X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FGenBankFile.java;h=1c17c0594903916d5f5d56b92948583abfbebe26;hb=refs%2Fheads%2FJAL-1260_droldan;hp=47150959bd1fbaa828c34766bdddae5db485cf26;hpb=2d63cfb4d8f84de5f40670bb301ee8a22db321ff;p=jalview.git

diff --git a/src/jalview/io/GenBankFile.java b/src/jalview/io/GenBankFile.java
index 4715095..1c17c05 100644
--- a/src/jalview/io/GenBankFile.java
+++ b/src/jalview/io/GenBankFile.java
@@ -32,842 +32,1108 @@ import java.util.regex.Pattern;
 
 import org.apache.james.mime4j.field.ParsedField;
 
-public class GenBankFile extends AlignFile {
-    private static final Logger log = Logger.getLogger(GenBankFile.class.getName());
-	private GenBankVersion version = new GenBankVersion();
-	private GenBankLocus locus = new GenBankLocus();
-	private GenBankSource source = new GenBankSource();
-    private static final Pattern patLocation = Pattern.compile("(\\d+)\\.\\.(\\d+)");
-    private static final Pattern patLocationComp = Pattern.compile("(complement)\\((\\d+)\\.\\.(\\d+)\\)");
-    private static final Pattern patLocus = Pattern.compile("^LOCUS +([a-z|A-Z|0-9|_]+) +([0-9]+) bp ( {3}|ss\\-|ds\\-|ms\\-)([a-z|A-Z|-|\\s]+) ([a-z| ]{8}) ([A-Z| ]{3}) ([0-9]+-[A-Z]+-[0-9]+)");
-    private static final Pattern patQualifierKey = Pattern.compile("/(.*?)=");
-    private static final Pattern patFeatureKey = Pattern.compile("^\\s{5}([A-Za-z0-9\\_\\']+)\\s+");
-    
-    private String definition;
-    private String accession;
-    private String keywords;
-    private String dblink;
-    private String baseCount;
-
-	private Vector<GenBankFeature> features;
-	private Vector<String> comments;
-	//Items under origin 
-	private Vector<GenBankSequence> sequences;
-	private Vector<GenBankReference> references;
-	
-	private SequenceI genBankSequence;
-
-	public GenBankFile() {
-	}
-
-	public GenBankFile(String inFile, String type) throws IOException {
-		super(inFile, type);
-	}
-
-	public GenBankFile(FileParse source) throws IOException {
-		super(source);
-	}
-
-	public void initData() {
-		super.initData();
-		features = new Vector<GenBankFeature>();
-		comments = new Vector<String>();
-		sequences = new Vector<GenBankSequence>();
-		references = new Vector<GenBankReference>();
-	}
-
-	public void parse() throws IOException {
-		String line;
-		boolean featureMode = false;					//FEATURES found
-		boolean seqMode = false;						//Parsing Sequences from SOURCE
-		boolean referenceMode = false;					//REFERENCE found
-		boolean sourceMode = false;						//SOURCE found
-		boolean commentMode = false;					//COMMENT found
-		boolean parsingAuthors = false;					//Parsing authors (multiline)
-		boolean parsingDefinition = false;				//Parsing definition (multiline)
-		boolean parsingKeywords = false;				//Parsing keywords (multiline)
-		boolean parsingDbLink = false;					//Parsing DBLINK (multiline)
-		boolean parsingTitle = false;					//Parsing title (multiline)
-		boolean parsingQualifier = false;				//Parsing feature qualifier (multine)
-		String currentQualifierName = "";
-		GenBankReference reference = null;
-		GenBankFeature feature = null;
-		List<String> sourceLines = new ArrayList<String>();
-
-		if (this.isValid()){
-			
-			while ((line = nextLine()) != null) {
-				// We only process lines if they have contents within
-				if (line.length() == 0)
-					continue;
-				
-				if (line.startsWith("FEATURES")){
-					featureMode = true;
-					seqMode = false;
-					referenceMode = false;
-					sourceMode = false;
-					commentMode = false;
-					feature = new GenBankFeature();
-					source = parseSource(sourceLines);
-				}
-	
-				
-				if (seqMode) {
-					if (!line.startsWith("//")){
-						GenBankSequence seq = processSequenceLine(line);
-						sequences.add(seq);
-					}
-					featureMode = false;
-					referenceMode = false;
-					sourceMode = false;
-				}
-				
-				if (line.startsWith("ORIGIN")){
-					if (feature.getType()!=null)
-						features.add(feature);
-					featureMode = false;
-					referenceMode = false;
-					sourceMode = false;
-					seqMode = true;					
-				}
-	
-				if (featureMode){
-					// Process feature line
-					if (!line.startsWith("FEATURES") && !line.startsWith("BASE COUNT")){
-						//Parse type			
-						if (!line.trim().startsWith("/")){							
-							Matcher featuresMatch = patFeatureKey.matcher(line);
-							if (featuresMatch.find()){
-								if (feature.getType()!=null)
-									features.add(feature);	//Hay que añadirlo sólo si no se está a mitad de un qualif o una feature
-								//It's a feature
-								String type = featuresMatch.group(0);
-								feature = new GenBankFeature();
-								feature.setType(type);							 
