JAL-3816 bump version number and cut release notes

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 606540f..4697262 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;
 
@@ -205,7 +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 = "";
@@ -332,17 +334,14 @@ 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 ?
@@ -527,6 +526,9 @@ 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));
           }
         }
@@ -666,7 +668,7 @@ 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)
             {
@@ -718,7 +720,7 @@ 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)
@@ -755,6 +757,12 @@ 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";
@@ -930,6 +938,11 @@ 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)
   {
@@ -942,8 +955,10 @@ 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);
       max = Math.max(max, s[in].getLength());
 
@@ -953,17 +968,33 @@ 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++;
@@ -996,7 +1027,8 @@ public class StockholmFile extends AlignFile
         String type = (String) dataRef.remove(idd);
         out.append(new Format("%-" + (maxid - 2) + "s")
                 .form("#=GS " + idd.toString() + " "));
-        if (type.contains("PFAM") || type.contains("RFAM"))
+        if (isAA && type.contains("UNIPROT")
+                || (!isAA && type.contains("EMBL")))
         {
 
           out.append(" AC " + type.substring(type.indexOf(";") + 1));
@@ -1127,7 +1159,13 @@ 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 = ' ';
@@ -1149,11 +1187,7 @@ public class StockholmFile extends AlignFile
       }
       if (charset)
       {
-        if (ssannotchar == ' ' && isrna)
-        {
-          ssannotchar = '.';
-        }
-        return ssannotchar;
+        return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar;
       }
     }