merge from develop

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index e6d3e83..f9d4c08 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,20 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.TreeMap;
-
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -52,6 +38,20 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
  * refactored elsewhere at some point.
@@ -448,6 +448,11 @@ public class AlignmentUtils
   protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,
           char[] aaSeqChars)
   {
+    if (cdnaSeqChars == null || aaSeqChars == null)
+    {
+      return false;
+    }
+
     int aaResidue = 0;
     for (int i = cdnaStart; i < cdnaSeqChars.length - 2
             && aaResidue < aaSeqChars.length; i += 3, aaResidue++)
@@ -862,7 +867,7 @@ public class AlignmentUtils
           {
             mapping.markMappedRegion(seq, pos, sr);
           }
-          newseq.append(sr.toString());
+          newseq.append(sr.getCharacters());
           if (first)
           {
             first = false;
@@ -1016,6 +1021,11 @@ public class AlignmentUtils
    */
   public static boolean isMappable(AlignmentI al1, AlignmentI al2)
   {
+    if (al1 == null || al2 == null)
+    {
+      return false;
+    }
+
     /*
      * Require one nucleotide and one protein
      */
@@ -1048,9 +1058,15 @@ public class AlignmentUtils
    * @param mappings
    * @return
    */
-  public static boolean isMappable(SequenceI dnaSeq, SequenceI proteinSeq,
+  protected static boolean isMappable(SequenceI dnaSeq,
+          SequenceI proteinSeq,
           Set<AlignedCodonFrame> mappings)
   {
+    if (dnaSeq == null || proteinSeq == null)
+    {
+      return false;
+    }
+
     SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
     SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
             : proteinSeq.getDatasetSequence();