-								GenBankLocation loc = parserFeatureLocation(feature, line.replace(type,""));
-								feature.setLocation(loc);
-								parsingQualifier = false;
-								continue;
-							}else if (parsingQualifier) {					//If not a feature, it's another part of a qualifier
-								String qValue = feature.getQualifier(currentQualifierName);
-								StringBuffer sb = new StringBuffer().append(qValue).append(ltrim(line));
-								feature.updateQualifier(currentQualifierName, sb.toString());
-								continue;					
-							}
-						}else{
-							//It's the begining of a qualifier line
-							Matcher matcher = patQualifierKey.matcher(line);
-							if (matcher.find()){
-							    String qName = matcher.group(1);
-							    currentQualifierName = qName.replace("/","");
-								line = line.replace(qName,"").replace("/", "").replace("=","");
-								feature.addQualifier(currentQualifierName, ltrim(line));
-								parsingQualifier = true;
-								continue;
-							}
-						}
-					}
-				}
-				// Process REFERENCE line
-				if (line.startsWith("REFERENCE")) {
-					if (!referenceMode){
-						//This is line is the REFERENCE line
-						referenceMode = true;
-						featureMode = false;
-						sourceMode = false;
-						seqMode = false;
-					}else{
-						//We were at referenceMode, then add current reference to the list and create a new one
-						references.add(reference);
-					}
-					reference = new GenBankReference();
-					String desc = processReferenceLine(line,"REFERENCE");
-					int[] ranges = parseReferenceDescriptor(desc);
-					reference.setDescriptor(desc);
-					reference.setOrder(ranges[0]);
-					reference.setBegin(ranges[1]);
-					reference.setEnd(ranges[2]);
-					parsingAuthors = false;
-					parsingTitle = false;
-					continue;
-				}
-				
-				if (line.startsWith("  AUTHORS")){
-					if (referenceMode){
-						reference.setAuthors(processReferenceLine(line,"AUTHORS"));
-						parsingAuthors = true;
-						parsingTitle = false;
-					}
-					 continue;
-				}
-				if (line.startsWith("  TITLE")){
-					if (referenceMode){
-						reference.setTitle(processReferenceLine(line,"TITLE"));
-						parsingAuthors = false;
-						parsingTitle = true;
-					}
-					 continue;
-				}
-				if (line.startsWith("  JOURNAL")){
-					if (referenceMode){
-						reference.setJournal(processReferenceLine(line,"JOURNAL"));
-						parsingTitle = false;
-						parsingAuthors = false;
-					}
-					continue;
-				}
-				if (line.startsWith("   PUBMED")){
-					if (referenceMode){
-						reference.setPubmed(processReferenceLine(line,"PUBMED"));
-						parsingTitle = false;
-						parsingAuthors = false;
-					}
-					 continue;
-				}
-
-				if (line.startsWith("   MEDLINE")){
-					if (referenceMode){
-						reference.setMedline(processReferenceLine(line,"MEDLINE"));
-						parsingTitle = false;
-						parsingAuthors = false;
-					}
-					 continue;
-				}
-				if (line.startsWith("  REMARK")){
-					if (referenceMode){
-						reference.setRemark(processReferenceLine(line,"REMARK"));
-						parsingTitle = false;
-						parsingAuthors = false;
-					}
-					 continue;
-				}
-				if (line.startsWith("  CONSRTM")){
-					if (referenceMode){
-						reference.setConsortia(processReferenceLine(line,"CONSRTM"));
-						parsingTitle = false;
-						parsingAuthors = false;
-					}
-					 continue;
-				}
-				
-	
-				if (line.startsWith("SOURCE")) {
-					parsingKeywords = false;
-					sourceMode = true;
-					commentMode = false;
-					if (sourceMode){
-						sourceLines.add(line);
-					}
-					 continue;
-				}
-				if (line.indexOf("ORGANISM")!=-1) {
-					if (sourceMode){
-						sourceLines.add(line);
-						 continue;
-					}
-				}
-				
-				if (line.startsWith("COMMENT")){
-					if (reference!=null)
-						references.add(reference);
-					commentMode = true;
-					sourceMode = false;
-					referenceMode = false;
-					sourceMode = false;
-					seqMode = false;
-					comments.add(processCommentLine(line));
-					 continue;
-				}			
-				// Process LOCUS line
-				if (line.startsWith("LOCUS")) {
-					locus = parseLocus(line);
-					continue;
-				}
-				// Process BASE COUNT line
-				if (line.startsWith("BASE COUNT")) {
-					baseCount = processHeaderLine(line,"BASE COUNT");
-					featureMode = false;
-					continue;
-				}
-				// Process DEFINITION line
-				if (line.startsWith("DEFINITION")) {
-					definition = processHeaderLine(line,"DEFINITION");
-					parsingDefinition = true;
-					 continue;
-				}
-				// Process ACCESSION line
-				if (line.startsWith("ACCESSION")) {
-					accession = processHeaderLine(line,"ACCESSION");
-					parsingDefinition = false;
