From 70cb8184fe397a90f60ecc06d419ff2f7fbbb433 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 30 Apr 2007 13:23:14 +0000
Subject: [PATCH] parse alignment properties and add annotation rows for
 general alignment position annotation.

---
 src/jalview/io/StockholmFile.java |  106 ++++++++++++++++++++++++++++++++++---
 1 file changed, 100 insertions(+), 6 deletions(-)

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 10ddf53..9104a5f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -62,12 +62,13 @@ public class StockholmFile
   public void parse()
       throws IOException
   {
+    StringBuffer treeString=new StringBuffer();
+    String treeName = null;
     // --------------- Variable Definitions -------------------
     String line;
     String version;
     //  String id;
-    Hashtable alAnn = new Hashtable(); // Alignment wide annotations
-    Hashtable seqAnn = new Hashtable(); // Sequence related annotations
+     Hashtable seqAnn = new Hashtable(); // Sequence related annotations
     Hashtable seqs = new Hashtable();
     Regex p, r, rend, s, x;
 
@@ -122,6 +123,14 @@ public class StockholmFile
           int start = 1;
           int end = -1;
           String sid = acc;
+          // Retrieve hash of annotations for this accession
+          Hashtable accAnnotations = null;
+          
+          if (seqAnn!=null && seqAnn.containsKey(acc))
+          {
+            accAnnotations = (Hashtable) seqAnn.get(acc);
+          }
+          
           // Split accession in id and from/to
           if (p.search(acc))
           {
@@ -132,11 +141,29 @@ public class StockholmFile
           //logger.debug(sid + ", " + start + ", " + end);
 
           Sequence seqO = new Sequence(sid, seq, start, end);
+          // Add Description (if any)
+          if (accAnnotations!=null && accAnnotations.containsKey("DE"))
+          {
+            String desc = (String) accAnnotations.get("DE");
+            seqO.setDescription((desc==null)?"" : desc);
+          }
+          // Add DB References (if any)
+          if (accAnnotations!=null && accAnnotations.containsKey("DR"))
+          {
+            String dbr = (String) accAnnotations.get("DR");
+            if (dbr!=null && dbr.indexOf(";")>-1)
+            {
+              String src = dbr.substring(0, dbr.indexOf(";"));
+              String acn = dbr.substring(dbr.indexOf(";")+1);
+              DBRefEntry dbref = new DBRefEntry(jalview.util.DBRefUtils.getCanonicalName(src), acn, "");
+              seqO.addDBRef(dbref);
+            }
+          }
           Hashtable features = null;
           // We need to adjust the positions of all features to account for gaps
           try
           {
-            features = (Hashtable) ( (Hashtable) seqAnn.get(acc)).get(
+            features = (Hashtable) accAnnotations.get(
                 "features");
           }
           catch (java.lang.NullPointerException e)
@@ -150,6 +177,9 @@ public class StockholmFile
             Enumeration i = features.keys();
             while (i.hasMoreElements())
             {
+              // TODO: parse out secondary structure annotation as annotation row
+              // TODO: parse out scores as annotation row
+              // TODO: map coding region to core jalview feature types
               String type = i.nextElement().toString();
               Hashtable content = (Hashtable) features.get(type);
 
@@ -258,7 +288,23 @@ public class StockholmFile
           Regex an = new Regex("(\\w+)\\s*(.*)");
           if (an.search(annContent))
           {
-            alAnn.put(an.stringMatched(1), an.stringMatched(2));
+            if (an.stringMatched(1).equals("NH"))
+            {
+              treeString.append(an.stringMatched(2));
+            } else 
+            if (an.stringMatched(1).equals("TN")) {
+              if (treeString.length()>0)
+              {
+                if (treeName==null)
+                {
+                  treeName = "Tree "+(getTreeCount()+1);
+                }
+                addNewickTree(treeName, treeString.toString());
+              }
+              treeName = an.stringMatched(2);
+              treeString = new StringBuffer();
+            }
+            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
           }
         }
         else if (annType.equals("GS"))
@@ -279,7 +325,8 @@ public class StockholmFile
             String acc = s.stringMatched(1);
             String type = s.stringMatched(2);
             String content = s.stringMatched(3);
-
+            // TODO: store DR in a vector.
+            // TODO: store AC according to generic file db annotation.
             Hashtable ann;
             if (seqAnn.containsKey(acc))
             {
@@ -299,8 +346,14 @@ public class StockholmFile
         }
         else if (annType.equals("GC"))
         {
-          System.out.println(annContent);
           // Generic per-Column annotation, exactly 1 char per column
+          // always need a label.
+          if (x.search(annContent))
+          {
+            // parse out and create alignment annotation directly.
+            AlignmentAnnotation annotation = parseAnnotationRow(x.stringMatched(1), x.stringMatched(2));
+            annotations.addElement(annotation);
+          }
         }
         else if (annType.equals("GR"))
         {
@@ -393,8 +446,49 @@ public class StockholmFile
         }
       }
     }
+    if (treeString.length()>0)
+    {
+      if (treeName==null)
+      {
+        treeName = "Tree "+(1+getTreeCount());
+      }
+      addNewickTree(treeName, treeString.toString());
+    }
   }
 
+  private AlignmentAnnotation parseAnnotationRow(String label, String annots)
+  {
+    String type = (label.indexOf("_cons")==label.length()-5) ? label.substring(0, label.length()-5)
+            : label;
+    boolean ss = false;
+    type = id2type(type);
+    if (type.equals("secondary structure"))
+    {
+      ss=true;
+    }
+    // decide on secondary structure or not.
+    Annotation[] els = new Annotation[annots.length()];
+    for (int i = 0; i<annots.length(); i++)
+    {
+      String pos = annots.substring(i,i+1);
+      Annotation ann;
+      ann = new Annotation(pos, "", ' ', Float.NaN);
+      if (ss)
+      {
+        ann.secondaryStructure = jalview.schemes.ResidueProperties.getDssp3state(pos).charAt(0);
+        if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0)=='C')
+        {
+          ann.displayCharacter = "";
+        } else {
+          ann.displayCharacter += " ";
+        }
+      }
+      
+      els[i] = ann;
+    }
+    return new AlignmentAnnotation(label, label, els);
+  }
+  
   public static String print(SequenceI[] s)
   {
     return "not yet implemented";
-- 
1.7.10.2