Support for SnapGene Server

Added read/write/detectFeatures for SnapGene server
Support default displayId's for conversion
Update some javadocs
File type for dna/json/turtle determined now by file suffix
Added support to read/write SnapGene DNA files
Added options for SnapGene output to validate

Author: cjmyers

core2/pom.xml

@@ -96,6 +96,11 @@
 		<artifactId>guava</artifactId>
 		<version>19.0</version>
 	  </dependency>
+	  <dependency>
+  		<groupId>org.apache.commons</groupId>
+  		<artifactId>commons-lang3</artifactId>
+  		<version>3.7</version>
+	  </dependency>
 	</dependencies>
 
 	<repositories>

core2/src/main/java/org/sbolstandard/core2/FASTA.java

@@ -134,7 +134,7 @@ private static Sequence createSequence(SBOLDocument doc,String URIprefix,String
 	 * @throws SBOLValidationException if an SBOL validation rule was violated in {@link #createSequence(SBOLDocument, String, String, String, String, URI)}.
 	 * @throws IOException
 	 */
-	static void read(SBOLDocument doc,String stringBuffer,String URIprefix,String version,URI encoding) throws SBOLValidationException, IOException
+	static void read(SBOLDocument doc,String stringBuffer,String URIprefix,String displayId,String version,URI encoding) throws SBOLValidationException, IOException
 	{
 		// reset the global static variables needed for parsing
 		nextLine = null;
@@ -145,7 +145,6 @@ static void read(SBOLDocument doc,String stringBuffer,String URIprefix,String ve
 		String elements = null;
 		String description = "";
 		boolean sequenceMode = false;
-		String displayId;
 		BufferedReader br = new BufferedReader(new StringReader(stringBuffer));
 
 		while ((strLine = readFASTALine(br)) != null)   {
@@ -154,31 +153,37 @@ static void read(SBOLDocument doc,String stringBuffer,String URIprefix,String ve
 			if (strLine.startsWith(">")) {
 				if (sequenceMode) {
 					sequenceMode = false;
-					if (description.contains(":")) {
-						displayId = description.substring(0, description.indexOf(":")).trim();
-						description = description.substring(description.indexOf(":")+1).trim();
-					} else {
-						displayId = description;
+					if (displayId == null || displayId.equals("")) {
+						if (description.contains(":")) {
+							displayId = description.substring(0, description.indexOf(":")).trim();
+							description = description.substring(description.indexOf(":")+1).trim();
+						} else {
+							displayId = description;
+						}
 					}
 					displayId = URIcompliance.fixDisplayId(displayId);
 					Sequence sequence = createSequence(doc,URIprefix,displayId,version,sbSequence.toString(),encoding);
 					sequence.setDescription(description);
+					displayId = "";
 					description = "";
 					sbSequence = new StringBuilder();
 				}
 				description += strLine.replaceFirst(">", "").trim();
 			} else if (strLine.startsWith(";")) {
 				if (sequenceMode) {
 					sequenceMode = false;
-					if (description.contains(":")) {
-						displayId = description.substring(0, description.indexOf(":")).trim();
-						description = description.substring(description.indexOf(":")+1).trim();
-					} else {
-						displayId = description;
+					if (displayId == null || displayId.equals("")) {
+						if (description.contains(":")) {
+							displayId = description.substring(0, description.indexOf(":")).trim();
+							description = description.substring(description.indexOf(":")+1).trim();
+						} else {
+							displayId = description;
+						}
 					}
 					displayId = URIcompliance.fixDisplayId(displayId);
 					Sequence sequence = createSequence(doc,URIprefix,displayId,version,sbSequence.toString(),encoding);
 					sequence.setDescription(description);
+					displayId = "";
 					description = "";
 					sbSequence = new StringBuilder();
 				}

core2/src/main/java/org/sbolstandard/core2/GenBank.java

@@ -873,7 +873,7 @@ private static String fixTag(String tag) {
 	 * <li>{@link #createSubComponentDefinitions(SBOLDocument, ComponentDefinition, URI, String, String)}.</li>
 	 * </ul>
 	 */
-	static void read(SBOLDocument doc,String stringBuffer,String URIPrefix,String defaultVersion) throws IOException, SBOLConversionException, SBOLValidationException {
+	static void read(SBOLDocument doc,String stringBuffer,String URIPrefix,String displayId,String defaultVersion) throws IOException, SBOLConversionException, SBOLValidationException {
 		so = new SequenceOntology();
 
 		// reset the global static variables needed for parsing
@@ -890,7 +890,7 @@ static void read(SBOLDocument doc,String stringBuffer,String URIPrefix,String de
 		URI lastRole = null;
 		while (true) {
 			boolean cont = false;
-			String id = "";
+			String id = displayId;
 			String accession = "";
 			String version = defaultVersion;
 			featureMode = false;
@@ -914,14 +914,16 @@ static void read(SBOLDocument doc,String stringBuffer,String URIPrefix,String de
 					//String[] strSplit = strLine.split("\\s+");
 
 					// ID of the sequence
-					if (strLine.length() > 28) {
-						id = strLine.substring(12, 28).trim();
-						annotation = new Annotation(new QName(GBNAMESPACE, LOCUS, GBPREFIX), id);
-						id = URIcompliance.fixDisplayId(id);
-						annotations.add(annotation);
-					} else {
-						// TODO: Exception?
-						id = "id_is_missing";
+					if (id == null || id.equals("")) {
+						if (strLine.length() > 28) {
+							id = strLine.substring(12, 28).trim();
+							annotation = new Annotation(new QName(GBNAMESPACE, LOCUS, GBPREFIX), id);
+							id = URIcompliance.fixDisplayId(id);
+							annotations.add(annotation);
+						} else {
+							// TODO: Exception?
+							id = "id_is_missing";
+						}
 					}
 
 					// Base count of the sequence

core2/src/main/java/org/sbolstandard/core2/SBOLDocument.java

@@ -90,6 +90,10 @@ public class SBOLDocument {
 	 * Constant representing GenBank file format
 	 */
 	public static final String GENBANK = "GENBANK";
+	/**
+	 * Constant representing SnapGene file format
+	 */
+	public static final String SNAPGENE = "SNAPGENE";
 
 	/**
 	 * Creates a new SBOLDocument instance with one empty list for the namespaces