parse alignment properties and add annotation rows for general alignment position...

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 10ddf53..9104a5f 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -62,12 +62,13 @@ public class StockholmFile
   public void parse()\r
       throws IOException\r
   {\r
+    StringBuffer treeString=new StringBuffer();\r
+    String treeName = null;\r
     // --------------- Variable Definitions -------------------\r
     String line;\r
     String version;\r
     //  String id;\r
-    Hashtable alAnn = new Hashtable(); // Alignment wide annotations\r
-    Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
+     Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
     Hashtable seqs = new Hashtable();\r
     Regex p, r, rend, s, x;\r
 \r
@@ -122,6 +123,14 @@ public class StockholmFile
           int start = 1;\r
           int end = -1;\r
           String sid = acc;\r
+          // Retrieve hash of annotations for this accession\r
+          Hashtable accAnnotations = null;\r
+          \r
+          if (seqAnn!=null && seqAnn.containsKey(acc))\r
+          {\r
+            accAnnotations = (Hashtable) seqAnn.get(acc);\r
+          }\r
+          \r
           // Split accession in id and from/to\r
           if (p.search(acc))\r
           {\r
@@ -132,11 +141,29 @@ public class StockholmFile
           //logger.debug(sid + ", " + start + ", " + end);\r
 \r
           Sequence seqO = new Sequence(sid, seq, start, end);\r
+          // Add Description (if any)\r
+          if (accAnnotations!=null && accAnnotations.containsKey("DE"))\r
+          {\r
+            String desc = (String) accAnnotations.get("DE");\r
+            seqO.setDescription((desc==null)?"" : desc);\r
+          }\r
+          // Add DB References (if any)\r
+          if (accAnnotations!=null && accAnnotations.containsKey("DR"))\r
+          {\r
+            String dbr = (String) accAnnotations.get("DR");\r
+            if (dbr!=null && dbr.indexOf(";")>-1)\r
+            {\r
+              String src = dbr.substring(0, dbr.indexOf(";"));\r
+              String acn = dbr.substring(dbr.indexOf(";")+1);\r
+              DBRefEntry dbref = new DBRefEntry(jalview.util.DBRefUtils.getCanonicalName(src), acn, "");\r
+              seqO.addDBRef(dbref);\r
+            }\r
+          }\r
           Hashtable features = null;\r
           // We need to adjust the positions of all features to account for gaps\r
           try\r
           {\r
-            features = (Hashtable) ( (Hashtable) seqAnn.get(acc)).get(\r
+            features = (Hashtable) accAnnotations.get(\r
                 "features");\r
           }\r
           catch (java.lang.NullPointerException e)\r
@@ -150,6 +177,9 @@ public class StockholmFile
             Enumeration i = features.keys();\r
             while (i.hasMoreElements())\r
             {\r
+              // TODO: parse out secondary structure annotation as annotation row\r
+              // TODO: parse out scores as annotation row\r
+              // TODO: map coding region to core jalview feature types\r
               String type = i.nextElement().toString();\r
               Hashtable content = (Hashtable) features.get(type);\r
 \r
@@ -258,7 +288,23 @@ public class StockholmFile
           Regex an = new Regex("(\\w+)\\s*(.*)");\r
           if (an.search(annContent))\r
           {\r
-            alAnn.put(an.stringMatched(1), an.stringMatched(2));\r
+            if (an.stringMatched(1).equals("NH"))\r
+            {\r
+              treeString.append(an.stringMatched(2));\r
+            } else \r
+            if (an.stringMatched(1).equals("TN")) {\r
+              if (treeString.length()>0)\r
+              {\r
+                if (treeName==null)\r
+                {\r
+                  treeName = "Tree "+(getTreeCount()+1);\r
+                }\r
+                addNewickTree(treeName, treeString.toString());\r
+              }\r
+              treeName = an.stringMatched(2);\r
+              treeString = new StringBuffer();\r
+            }\r
+            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
           }\r
         }\r
         else if (annType.equals("GS"))\r
@@ -279,7 +325,8 @@ public class StockholmFile
             String acc = s.stringMatched(1);\r
             String type = s.stringMatched(2);\r
             String content = s.stringMatched(3);\r
-\r
+            // TODO: store DR in a vector.\r
+            // TODO: store AC according to generic file db annotation.\r
             Hashtable ann;\r
             if (seqAnn.containsKey(acc))\r
             {\r
@@ -299,8 +346,14 @@ public class StockholmFile
         }\r
         else if (annType.equals("GC"))\r
         {\r
-          System.out.println(annContent);\r
           // Generic per-Column annotation, exactly 1 char per column\r
+          // always need a label.\r
+          if (x.search(annContent))\r
+          {\r
+            // parse out and create alignment annotation directly.\r
+            AlignmentAnnotation annotation = parseAnnotationRow(x.stringMatched(1), x.stringMatched(2));\r
+            annotations.addElement(annotation);\r
+          }\r
         }\r
         else if (annType.equals("GR"))\r
         {\r
@@ -393,8 +446,49 @@ public class StockholmFile
         }\r
       }\r
     }\r
+    if (treeString.length()>0)\r
+    {\r
+      if (treeName==null)\r
+      {\r
+        treeName = "Tree "+(1+getTreeCount());\r
+      }\r
+      addNewickTree(treeName, treeString.toString());\r
+    }\r
   }\r
 \r
+  private AlignmentAnnotation parseAnnotationRow(String label, String annots)\r
+  {\r
+    String type = (label.indexOf("_cons")==label.length()-5) ? label.substring(0, label.length()-5)\r
+            : label;\r
+    boolean ss = false;\r
+    type = id2type(type);\r
+    if (type.equals("secondary structure"))\r
+    {\r
+      ss=true;\r
+    }\r
+    // decide on secondary structure or not.\r
+    Annotation[] els = new Annotation[annots.length()];\r
+    for (int i = 0; i<annots.length(); i++)\r
+    {\r
+      String pos = annots.substring(i,i+1);\r
+      Annotation ann;\r
+      ann = new Annotation(pos, "", ' ', Float.NaN);\r
+      if (ss)\r
+      {\r
+        ann.secondaryStructure = jalview.schemes.ResidueProperties.getDssp3state(pos).charAt(0);\r
+        if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0)=='C')\r
+        {\r
+          ann.displayCharacter = "";\r
+        } else {\r
+          ann.displayCharacter += " ";\r
+        }\r
+      }\r
+      \r
+      els[i] = ann;\r
+    }\r
+    return new AlignmentAnnotation(label, label, els);\r
+  }\r
+  \r
   public static String print(SequenceI[] s)\r
   {\r
     return "not yet implemented";\r