-					continue;
-				}
-				// Process VERSION line
-				if (line.startsWith("VERSION")) {
-					version = parseVersion(line);
-					//headers.put("VERSION", processHeaderLine(line,"VERSION"));
-					 continue;
-				}
-				// Process DBLINK line
-				if (line.startsWith("DBLINK")) {
-					dblink =  processHeaderLine(line,"DBLINK");
-					parsingDbLink = true;
-					 continue;
-				}
-				// Process KEYWORDS line
-				if (line.startsWith("KEYWORDS")) {
-					keywords = processHeaderLine(line,"KEYWORDS");
-					parsingKeywords = true;
-					parsingDbLink = false;					
-					 continue;
-				}				
-				if (sourceMode){
-					sourceLines.add(line);
-					continue;
-				}
-				if (parsingDefinition){
-					StringBuffer sb = new StringBuffer().append(definition).append(line);
-					definition = sb.toString();
-					continue;
-				}
-				if (referenceMode && parsingAuthors){
-					if (reference!=null){
-						StringBuffer authors = new StringBuffer().append(reference.getAuthors()).append(line);						
-						reference.setAuthors(authors.toString());
-					}
-					continue;
-				}
-				if (referenceMode && parsingTitle){
-					if (reference!=null){
-						StringBuffer title = new StringBuffer().append(reference.getTitle()).append(line);						
-						reference.setTitle(title.toString());
-					}
-					continue;
-				}
-				if (parsingKeywords){
-					StringBuffer sb = new StringBuffer().append(keywords).append(line);
-					keywords = sb.toString();
-					continue;					
-				}
-				if (parsingDbLink){
-					StringBuffer sb = new StringBuffer().append(dblink).append(line);
-					dblink = sb.toString();
-					continue;					
-				}
-				if (commentMode){
-					comments.add(line);
-				}
-			}
-			setEntries();
-		}else{
-			//File is not valid
-			throw new IOException("GenBankFile is not valid.");
-		}
-	}	
-
-	protected void setEntries(){
-	    StringBuffer result = new StringBuffer();
-	    //Mapping GenBank info into Jalview data model
-	    genBankSequence = new Sequence(accession,DnaUtils.getNucleotidesFromSequenceVector(sequences));
-	    //Mapping DBRefEntry
-	    DBRefEntry dbRef = new DBRefEntry();
-	    dbRef.setSource(DBRefSource.GENBANK);
-	    dbRef.setVersion(version == null ? "" : version.toString());
-	    dbRef.setAccessionId(accession);
-	    // add map to indicate the sequence is a valid coordinate frame for the dbref
-	    dbRef.setMap(new Mapping(null, new int[]
-	      { 1, genBankSequence.getLength() }, new int[]
-	      { 1, genBankSequence.getLength() }, 1, 1));
-	    genBankSequence.addDBRef(dbRef);
-	    
-	    //add header info as non-positional features
-	    //add LOCUS
-	    SequenceFeature locusF = new SequenceFeature("LOCUS", (locus == null ? "" : locus.toString()), null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(locusF);
-	    //add DEFNITION
-	    SequenceFeature defF = new SequenceFeature("DEFINITION", definition, null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(defF);
-	    //add ACCESSION
-	    SequenceFeature accessionF = new SequenceFeature("ACCESSION", accession, null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(accessionF);
-	    //add VERSION
-	    SequenceFeature versionF = new SequenceFeature("VERSION", (version == null ? "" : version.toString()), null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(versionF);
-	    //add DBLINK
-	    SequenceFeature dblinkF = new SequenceFeature("DBLINK", (dblink == null ? "" : dblink.toString()), null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(dblinkF);
-	    //add KEYWORDS
-	    SequenceFeature keywordsF = new SequenceFeature("KEYWORDS", keywords, null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(keywordsF);
-	    //add SOURCE
-	    SequenceFeature sourceF = new SequenceFeature("SOURCE", (source == null ? "" : source.toString()), null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(sourceF);
-	    //add BASE COUNT
-	    SequenceFeature baseCountF = new SequenceFeature("BASE COUNT", (baseCount == null ? "" : baseCount.toString()), null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-	    genBankSequence.addSequenceFeature(baseCountF);
-	    
-	    // add literature and database cross references in the file
-	    for (GenBankReference gbRef:references){
-	    	//They are non-positional features
-	    	SequenceFeature refFeature = new SequenceFeature("REFERENCE", gbRef.toString(),null,gbRef.getBegin(),gbRef.getEnd(),DBRefSource.GENBANK);
-	    	genBankSequence.addSequenceFeature(refFeature);
-	    }
-	    //add COMMENTS
-	    if (comments.size()>0){
-	    	StringBuffer sb = new StringBuffer();
-		    for (String comment: comments){
