JAL-2089 Merge branch releases/Release_2_10_Branch to master

[jalview.git] / src / jalview / util / DBRefUtils.java

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index f414a9c..32883d1 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -302,7 +302,8 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
+      if (refa.getSource() != null
+              && refb.getSource() != null
               && DBRefUtils.getCanonicalName(refb.getSource()).equals(
                       DBRefUtils.getCanonicalName(refa.getSource())))
       {
@@ -334,7 +335,8 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
+      if (refa.getSource() != null
+              && refb.getSource() != null
               && DBRefUtils.getCanonicalName(refb.getSource()).equals(
                       DBRefUtils.getCanonicalName(refa.getSource())))
       {
@@ -371,7 +373,8 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
+      if (refa.getSource() != null
+              && refb.getSource() != null
               && DBRefUtils.getCanonicalName(refb.getSource()).equals(
                       DBRefUtils.getCanonicalName(refa.getSource())))
       {
@@ -411,7 +414,8 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
+      if (refa.getSource() != null
+              && refb.getSource() != null
               && DBRefUtils.getCanonicalName(refb.getSource()).equals(
                       DBRefUtils.getCanonicalName(refa.getSource())))
       {
@@ -614,21 +618,21 @@ public class DBRefUtils
    * sequences if they have an appropriate primary ref
    * <table>
    * <tr>
-   * <td>Seq Type</td>
-   * <td>Primary DB</td>
-   * <td>Direct which will be promoted</td>
+   * <th>Seq Type</th>
+   * <th>Primary DB</th>
+   * <th>Direct which will be promoted</th>
    * </tr>
-   * <tr>
+   * <tr align=center>
    * <td>peptides</td>
    * <td>Ensembl</td>
    * <td>Uniprot</td>
    * </tr>
-   * <tr>
+   * <tr align=center>
    * <td>peptides</td>
    * <td>Ensembl</td>
    * <td>Uniprot</td>
    * </tr>
-   * <tr>
+   * <tr align=center>
    * <td>dna</td>
    * <td>Ensembl</td>
    * <td>ENA</td>
@@ -646,8 +650,16 @@ public class DBRefUtils
       return;
     }
     List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
-    selfs.addAll(Arrays.asList(selectDbRefs(!sequence.isProtein(),
-            sequence.getDBRefs())));
+    {
+      DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+              sequence.getDBRefs());
+      if (selfArray == null || selfArray.length == 0)
+      {
+        // nothing to do
+        return;
+      }
+      selfs.addAll(Arrays.asList(selfArray));
+    }
 
     // filter non-primary refs
     for (DBRefEntry p : pr)