patch for secondary issue in JAL-664 re parsing empty fields in description line

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

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index e4483a5..3af2f93 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.io;
 
@@ -120,7 +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)
@@ -138,6 +138,7 @@ public class ModellerDescription
 
       if (i < seqTypes.length)
       {
+        st.nextToken(); // skip ':'
         // valid seqType for modeller
         type = i;
         i = 1; // continue parsing fields
@@ -145,6 +146,8 @@ public class ModellerDescription
         {
           if ((field = st.nextToken(":")) != null)
           {
+            if (!field.equals(":"))
+            {
             // validate residue field value
             if (Types[i] == 1)
             {
@@ -163,6 +166,12 @@ public class ModellerDescription
               ;
             }
             fields.put(Fields[i++], field);
+            if (st.hasMoreTokens()) {
+              st.nextToken(); // skip token sep.
+            }
+            } else {
+              i++;
+            }
           }
         }
         if (i == TAIL)
@@ -170,7 +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);
         }
@@ -216,7 +226,7 @@ public class ModellerDescription
    * make a possibly updated modeller field line for the sequence object
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    */
   ModellerDescription(SequenceI seq)
   {
@@ -230,12 +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());
       }
@@ -246,7 +257,7 @@ public class ModellerDescription
       setStartCode(seq.getStart());
       setEndCode(seq.getEnd());
       fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten
-                                                  // below...
+      // below...
       // type - decide based on evidence of PDB database references - this also
       // sets the local reference field
       int t = 0; // sequence
@@ -338,7 +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();
     }
@@ -367,7 +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();
     }
@@ -378,14 +389,15 @@ public class ModellerDescription
    * returns true if sequence object was modifed with a valid modellerField set
    * 
    * @param newSeq
-   *                SequenceI
+   *          SequenceI
    * @return boolean
    */
   boolean updateSequenceI(SequenceI newSeq)
   {
     if (isModellerFieldset())
     {
-      if (getStartCode().val != null)
+      resCode rc=getStartCode();
+      if (rc!=null && rc.val != null)
       {
         newSeq.setStart(getStartNum());
       }
@@ -393,7 +405,8 @@ public class ModellerDescription
       {
         newSeq.setStart(1);
       }
-      if (getEndCode().val != null)
+      rc=getEndCode();
+      if (rc!=null && rc.val != null)
       {
         newSeq.setEnd(getEndNum());
       }