updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

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

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 457a6ae..bd0a900 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,8 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, 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 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.
+ *
+ * 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
+ */
 package jalview.io;
 
 import jalview.datamodel.SequenceI;
 import java.util.Vector;
-import com.stevesoft.pat.Regex;
 public class ModellerDescription
 {
     /**
@@ -70,7 +87,7 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
     {
@@ -81,8 +98,8 @@ public class ModellerDescription
     {
       value = r.stringMatched(1);
     }
-    jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
-                                "'");
+   // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+   //                             "'");
     try
     {
       val = Integer.valueOf(value);
@@ -107,7 +124,7 @@ public class ModellerDescription
       field = st.nextToken(":");
       do
       {
-        if (seqTypes[i].compareToIgnoreCase(field) == 0)
+        if (seqTypes[i].equalsIgnoreCase(field) )
         {
           break;
         }
@@ -133,8 +150,8 @@ public class ModellerDescription
               }
               else
               {
-                jalview.bin.Cache.log.debug(
-                    "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
+          //      jalview.bin.Cache.log.debug(
+         //           "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
                 type = -1; /* invalid field! - throw the FieldSet away */
               }
               ;
@@ -225,19 +242,17 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null &&
           seq.getDatasetSequence().getDBRef() != null)
       {
-        Vector dbr = seq.getDatasetSequence().getDBRef();
+        jalview.datamodel.DBRefEntry [] dbr = seq.getDatasetSequence().getDBRef();
         int i, j;
-        for (i = 0, j = dbr.size(); i < j; i++)
+        for (i = 0, j = dbr.length; i < j; i++)
         {
-          jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)
-              dbr.get(i);
-          if (dref != null)
+          if (dbr[i] != 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 (dref.getSource().equals("PDB"))
+            if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
             {
-              fields.put(Fields[LOCALID], dref.getAccessionId());
+              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
               t = 2;
               break;
             }