JAL-3532 TODO comment

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index f5b5177..b9f1274 100644 (file)
--- 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;
 
@@ -83,6 +85,14 @@ public class StockholmFile extends AlignFile
   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;
@@ -197,7 +207,7 @@ 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 = "";
@@ -519,6 +529,9 @@ 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));
           }
         }
@@ -658,7 +671,7 @@ 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 +723,7 @@ 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)
@@ -824,9 +837,14 @@ public class StockholmFile extends AlignFile
     }
     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"))
     {
@@ -844,7 +862,7 @@ 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);
@@ -917,6 +935,11 @@ public class StockholmFile extends AlignFile
     return annot;
   }
 
+  private String dbref_to_ac_record(DBRefEntry ref)
+  {
+    return ref.getSource().toString() + " ; "
+            + ref.getAccessionId().toString();
+  }
   @Override
   public String print(SequenceI[] s, boolean jvSuffix)
   {
@@ -931,6 +954,7 @@ public class StockholmFile extends AlignFile
     Hashtable dataRef = null;
     while ((in < s.length) && (s[in] != null))
     {
+      boolean isAA = s[in].isProtein();
       String tmp = printId(s[in], jvSuffix);
       max = Math.max(max, s[in].getLength());
 
@@ -940,17 +964,33 @@ 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)
+        {
+          dataRef.put(tmp, dbref_to_ac_record(primrefs.get(0)));
+        }
+        else
         {
-          if (dataRef == null)
+          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++;
@@ -1114,22 +1154,36 @@ public class StockholmFile extends AlignFile
     String ch = (annot == null)
             ? ((sequenceI == null) ? "-"
                     : Character.toString(sequenceI.getCharAt(k)))
-            : annot.displayCharacter;
+            : (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)
@@ -1144,7 +1198,9 @@ public class StockholmFile extends AlignFile
     {
       seq = ch.charAt(1);
     }
-    return seq;
+
+    return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+            : seq;
   }
 
   public String print()