Implementation of exceptional complex location in case of location spanning the end point. Location contract wants sublocations

paolopavan · paolopavan · commit e49b69be3fc1 · 2020-04-25T22:50:03.000+01:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -68,7 +68,7 @@ public class GenbankSequenceParser<S extends AbstractSequence<C>, C extends Comp
 	private String header;
 	private String accession;
 	private boolean isCircularSequence;
-	private long sequenceLength;
+	private int sequenceLength;
 	public LinkedHashMap<String, ArrayList<DBReferenceInfo>> mapDB;
 	/**
 	 * this data structure collects list of features extracted from the
@@ -162,7 +162,7 @@ private String parse(BufferedReader bufferedReader) {
 				if (m.matches()) {
 					headerParser.setName(m.group(1));
 					headerParser.setAccession(m.group(1)); // default if no accession found
-					sequenceLength = Long.valueOf(m.group(2));
+					sequenceLength = Integer.valueOf(m.group(2));
 					String lengthUnits = m.group(3);
 					String type = m.group(6);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -51,7 +51,7 @@
 public class InsdcParser <S extends AbstractSequence<C>, C extends Compound>{
 
 	private boolean isSequenceCircular;
-	private long sequenceLength;
+	private int sequenceLength;
 
 	private final DataSource dataSource;
 
@@ -133,7 +133,7 @@ public void setSequenceCircular(boolean sequenceCircular) {
 		isSequenceCircular = sequenceCircular;
 	}
 
-	public void setSequenceLength(long sequenceLength) {
+	public void setSequenceLength(int sequenceLength) {
 		this.sequenceLength = sequenceLength;
 	}
 
@@ -249,11 +249,34 @@ private List<Location> parseLocationString(String string, int versus) throws Par
 					featureGlobalEnd = end;
 				}
 
-				AbstractLocation l = new SimpleLocation(
-						new SimplePoint(start),
-						new SimplePoint(end),
-						s
-				);
+				AbstractLocation l;
+				if (start < end) {
+					l = new SimpleLocation(
+							new SimplePoint(start),
+							new SimplePoint(end),
+							s
+					);
+				} else {
+					// in case of location spanning the end point, Location contract wants sublocations
+					AbstractLocation l5prime = new SimpleLocation(
+							new SimplePoint(1),
+							new SimplePoint(end),
+							Strand.POSITIVE
+					);
+					AbstractLocation l3prime = new SimpleLocation(
+							new SimplePoint(start),
+							new SimplePoint(sequenceLength),
+							Strand.POSITIVE
+					);
+
+					l = new SimpleLocation(
+							new SimplePoint(start),
+							new SimplePoint(end), // seq length
+							s,
+							isSequenceCircular,
+							Arrays.asList(l5prime, l3prime)
+					);
+				}
 
 				if(m.group(4) != null && m.group(4).equals("^")) l.setBetweenCompounds(true);
 
