javatidy

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 1c14240..94aa5c9 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,23 +1,24 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ *\r
  * This file is part of Jalview.\r
- * \r
+ *\r
  * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
+ * modify it under the terms of the GNU General Public License\r
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ *\r
+ * Jalview is distributed in the hope that it will be useful, but\r
+ * WITHOUT ANY WARRANTY; without even the implied warranty\r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
  * PURPOSE.  See the GNU General Public License for more details.\r
- * \r
+ *\r
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.analysis;\r
 \r
 import java.util.Enumeration;\r
+import java.util.List;\r
 import java.util.Vector;\r
 import java.util.Hashtable;\r
 \r
@@ -34,15 +35,15 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 /**\r
  * Functions for cross-referencing sequence databases. user must first specify\r
  * if cross-referencing from protein or dna (set dna==true)\r
- * \r
+ *\r
  * @author JimP\r
- * \r
+ *\r
  */\r
 public class CrossRef\r
 {\r
   /**\r
    * get the DNA or protein references for a protein or dna sequence\r
-   * \r
+   *\r
    * @param dna\r
    * @param rfs\r
    * @return\r
@@ -66,12 +67,12 @@ public class CrossRef
   public static Hashtable classifyDbRefs(DBRefEntry[] rfs)\r
   {\r
     Hashtable classes = new Hashtable();\r
-    classes.put(DBRefSource.PROTEINDBS, jalview.util.DBRefUtils.selectRefs(\r
-            rfs, DBRefSource.PROTEINDBS));\r
+    classes.put(DBRefSource.PROTEINDBS,\r
+            jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS));\r
     classes.put(DBRefSource.DNACODINGDBS, jalview.util.DBRefUtils\r
             .selectRefs(rfs, DBRefSource.DNACODINGDBS));\r
-    classes.put(DBRefSource.DOMAINDBS, jalview.util.DBRefUtils.selectRefs(\r
-            rfs, DBRefSource.DOMAINDBS));\r
+    classes.put(DBRefSource.DOMAINDBS,\r
+            jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.DOMAINDBS));\r
     // classes.put(OTHER, )\r
     return classes;\r
   }\r
@@ -90,7 +91,7 @@ public class CrossRef
   /**\r
    * Indirect references are references from other sequences from the dataset to\r
    * any of the direct DBRefEntrys on the given sequences.\r
-   * \r
+   *\r
    * @param dna\r
    *          true if seqs are DNA seqs\r
    * @param seqs\r
@@ -201,7 +202,7 @@ public class CrossRef
   }\r
 \r
   /**\r
-   * \r
+   *\r
    * @param dna\r
    * @param seqs\r
    * @return\r
@@ -213,7 +214,7 @@ public class CrossRef
   }\r
 \r
   /**\r
-   * \r
+   *\r
    * @param seqs\r
    * @param dna\r
    * @param source\r
@@ -415,7 +416,7 @@ public class CrossRef
    * find references to lrfs in the cross-reference set of each sequence in\r
    * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry\r
    * based on source and accession string only - Map and Version are nulled.\r
-   * \r
+   *\r
    * @param sequenceI\r
    * @param lrfs\r
    * @param dataset\r
@@ -443,7 +444,7 @@ public class CrossRef
   /**\r
    * search a given sequence dataset for references matching cross-references to\r
    * the given sequence\r
-   * \r
+   *\r
    * @param sequenceI\r
    * @param xrf\r
    * @param dataset\r
@@ -462,7 +463,7 @@ public class CrossRef
    * TODO: generalise to different protein classifications Search dataset for\r
    * DBRefEntrys matching the given one (xrf) and add the associated sequence to\r
    * rseq.\r
-   * \r
+   *\r
    * @param sequenceI\r
    * @param xrf\r
    * @param dataset\r
@@ -486,10 +487,10 @@ public class CrossRef
       System.err.println("Empty dataset sequence set - NO VECTOR");\r
       return false;\r
     }\r
-    Enumeration e = dataset.getSequences().elements();\r
-    while (e.hasMoreElements())\r
+    List<SequenceI> ds;\r
+    synchronized (ds=dataset.getSequences())\r
     {\r
-      SequenceI nxt = (SequenceI) e.nextElement();\r
+      for (SequenceI nxt:ds)\r
       if (nxt != null)\r
       {\r
         if (nxt.getDatasetSequence() != null)\r
@@ -518,7 +519,7 @@ public class CrossRef
           }\r
           else\r
           {\r
-            poss = CrossRef.findXDbRefs(dna, poss); // \r
+            poss = CrossRef.findXDbRefs(dna, poss); //\r
             cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);\r
           }\r
           if (cands != null)\r
@@ -566,7 +567,7 @@ public class CrossRef
   /**\r
    * precalculate different products that can be found for seqs in dataset and\r
    * return them.\r
-   * \r
+   *\r
    * @param dna\r
    * @param seqs\r
    * @param dataset\r