X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=a56f2af0b1165c911f9f89eaff30e0b8b0ccc688;hb=08c7bee16c16563cc7cec7ea4d336b3e0c4c937a;hp=21b2aafe05c0f685003255425cfd7f2214e89ab5;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 21b2aaf..a56f2af 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,23 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
 
 public class ModellerDescription
 {
@@ -26,13 +34,12 @@ public class ModellerDescription
    * single line, and sequence start/end and other properties. See PIRFile IO
    * for its use.
    */
-  final String[] seqTypes =
-  { "sequence", "structure", "structureX", "structureN" };
+  final String[] seqTypes = { "sequence", "structure", "structureX",
+      "structureN" };
 
-  final String[] Fields =
-  { "objectType", "objectId", "startField", "startCode", "endField",
-      "endCode", "description1", "description2", "resolutionField",
-      "tailField" };
+  final String[] Fields = { "objectType", "objectId", "startField",
+      "startCode", "endField", "endCode", "description1", "description2",
+      "resolutionField", "tailField" };
 
   final int TYPE = 0;
 
@@ -57,11 +64,10 @@ public class ModellerDescription
   /**
    * 0 is free text or empty 1 is something that parses to an integer, or \@
    */
-  final int Types[] =
-  { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
+  final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
 
-  final char Padding[] =
-  { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+  final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
+      '.' };
 
   java.util.Hashtable fields = new java.util.Hashtable();
 
@@ -84,7 +90,7 @@ public class ModellerDescription
 
     resCode(int v)
     {
-      val = new Integer(v);
+      val = Integer.valueOf(v);
       field = val.toString();
     }
   };
@@ -92,7 +98,7 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+    Regex r = new Regex(
             "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
@@ -119,8 +125,9 @@ 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 +155,31 @@ 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 +190,7 @@ 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 +250,15 @@ 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());
       }
@@ -262,23 +274,22 @@ public class ModellerDescription
       // sets the local reference field
       int t = 0; // sequence
       if (seq.getDatasetSequence() != null
-              && seq.getDatasetSequence().getDBRef() != null)
+              && seq.getDatasetSequence().getDBRefs() != null)
       {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
-                .getDBRef();
-        int i, j;
-        for (i = 0, j = dbr.length; i < j; i++)
+        List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
+        for (int i = 0, ni = dbr.size(); i < ni; i++)
         {
-          if (dbr[i] != null)
+        	DBRefEntry dbri = dbr.get(i);
+          if (dbri != null)
           {
             // JBPNote PDB dbRefEntry needs properties to propagate onto
             // ModellerField
             // JBPNote Need to get info from the user about whether the sequence
             // is the one being modelled, or if it is a template.
-            if (dbr[i].getSource()
+            if (dbri.getSource()
                     .equals(jalview.datamodel.DBRefSource.PDB))
             {
-              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
+              fields.put(Fields[LOCALID], dbri.getAccessionId());
               t = 2;
               break;
             }
@@ -349,7 +360,7 @@ 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 +389,7 @@ 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 +407,8 @@ 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 +416,8 @@ 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());
       }