.label;
           }
           else
           {
-            key = type2id(aa.label.toLowerCase());
-            if (key == null)
-            {
-              label = aa.label;
-            }
-            else
-            {
-              label = key + "_cons";
-            }
-          }
-          if (label == null)
-          {
-            label = aa.label;
+            label = key + "_cons";
           }
-          label = label.replace(" ", "_");
+        }
+        if (label == null)
+        {
+          label = aa.label;
+        }
+        label = label.replace(" ", "_");
 
-          out.append(new Format("%-" + maxid + "s")
-                  .form("#=GC " + label + " "));
-          boolean isrna = aa.isValidStruc();
-          for (int j = 0; j < aa.annotations.length; j++)
-          {
-            seq += outputCharacter(key, j, isrna, aa.annotations, null);
-          }
-          out.append(seq);
-          out.append(newline);
+        out.append(
+                new Format("%-" + maxid + "s").form("#=GC " + label + " "));
+        boolean isrna = aa.isValidStruc();
+        for (int j = 0; j < aa.annotations.length; j++)
+        {
+          seq += outputCharacter(key, j, isrna, aa.annotations, null);
         }
+        out.append(seq);
+        out.append(newline);
       }
     }
 
@@ -1106,6 +1155,7 @@ public class StockholmFile extends AlignFile
     return out.toString();
   }
 
+
   /**
    * add an annotation character to the output row
    * 
@@ -1121,23 +1171,39 @@ public class StockholmFile extends AlignFile
   {
     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 == null
+                    ? String.valueOf(annot.secondaryStructure)
+                    : annot.displayCharacter);
+    if (ch == null)
+    {
+      ch = " ";
+    }
     if (key != null && key.equals("SS"))
     {
+      char ssannotchar = ' ';
+      boolean charset = false;
       if (annot == null)
       {
         // sensible gap character
-        return ' ';
+        ssannotchar = ' ';
+        charset = true;
       }
       else
       {
         // valid secondary structure AND no alternative label (e.g. ' B')
         if (annot.secondaryStructure > ' ' && ch.length() < 2)
         {
-          return annot.secondaryStructure;
+          ssannotchar = annot.secondaryStructure;
+          charset = true;
         }
       }
+      if (charset)
+      {
+        return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar;
+      }
     }
 
     if (ch.length() == 0)
@@ -1152,9 +1218,31 @@ public class StockholmFile extends AlignFile
     {
       seq = ch.charAt(1);
     }
-    return seq;
+
+    return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+            : seq;
   }
 
+  /**
+   * make a friendly ID string.
+   * 
+   * @param dataName
+   * @return truncated dataName to after last '/'
+   */
+  private String safeName(String dataName)
+  {
+    int b = 0;
+    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+    {
+      dataName = dataName.substring(b + 1).trim();
+
+    }
+    int e = (dataName.length() - dataName.indexOf(".")) + 1;
+    dataName = dataName.substring(1, e).trim();
+    return dataName;
+  }
+  
+  
   public String print()
   {
     out = new StringBuffer();
@@ -1162,6 +1250,7 @@ public class StockholmFile extends AlignFile
     out.append(newline);
     print(getSeqsAsArray(), false);
 
+    out.append("//");
     out.append(newline);
     return out.toString();
   }
@@ -1191,15 +1280,15 @@ public class StockholmFile extends AlignFile
 
     }
   }
-
+  
   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);
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type code " + id);
     return id;
   }
 
@@ -1220,27 +1309,8 @@ public class StockholmFile extends AlignFile
     {
       return key;
     }
-    System.err.println("Warning : Unknown Stockholm annotation type: "
-            + type);
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type: " + type);
     return key;
   }
-
-  /**
-   * make a friendly ID string.
-   * 
-   * @param dataName
-   * @return truncated dataName to after last '/'
-   */
-  private String safeName(String dataName)
-  {
-    int b = 0;
-    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
-    {
-      dataName = dataName.substring(b + 1).trim();
-
-    }
-    int e = (dataName.length() - dataName.indexOf(".")) + 1;
-    dataName = dataName.substring(1, e).trim();
-    return dataName;
-  }
 }