-		    	sb.append(comment).append(newline);
-		    }
-		    SequenceFeature commentF = new SequenceFeature("COMMENT", sb.toString(), null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
-		    genBankSequence.addSequenceFeature(commentF);
-	    }
-	    //Mapping FEATURES
-	    for (GenBankFeature feature:features){
-	    	if (feature.getType()!=null){
-		    	SequenceFeature sf = new SequenceFeature();
-		    	sf.setType(feature.getType());
-		    	sf.setDescription(feature.getType());
-		    	
-		    	sf.setBegin(feature.getLocation()==null ? 0 : feature.getLocation().getMinor());
-		    	sf.setEnd(feature.getLocation()==null ? 0 : feature.getLocation().getMajor());
-		    	Enumeration<String> names = feature.getQualifiersNames();
-		    	while (names.hasMoreElements()){
-		    		String qName = names.nextElement();
-		    		String qValue = feature.getQualifier(qName);
-		    		sf.setValue(qName, qValue);
-		    	}
-		    	genBankSequence.addSequenceFeature(sf);
-	    	}
-	    }
-	    SequenceI[] parsedSeqs = new SequenceI[1];
-	    parsedSeqs[0] = genBankSequence;
-	    this.setSeqs(parsedSeqs);
-	}
-    private GenBankVersion parseVersion(String line) {
-        //VERSION U00096.2 GI:48994873
-    	if (line.trim().equalsIgnoreCase("VERSION")){
-    		return null;
-    	}else{
-	        GenBankVersion ver = new GenBankVersion();
-	        String v = line.substring(11, line.indexOf(" ", 12)).trim();
-	        ver.setVersion(v);
-	        int posGI = line.indexOf("GI:", 11 + v.length());
-	        if (posGI > -1) {
-	            ver.setGI(line.substring(posGI));
-	        }
-	        return ver;
-    	}
+public class GenBankFile extends AlignFile
+{
+  private static final Logger log = Logger.getLogger(GenBankFile.class
+          .getName());
+
+  private GenBankVersion version = new GenBankVersion();
+
+  private GenBankLocus locus = new GenBankLocus();
+
+  private GenBankSource source = new GenBankSource();
+
+  private static final Pattern patLocation = Pattern
+          .compile("(\\d+)\\.\\.(\\d+)");
+
+  private static final Pattern patLocationComp = Pattern
+          .compile("(complement)\\((\\d+)\\.\\.(\\d+)\\)");
+
+  private static final Pattern patLocus = Pattern
+          .compile("^LOCUS +([a-z|A-Z|0-9|_]+) +([0-9]+) bp ( {3}|ss\\-|ds\\-|ms\\-)([a-z|A-Z|-|\\s]+) ([a-z| ]{8}) ([A-Z| ]{3}) ([0-9]+-[A-Z]+-[0-9]+)");
+
+  private static final Pattern patQualifierKey = Pattern.compile("/(.*?)=");
+
+  private static final Pattern patFeatureKey = Pattern
+          .compile("^\\s{5}([A-Za-z0-9\\_\\']+)\\s+");
+
+  private String definition;
+
+  private String accession;
+
+  private String keywords;
+
+  private String dblink;
+
+  private String baseCount;
+
+  private Vector<GenBankFeature> features;
+
+  private Vector<String> comments;
+
+  // Items under origin
+  private Vector<GenBankSequence> sequences;
+
+  private Vector<GenBankReference> references;
+
+  private SequenceI genBankSequence;
+
+  public GenBankFile()
+  {
+  }
+
+  public GenBankFile(String inFile, String type) throws IOException
+  {
+    super(inFile, type);
+  }
+
+  public GenBankFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
+  public void initData()
+  {
+    super.initData();
+    features = new Vector<GenBankFeature>();
+    comments = new Vector<String>();
+    sequences = new Vector<GenBankSequence>();
+    references = new Vector<GenBankReference>();
+  }
+
+  public void parse() throws IOException
+  {
+    String line;
+    boolean featureMode = false; // FEATURES found
+    boolean seqMode = false; // Parsing Sequences from SOURCE
+    boolean referenceMode = false; // REFERENCE found
+    boolean sourceMode = false; // SOURCE found
+    boolean commentMode = false; // COMMENT found
+    boolean parsingAuthors = false; // Parsing authors (multiline)
+    boolean parsingDefinition = false; // Parsing definition (multiline)
+    boolean parsingKeywords = false; // Parsing keywords (multiline)
+    boolean parsingDbLink = false; // Parsing DBLINK (multiline)
+    boolean parsingTitle = false; // Parsing title (multiline)
+    boolean parsingQualifier = false; // Parsing feature qualifier (multine)
+    String currentQualifierName = "";
+    GenBankReference reference = null;
+    GenBankFeature feature = null;
+    List<String> sourceLines = new ArrayList<String>();
+
+    if (this.isValid())
+    {
+
+      while ((line = nextLine()) != null)
+      {
+        // We only process lines if they have contents within
+        if (line.length() == 0)
+          continue;
+
+        if (line.startsWith("FEATURES"))
+        {
+          featureMode = true;
+          seqMode = false;
