*/
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;
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.
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++)
{
mapping.markMappedRegion(seq, pos, sr);
}
- newseq.append(sr.toString());
+ newseq.append(sr.getCharacters());
if (first)
{
first = false;
*/
public static boolean isMappable(AlignmentI al1, AlignmentI al2)
{
+ if (al1 == null || al2 == null)
+ {
+ return false;
+ }
+
/*
* Require one nucleotide and one protein
*/
* @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();
/**
* Returns true if seq1 has a cross-reference to seq2. Currently this assumes
- * that sequence name is structured as Source|AccessId.
+ * that sequence name is structured as Source|AccessionId.
*
* @param seq1
* @param seq2