formatting

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

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 3b58519..e7e6a38 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -119,8 +119,9 @@ 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, ":",true);
-    
+    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":",
+            true);
+
     String field;
     int type = -1;
     if (st.countTokens() > 0)
@@ -148,28 +149,31 @@ public class ModellerDescription
           {
             if (!field.equals(":"))
             {
-            // validate residue field value
-            if (Types[i] == 1)
-            {
-              resCode val = validResidueCode(field);
-              if (val != null)
+              // validate residue field value
+              if (Types[i] == 1)
               {
-                fields.put(new String(Fields[i] + "num"), val);
+                resCode val = validResidueCode(field);
+                if (val != null)
+                {
+                  fields.put(new String(Fields[i] + "num"), val);
+                }
+                else
+                {
+                  // jalview.bin.Cache.log.debug(
+                  // "Ignoring non-Modeller description: invalid integer-like
+                  // field '" + field + "'");
+                  type = -1; /* invalid field! - throw the FieldSet away */
+                }
+                ;
               }
-              else
+              fields.put(Fields[i++], field);
+              if (st.hasMoreTokens())
               {
-                // jalview.bin.Cache.log.debug(
-                // "Ignoring non-Modeller description: invalid integer-like
-                // field '" + field + "'");
-                type = -1; /* invalid field! - throw the FieldSet away */
+                st.nextToken(); // skip token sep.
               }
-              ;
             }
-            fields.put(Fields[i++], field);
-            if (st.hasMoreTokens()) {
-              st.nextToken(); // skip token sep.
-            }
-            } else {
+            else
+            {
               i++;
             }
           }
@@ -180,7 +184,7 @@ public class ModellerDescription
           while (st.hasMoreTokens())
           {
             String tl = st.nextToken(":");
-            field += tl.equals(":") ? tl : (":" + tl); 
+            field += tl.equals(":") ? tl : (":" + tl);
           }
           fields.put(Fields[TAIL], field);
         }
@@ -240,13 +244,15 @@ public class ModellerDescription
     {
       // Set start and end before we update the type (in the case of a
       // synthesized field set)
-      if (getStartCode()==null || (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 (getEndCode()==null || (getEndNum() != seq.getEnd() && getStartCode()!=null && getStartCode().val != null))
+      if (getEndCode() == null
+              || (getEndNum() != seq.getEnd() && getStartCode() != null && getStartCode().val != null))
       {
         setEndCode(seq.getEnd());
       }
@@ -349,7 +355,7 @@ public class ModellerDescription
   {
     int start = 0;
     resCode val = getStartCode();
-    if (val!=null && val.val != null)
+    if (val != null && val.val != null)
     {
       return val.val.intValue();
     }
@@ -378,7 +384,7 @@ public class ModellerDescription
   {
     int end = 0;
     resCode val = getEndCode();
-    if (val!=null && val.val != null)
+    if (val != null && val.val != null)
     {
       return val.val.intValue();
     }
@@ -396,8 +402,8 @@ public class ModellerDescription
   {
     if (isModellerFieldset())
     {
-      resCode rc=getStartCode();
-      if (rc!=null && rc.val != null)
+      resCode rc = getStartCode();
+      if (rc != null && rc.val != null)
       {
         newSeq.setStart(getStartNum());
       }
@@ -405,8 +411,8 @@ public class ModellerDescription
       {
         newSeq.setStart(1);
       }
-      rc=getEndCode();
-      if (rc!=null && rc.val != null)
+      rc = getEndCode();
+      if (rc != null && rc.val != null)
       {
         newSeq.setEnd(getEndNum());
       }