+          referenceMode = false;
+          sourceMode = false;
+          commentMode = false;
+          feature = new GenBankFeature();
+          source = parseSource(sourceLines);
+        }
+
+        if (seqMode)
+        {
+          if (!line.startsWith("//"))
+          {
+            GenBankSequence seq = processSequenceLine(line);
+            sequences.add(seq);
+          }
+          featureMode = false;
+          referenceMode = false;
+          sourceMode = false;
+        }
+
+        if (line.startsWith("ORIGIN"))
+        {
+          if (feature.getType() != null)
+            features.add(feature);
+          featureMode = false;
+          referenceMode = false;
+          sourceMode = false;
+          seqMode = true;
+        }
+
+        if (featureMode)
+        {
+          // Process feature line
+          if (!line.startsWith("FEATURES")
+                  && !line.startsWith("BASE COUNT"))
+          {
+            // Parse type
+            if (!line.trim().startsWith("/"))
+            {
+              Matcher featuresMatch = patFeatureKey.matcher(line);
+              if (featuresMatch.find())
+              {
+                if (feature.getType() != null)
+                  features.add(feature); // Hay que a�adirlo s�lo si no se est�
+                                         // a mitad de un qualif o una feature
+                // It's a feature
+                String type = featuresMatch.group(0);
+                feature = new GenBankFeature();
+                feature.setType(type);
+                GenBankLocation loc = parserFeatureLocation(feature,
+                        line.replace(type, ""));
+                feature.setLocation(loc);
+                parsingQualifier = false;
+                continue;
+              }
+              else if (parsingQualifier)
+              { // If not a feature, it's another part of a qualifier
+                String qValue = feature.getQualifier(currentQualifierName);
+                StringBuffer sb = new StringBuffer().append(qValue).append(
+                        ltrim(line));
+                feature.updateQualifier(currentQualifierName, sb.toString());
+                continue;
+              }
+            }
+            else
+            {
+              // It's the begining of a qualifier line
+              Matcher matcher = patQualifierKey.matcher(line);
+              if (matcher.find())
+              {
+                String qName = matcher.group(1);
+                currentQualifierName = qName.replace("/", "");
+                line = line.replace(qName, "").replace("/", "")
+                        .replace("=", "");
+                feature.addQualifier(currentQualifierName, ltrim(line));
+                parsingQualifier = true;
+                continue;
+              }
+            }
+          }
+        }
+        // Process REFERENCE line
+        if (line.startsWith("REFERENCE"))
+        {
+          if (!referenceMode)
+          {
+            // This is line is the REFERENCE line
+            referenceMode = true;
+            featureMode = false;
+            sourceMode = false;
+            seqMode = false;
+          }
+          else
+          {
+            // We were at referenceMode, then add current reference to the list
+            // and create a new one
+            references.add(reference);
+          }
+          reference = new GenBankReference();
+          String desc = processReferenceLine(line, "REFERENCE");
+          int[] ranges = parseReferenceDescriptor(desc);
+          reference.setDescriptor(desc);
+          reference.setOrder(ranges[0]);
+          reference.setBegin(ranges[1]);
+          reference.setEnd(ranges[2]);
+          parsingAuthors = false;
+          parsingTitle = false;
+          continue;
+        }
+
+        if (line.startsWith("  AUTHORS"))
+        {
+          if (referenceMode)
+          {
+            reference.setAuthors(processReferenceLine(line, "AUTHORS"));
+            parsingAuthors = true;
+            parsingTitle = false;
+          }
+          continue;
+        }
+        if (line.startsWith("  TITLE"))
+        {
+          if (referenceMode)
+          {
+            reference.setTitle(processReferenceLine(line, "TITLE"));
+            parsingAuthors = false;
+            parsingTitle = true;
+          }
+          continue;
+        }
+        if (line.startsWith("  JOURNAL"))
+        {
+          if (referenceMode)
+          {
+            reference.setJournal(processReferenceLine(line, "JOURNAL"));
+            parsingTitle = false;
+            parsingAuthors = false;
+          }
+          continue;
