Need to propagate down also this bit of information. Since two parameters more may be less readable I changed strategy and configured parser class.

paolopavan · paolopavan · commit d724aec7d36d · 2020-04-25T22:43:02.000+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
@@ -182,6 +182,10 @@ private String parse(BufferedReader bufferedReader) {
 
 					isCircularSequence = m.group(7).equalsIgnoreCase("circular");
 
+					// configure location parser with needed information
+					locationParser.setSequenceLength(sequenceLength);
+					locationParser.setSequenceCircular(isCircularSequence);
+
 					log.debug("compound type: {}", compoundType.getClass().getSimpleName());
 
 				} else {
@@ -284,7 +288,7 @@ private String parse(BufferedReader bufferedReader) {
 						// new feature!
 						gbFeature = new TextFeature(key, val, key, key);
 						Location l =
-								locationParser.parse(val, isCircularSequence);
+								locationParser.parse(val);
 						gbFeature.setLocation((AbstractLocation)l);
 
 						if (!featureCollection.containsKey(key)) {
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
@@ -35,6 +35,7 @@
 import java.io.IOException;
 import java.io.Reader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -49,6 +50,9 @@
  */
 public class InsdcParser <S extends AbstractSequence<C>, C extends Compound>{
 
+	private boolean isSequenceCircular;
+	private long sequenceLength;
+
 	private final DataSource dataSource;
 
 		/**
@@ -80,7 +84,6 @@ public class InsdcParser <S extends AbstractSequence<C>, C extends Compound>{
 	 * Not really sure that they are not declared obsolete but they are still in
 	 * several files.
 	 */
-	//protected static final Pattern genbankSplitPattern = Pattern.compile("^\\s?(join|order|bond|complement|)\\(?([^\\)]+)\\)?");
 	protected static final Pattern genbankSplitPattern = Pattern.compile("^\\s?(join|order|bond|complement|)\\(?(.+)\\)?");
 	/**
 	 * designed to recursively split a location string in tokens. Valid tokens
@@ -126,7 +129,13 @@ public DataSource getDataSource() {
 		return dataSource;
 	}
 
+	public void setSequenceCircular(boolean sequenceCircular) {
+		isSequenceCircular = sequenceCircular;
+	}
 
+	public void setSequenceLength(long sequenceLength) {
+		this.sequenceLength = sequenceLength;
+	}
 
 	/**
 	 * Main method for parsing a location from a String instance
@@ -135,12 +144,12 @@ public DataSource getDataSource() {
 	 * @return The parsed location
 	 * @throws ParserException thrown in the event of any error during parsing
 	 */
-	public Location parse(String locationString, boolean isSequenceCircular) throws ParserException {
+	public Location parse(String locationString) throws ParserException {
 		featureGlobalStart = Integer.MAX_VALUE;
 		featureGlobalEnd = 1;
 
 		Location l;
-		List<Location> ll = parseLocationString(locationString, 1, isSequenceCircular);
+		List<Location> ll = parseLocationString(locationString, 1);
 
 		if (ll.size() == 1) {
 			l = ll.get(0);
@@ -155,10 +164,6 @@ public Location parse(String locationString, boolean isSequenceCircular) throws
 		return l;
 	}
 
-	public Location parse(String locationString) throws ParserException {
-		return parse(locationString, false);
-	}
-
 		/**
          * Reader based version of the parse methods.
          *
@@ -173,7 +178,7 @@ public List<AbstractLocation> parse(Reader reader) throws IOException, ParserExc
 		return null;
 	}
 
-	private List<Location> parseLocationString(String string, int versus, boolean isSequenceCircular) throws ParserException {
+	private List<Location> parseLocationString(String string, int versus) throws ParserException {
 		Matcher m;
 		List<Location> boundedLocationsCollection = new ArrayList<Location>();
 
@@ -192,7 +197,7 @@ private List<Location> parseLocationString(String string, int versus, boolean is
 				//recursive case
 				int localVersus = splitQualifier.equalsIgnoreCase("complement") ? -1 : 1;
 				List<Location> subLocations = parseLocationString(
-						splitString, versus * localVersus, isSequenceCircular);
+						splitString, versus * localVersus);
 
 				switch (complexFeaturesAppendMode) {
 					case FLATTEN:
