From c2240c3de557b1845565cc458b5738e88103c3aa Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 12 Oct 2010 12:59:58 +0000
Subject: [PATCH] patch for secondary issue in JAL-664 re parsing empty fields
 in description line

---
 src/jalview/io/ModellerDescription.java |   30 ++++++++++++++++++++++--------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index b590a6d..3af2f93 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -119,7 +119,8 @@ public class ModellerDescription
   private java.util.Hashtable parseDescription(String desc)
   {
     java.util.Hashtable fields = new java.util.Hashtable();
-    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
+    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":",true);
+    
     String field;
     int type = -1;
     if (st.countTokens() > 0)
@@ -137,6 +138,7 @@ public class ModellerDescription
 
       if (i < seqTypes.length)
       {
+        st.nextToken(); // skip ':'
         // valid seqType for modeller
         type = i;
         i = 1; // continue parsing fields
@@ -144,6 +146,8 @@ public class ModellerDescription
         {
           if ((field = st.nextToken(":")) != null)
           {
+            if (!field.equals(":"))
+            {
             // validate residue field value
             if (Types[i] == 1)
             {
@@ -162,6 +166,12 @@ public class ModellerDescription
               ;
             }
             fields.put(Fields[i++], field);
+            if (st.hasMoreTokens()) {
+              st.nextToken(); // skip token sep.
+            }
+            } else {
+              i++;
+            }
           }
         }
         if (i == TAIL)
@@ -169,7 +179,8 @@ public class ModellerDescription
           // slurp remaining fields
           while (st.hasMoreTokens())
           {
-            field += ":" + st.nextToken(":");
+            String tl = st.nextToken(":");
+            field += tl.equals(":") ? tl : (":" + tl); 
           }
           fields.put(Fields[TAIL], field);
         }
@@ -229,12 +240,13 @@ public class ModellerDescription
     {
       // Set start and end before we update the type (in the case of a
       // synthesized field set)
-      if (getStartNum() != seq.getStart() && getStartCode().val != null)
+      if (getStartCode()==null || (getStartNum() != seq.getStart() && getStartCode().val != null))
       {
+        // unset or user updated sequence start position
         setStartCode(seq.getStart());
       }
 
-      if (getEndNum() != seq.getEnd() && getStartCode().val != null)
+      if (getEndCode()==null || (getEndNum() != seq.getEnd() && getStartCode()!=null && getStartCode().val != null))
       {
         setEndCode(seq.getEnd());
       }
@@ -337,7 +349,7 @@ public class ModellerDescription
   {
     int start = 0;
     resCode val = getStartCode();
-    if (val.val != null)
+    if (val!=null && val.val != null)
     {
       return val.val.intValue();
     }
@@ -366,7 +378,7 @@ public class ModellerDescription
   {
     int end = 0;
     resCode val = getEndCode();
-    if (val.val != null)
+    if (val!=null && val.val != null)
     {
       return val.val.intValue();
     }
@@ -384,7 +396,8 @@ public class ModellerDescription
   {
     if (isModellerFieldset())
     {
-      if (getStartCode().val != null)
+      resCode rc=getStartCode();
+      if (rc!=null && rc.val != null)
       {
         newSeq.setStart(getStartNum());
       }
@@ -392,7 +405,8 @@ public class ModellerDescription
       {
         newSeq.setStart(1);
       }
-      if (getEndCode().val != null)
+      rc=getEndCode();
+      if (rc!=null && rc.val != null)
       {
         newSeq.setEnd(getEndNum());
       }
-- 
1.7.10.2