+        }
+        if (line.startsWith("   PUBMED"))
+        {
+          if (referenceMode)
+          {
+            reference.setPubmed(processReferenceLine(line, "PUBMED"));
+            parsingTitle = false;
+            parsingAuthors = false;
+          }
+          continue;
+        }
+
+        if (line.startsWith("   MEDLINE"))
+        {
+          if (referenceMode)
+          {
+            reference.setMedline(processReferenceLine(line, "MEDLINE"));
+            parsingTitle = false;
+            parsingAuthors = false;
+          }
+          continue;
+        }
+        if (line.startsWith("  REMARK"))
+        {
+          if (referenceMode)
+          {
+            reference.setRemark(processReferenceLine(line, "REMARK"));
+            parsingTitle = false;
+            parsingAuthors = false;
+          }
+          continue;
+        }
+        if (line.startsWith("  CONSRTM"))
+        {
+          if (referenceMode)
+          {
+            reference.setConsortia(processReferenceLine(line, "CONSRTM"));
+            parsingTitle = false;
+            parsingAuthors = false;
+          }
+          continue;
+        }
+
+        if (line.startsWith("SOURCE"))
+        {
+          parsingKeywords = false;
+          sourceMode = true;
+          commentMode = false;
+          if (sourceMode)
+          {
+            sourceLines.add(line);
+          }
+          continue;
+        }
+        if (line.indexOf("ORGANISM") != -1)
+        {
+          if (sourceMode)
+          {
+            sourceLines.add(line);
+            continue;
+          }
+        }
+
+        if (line.startsWith("COMMENT"))
+        {
+          if (reference != null)
+            references.add(reference);
+          commentMode = true;
+          sourceMode = false;
+          referenceMode = false;
+          sourceMode = false;
+          seqMode = false;
+          comments.add(processCommentLine(line));
+          continue;
+        }
+        // Process LOCUS line
+        if (line.startsWith("LOCUS"))
+        {
+          locus = parseLocus(line);
+          continue;
+        }
+        // Process BASE COUNT line
+        if (line.startsWith("BASE COUNT"))
+        {
+          baseCount = processHeaderLine(line, "BASE COUNT");
+          featureMode = false;
+          continue;
+        }
+        // Process DEFINITION line
+        if (line.startsWith("DEFINITION"))
+        {
+          definition = processHeaderLine(line, "DEFINITION");
+          parsingDefinition = true;
+          continue;
+        }
+        // Process ACCESSION line
+        if (line.startsWith("ACCESSION"))
+        {
+          accession = processHeaderLine(line, "ACCESSION");
+          parsingDefinition = false;
+          continue;
+        }
+        // Process VERSION line
+        if (line.startsWith("VERSION"))
+        {
+          version = parseVersion(line);
+          // headers.put("VERSION", processHeaderLine(line,"VERSION"));
+          continue;
+        }
+        // Process DBLINK line
+        if (line.startsWith("DBLINK"))
+        {
+          dblink = processHeaderLine(line, "DBLINK");
+          parsingDbLink = true;
+          continue;
+        }
+        // Process KEYWORDS line
+        if (line.startsWith("KEYWORDS"))
+        {
+          keywords = processHeaderLine(line, "KEYWORDS");
+          parsingKeywords = true;
+          parsingDbLink = false;
+          continue;
+        }
+        if (sourceMode)
+        {
+          sourceLines.add(line);
+          continue;
+        }
+        if (parsingDefinition)
+        {
+          StringBuffer sb = new StringBuffer().append(definition).append(
+                  line);
+          definition = sb.toString();
+          continue;
+        }
+        if (referenceMode && parsingAuthors)
+        {
+          if (reference != null)
+          {
+            StringBuffer authors = new StringBuffer().append(
+                    reference.getAuthors()).append(line);
+            reference.setAuthors(authors.toString());
+          }
+          continue;
+        }
+        if (referenceMode && parsingTitle)
+        {
+          if (reference != null)
+          {
+            StringBuffer title = new StringBuffer().append(
+                    reference.getTitle()).append(line);
+            reference.setTitle(title.toString());
+          }
+          continue;
+        }
+        if (parsingKeywords)
+        {
+          StringBuffer sb = new StringBuffer().append(keywords)
+                  .append(line);
+          keywords = sb.toString();
+          continue;
+        }
+        if (parsingDbLink)
