X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;fp=src%2Fjalview%2Fio%2FStockholmFile.java;h=71e369eb6163e9bc31ecaa10336175c9d3e61f91;hb=e191ef5205d9700ee33955ff89e0b3a4597d17d1;hp=f5b517728c85ce77ad785c9030e7b7e475ed2046;hpb=1253fe4ed610223c3c3b4e4983ec542e818efdfe;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index f5b5177..71e369e 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -83,6 +83,8 @@ public class StockholmFile extends AlignFile
   public static final Regex DETECT_BRACKETS = new Regex(
           "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
 
+  public static final String RNASS_BRACKETS = "<>[]() {}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+
   StringBuffer out; // output buffer
 
   AlignmentI al;
@@ -197,7 +199,7 @@ 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 = "";
@@ -658,7 +660,7 @@ 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)
             {
@@ -710,7 +712,7 @@ 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)
@@ -814,6 +816,12 @@ public class StockholmFile extends AlignFile
     // convert1 = OPEN_PAREN.replaceAll(annots);
     // convert2 = CLOSE_PAREN.replaceAll(convert1);
     // annots = convert2;
+    
+    // DEBUG
+    System.out.println(
+            "*** parseAnnotationRow called with\n      annotation='"
+                    + annotation + "'\n      label='" + label
+                    + "'\n      annots='" + annots + "'");
 
     String type = label;
     if (label.contains("_cons"))
@@ -824,9 +832,12 @@ public class StockholmFile extends AlignFile
     }
     boolean ss = false, posterior = false;
     type = id2type(type);
+
+    boolean isrnass = false;
     if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
+      isrnass = DETECT_BRACKETS.search(annots);
     }
     if (type.equalsIgnoreCase("posterior probability"))
     {
@@ -844,7 +855,7 @@ 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);
@@ -1008,7 +1019,9 @@ public class StockholmFile extends AlignFile
 
           String key = type2id(alAnot[j].label);
           boolean isrna = alAnot[j].isValidStruc();
-
+          // bs debug
+          System.out.println("SEQUENCE " + i + "/" + s.length + " ISRNA="
+                  + isrna + ".");
           if (isrna)
           {
             // hardwire to secondary structure if there is RNA secondary
@@ -1030,6 +1043,9 @@ public class StockholmFile extends AlignFile
           {
             seq += outputCharacter(key, k, isrna, ann, s[i]);
           }
+          // bs debug
+          System.out.println("APPENDING SEQ: KEY=" + key + " ISRNA=" + isrna
+                  + ".\n" + "SEQ=" + seq + "\n");
           out.append(seq);
           out.append(newline);
         }
@@ -1038,6 +1054,8 @@ public class StockholmFile extends AlignFile
       out.append(new Format("%-" + maxid + "s")
               .form(printId(s[i], jvSuffix) + " "));
       out.append(s[i].getSequenceAsString());
+      // bs debug
+      System.out.println("ALSO APPENDING " + s[i].getSequenceAsString());
       out.append(newline);
       i++;
     }
@@ -1085,6 +1103,12 @@ public class StockholmFile extends AlignFile
         {
           seq += outputCharacter(key, j, isrna, aa.annotations, null);
         }
+        
+        // bs debug
+        System.out.println(
+                "PRINTING SEQ: KEY=" + key + " ISRNA=" + isrna + ".\n"
+                        + "SEQ=" + seq + "\n");
+        
         out.append(seq);
         out.append(newline);
       }
@@ -1117,18 +1141,30 @@ public class StockholmFile extends AlignFile
             : annot.displayCharacter;
     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)
+      {
+        if (ssannotchar == ' ' && isrna)
+        {
+          ssannotchar = '.';
         }
+        return ssannotchar;
       }
     }
 
@@ -1144,7 +1180,9 @@ public class StockholmFile extends AlignFile
     {
       seq = ch.charAt(1);
     }
-    return seq;
+
+    return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+            : seq;
   }
 
   public String print()