X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=fa6ef6d013ac861d592f08959574827cff4fe46f;hb=6ebb5015f90d293322fb3af0c7b20313359fe97d;hp=300a9ba2eecba039f26526e2bc9b99ef699d6822;hpb=0d6e36143a2d7471edb7ef386d0b79095e0cd63e;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 300a9ba..fa6ef6d 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,15 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 jalview.datamodel.*;
+
 public class ModellerDescription
 {
-    /**
-     * Translates between a String containing a set of colon-separated values
-     * on a single line, and sequence start/end and other properties.
-     * See PIRFile IO for its use.
-     */
-    final String[] seqTypes =
+  /**
+   * Translates between a String containing a set of colon-separated values
+   * on a single line, and sequence start/end and other properties.
+   * See PIRFile IO for its use.
+   */
+  final String[] seqTypes =
       {
       "sequence", "structure", "structureX", "structureN"};
   final String[] Fields =
@@ -69,7 +87,8 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.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))
     {
@@ -80,8 +99,8 @@ 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);
@@ -106,7 +125,7 @@ public class ModellerDescription
       field = st.nextToken(":");
       do
       {
-        if (seqTypes[i].equalsIgnoreCase(field) )
+        if (seqTypes[i].equalsIgnoreCase(field))
         {
           break;
         }
@@ -132,8 +151,8 @@ 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 */
               }
               ;
@@ -224,7 +243,7 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null &&
           seq.getDatasetSequence().getDBRef() != null)
       {
-        jalview.datamodel.DBRefEntry [] dbr = seq.getDatasetSequence().getDBRef();
+        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
         int i, j;
         for (i = 0, j = dbr.length; i < j; i++)
         {
@@ -370,4 +389,3 @@ public class ModellerDescription
     return false;
   }
 }
-