+        {
+          StringBuffer sb = new StringBuffer().append(dblink).append(line);
+          dblink = sb.toString();
+          continue;
+        }
+        if (commentMode)
+        {
+          comments.add(line);
+        }
+      }
+      setEntries();
     }
-    
-    private GenBankLocus parseLocus(String line){
-    	GenBankLocus loc = new GenBankLocus();
-        Matcher mat = patLocus.matcher(line);
-        if (mat.find()) {
-            String name = mat.group(1);
-            String len = mat.group(2);
-            String strand = mat.group(3);
-            String mtype = mat.group(4);
-            String linear = mat.group(5);
-            String division = mat.group(6);
-            String date = mat.group(7);
-    	
-	        loc.setName(name == null ? "" : name.trim());
-	        loc.setSequenceLength(len == null ? 0 : Integer.parseInt(len));
-	        loc.setStrand(strand == null ? "" : strand);
-	        loc.setMoleculeType(mtype == null ? "" : mtype);
-	        loc.setLinearSequence("linear".equals(linear));
-	        loc.setDivision(division == null ? "" : division);
-	        loc.setModificationDate(date == null ? "" :date);    		
-        }
-    	return loc;
+    else
+    {
+      // File is not valid
+      throw new IOException("GenBankFile is not valid.");
     }
-	private GenBankSource parseSource(List<String> lines){
-		StringBuffer sb = new StringBuffer();
-		for(String line:lines){
-			sb.append(line).append(newline);
-		}
-        // Source section
-        GenBankSource sou = new GenBankSource();
-        String aux = sb.toString().substring(11);
-        int fim1 = aux.indexOf("\n");
-        if (fim1 > -1) {
-            sou.setSource(aux.substring(0, fim1));
-            int ini2 = aux.indexOf("ORGANISM");
-            if (ini2 > -1) {
-                fim1 = aux.indexOf("\n", ini2 + 10);
-                if (fim1 > -1) {
-                    sou.setOrganism(aux.substring(ini2 + 10, fim1));
-                    sou.setTaxonomic(aux.substring(fim1).replaceAll("            ", "").replaceAll("\\s+", ""));
-                } else {
-                    sou.setOrganism(aux);
-                }
-            }
-        } else {
-            sou.setSource(aux);
-        }	
-        return sou;
-	}
-
-    /**
-     * Possible situations:
-     *
-     * 467 Points to a single base in the presented sequence 340..565 Points to
-     * a continuous range of bases bounded by and including the starting and
-     * ending bases &lt;345..500 Indicates that the exact lower boundary point
-     * of a feature is unknown. The location begins at some base previous to the
-     * first base specified (which need not be contained in the presented
-     * sequence) and continues to and includes the ending base &lt;1..888 The
-     * feature starts before the first sequenced base and continues to and
-     * includes base 888 1..&gt;888 The feature starts at the first sequenced
-     * base and continues beyond base 888 102.110 Indicates that the exact
-     * location is unknown but that it is one of the bases between bases 102 and
-     * 110, inclusive 123^124 Points to a site between bases 123 and 124
-     * join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
-     * form one contiguous sequence complement(34..126) Start at the base
-     * complementary to 126 and finish at the base complementary to base 34 (the
-     * feature is on the strand complementary to the presented strand)
-     * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and
-     * 4918 to 5163, then complements the joined segments (the feature is on the
-     * strand complementary to the presented strand)
-     * join(complement(4918..5163),complement(2691..4571)) Complements regions
-     * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
-     * feature is on the strand complementary to the presented strand)
-     * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
-     * this database) with primary accession number 'J00194'
-     * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
-     * with the region 100..202 of remote entry J00194
-     *
-     * @param fea
-     * @param localiza
-     */
-    private GenBankLocation parserFeatureLocation(GenBankFeature fea, String localiza) {
-        // remove os espaços, quebra de linhas etc
-        String buf = localiza.replaceAll("\\s", "");
-
-        // checks if there is a comma present between ranges
-        // complement(100..110),complement(90..100)
-        char[] buf2 = buf.toCharArray();
-        int abertos = 0;
-        java.util.List<String> lista = new java.util.ArrayList<String>();
