JAL-2507 capitalisation for annotation lines generated from stockholm annotation

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 8527f8b..c2f3683 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -33,6 +33,7 @@ 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;
 
@@ -45,7 +46,6 @@ import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.StringTokenizer;
 import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
@@ -366,6 +366,11 @@ public class StockholmFile extends AlignFile
 
               // add alignment annotation for this feature
               String key = type2id(type);
+
+              /*
+               * have we added annotation rows for this type ?
+               */
+              boolean annotsAdded = false;
               if (key != null)
               {
                 if (accAnnotations != null
@@ -374,6 +379,7 @@ 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 +392,11 @@ public class StockholmFile extends AlignFile
               while (j.hasMoreElements())
               {
                 String desc = j.nextElement().toString();
+                if ("annotations".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++)
@@ -572,22 +583,11 @@ 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 +602,12 @@ 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"))
@@ -631,15 +635,18 @@ public class StockholmFile extends AlignFile
               content = new Hashtable();
               features.put(this.id2type(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))
             {
@@ -656,7 +663,8 @@ public class StockholmFile extends AlignFile
             {
               alan.visible = false;
             }
-            // annotations.addAll(newStruc);
+            // new annotation overwrites any existing annotation...
+
             strucAnn.put(type, newStruc);
             seqAnn.put(acc, strucAnn);
           }
@@ -810,12 +818,16 @@ public class StockholmFile extends AlignFile
       type = (label.indexOf("_cons") == label.length() - 5) ? label
               .substring(0, label.length() - 5) : label;
     }
-    boolean ss = false;
+    boolean ss = false, posterior = false;
     type = id2type(type);
-    if (type.equals("secondary structure"))
+    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++)
@@ -831,12 +843,12 @@ 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))
           {
@@ -846,9 +858,29 @@ public class StockholmFile extends AlignFile
           {
             ann.displayCharacter = " " + ann.displayCharacter;
           }
+          }
         }
 
       }
+      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)
+          {
+            val = 10;
+          }
+        }
+        ann.value = val;
+      }
 
       els[i] = ann;
     }
@@ -1131,10 +1163,10 @@ public class StockholmFile extends AlignFile
     if (typeIds == null)
     {
       typeIds = new Hashtable();
-      typeIds.put("SS", "secondary structure");
-      typeIds.put("SA", "surface accessibility");
+      typeIds.put("SS", "Secondary Structure");
+      typeIds.put("SA", "Surface Accessibility");
       typeIds.put("TM", "transmembrane");
-      typeIds.put("PP", "posterior probability");
+      typeIds.put("PP", "Posterior Probability");
       typeIds.put("LI", "ligand binding");
       typeIds.put("AS", "active site");
       typeIds.put("IN", "intron");
@@ -1145,7 +1177,7 @@ public class StockholmFile extends AlignFile
       typeIds.put("DE", "description");
       typeIds.put("DR", "reference");
       typeIds.put("LO", "look");
-      typeIds.put("RF", "reference positions");
+      typeIds.put("RF", "Reference Positions");
 
     }
   }
@@ -1168,7 +1200,7 @@ public class StockholmFile extends AlignFile
     while (e.hasMoreElements())
     {
       Object ll = e.nextElement();
-      if (typeIds.get(ll).toString().equals(type))
+      if (typeIds.get(ll).toString().equalsIgnoreCase(type))
       {
         key = (String) ll;
         break;