-        int pinicial = 0;
-        for (int i = 0; i < buf2.length; i++) {
-            if (buf2[i] == '(') {
-                abertos++;
-            } else if (buf2[i] == ')') {
-                abertos--;
-            } else if (buf2[i] == ',' && abertos == 0) {
-                lista.add(buf.substring(pinicial, i));
-                pinicial = i + 1;
+  }
+
+  protected void setEntries()
+  {
+    StringBuffer result = new StringBuffer();
+    // Mapping GenBank info into Jalview data model
+    genBankSequence = new Sequence(accession,
+            DnaUtils.getNucleotidesFromSequenceVector(sequences));
+    // Mapping DBRefEntry
+    DBRefEntry dbRef = new DBRefEntry();
+    dbRef.setSource(DBRefSource.GENBANK);
+    dbRef.setVersion(version == null ? "" : version.toString());
+    dbRef.setAccessionId(accession);
+    // add map to indicate the sequence is a valid coordinate frame for the
+    // dbref
+    dbRef.setMap(new Mapping(null, new int[]
+    { 1, genBankSequence.getLength() }, new int[]
+    { 1, genBankSequence.getLength() }, 1, 1));
+    genBankSequence.addDBRef(dbRef);
+
+    // add header info as non-positional features
+    // add LOCUS
+    SequenceFeature locusF = new SequenceFeature("LOCUS",
+            (locus == null ? "" : locus.toString()), null, 1,
+            genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(locusF);
+    // add DEFNITION
+    SequenceFeature defF = new SequenceFeature("DEFINITION", definition,
+            null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(defF);
+    // add ACCESSION
+    SequenceFeature accessionF = new SequenceFeature("ACCESSION",
+            accession, null, 1, genBankSequence.getLength(),
+            DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(accessionF);
+    // add VERSION
+    SequenceFeature versionF = new SequenceFeature("VERSION",
+            (version == null ? "" : version.toString()), null, 1,
+            genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(versionF);
+    // add DBLINK
+    SequenceFeature dblinkF = new SequenceFeature("DBLINK",
+            (dblink == null ? "" : dblink.toString()), null, 1,
+            genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(dblinkF);
+    // add KEYWORDS
+    SequenceFeature keywordsF = new SequenceFeature("KEYWORDS", keywords,
+            null, 1, genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(keywordsF);
+    // add SOURCE
+    SequenceFeature sourceF = new SequenceFeature("SOURCE",
+            (source == null ? "" : source.toString()), null, 1,
+            genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(sourceF);
+    // add BASE COUNT
+    SequenceFeature baseCountF = new SequenceFeature("BASE COUNT",
+            (baseCount == null ? "" : baseCount.toString()), null, 1,
+            genBankSequence.getLength(), DBRefSource.GENBANK);
+    genBankSequence.addSequenceFeature(baseCountF);
+
+    // add literature and database cross references in the file
+    for (GenBankReference gbRef : references)
+    {
+      // They are non-positional features
+      SequenceFeature refFeature = new SequenceFeature("REFERENCE",
+              gbRef.toString(), null, gbRef.getBegin(), gbRef.getEnd(),
+              DBRefSource.GENBANK);
+      genBankSequence.addSequenceFeature(refFeature);
+    }
+    // add COMMENTS
+    if (comments.size() > 0)
+    {
+      StringBuffer sb = new StringBuffer();
+      for (String comment : comments)
+      {
+        sb.append(comment).append(newline);
+      }
+      SequenceFeature commentF = new SequenceFeature("COMMENT",
+              sb.toString(), null, 1, genBankSequence.getLength(),
+              DBRefSource.GENBANK);
+      genBankSequence.addSequenceFeature(commentF);
+    }
+    // Mapping FEATURES
+    for (GenBankFeature feature : features)
+    {
+      if (feature.getType() != null)
+      {
+        SequenceFeature sf = new SequenceFeature();
+        sf.setType(feature.getType());
+        sf.setDescription(feature.getType());
+
+        sf.setBegin(feature.getLocation() == null ? 0 : feature
+                .getLocation().getMinor());
+        sf.setEnd(feature.getLocation() == null ? 0 : feature.getLocation()
+                .getMajor());
+        Enumeration<String> names = feature.getQualifiersNames();
+        while (names.hasMoreElements())
+        {
+          String qName = names.nextElement();
+          String qValue = feature.getQualifier(qName);
+          sf.setValue(qName, qValue);
+        }
+        genBankSequence.addSequenceFeature(sf);
+      }
+    }
+    SequenceI[] parsedSeqs = new SequenceI[1];
+    parsedSeqs[0] = genBankSequence;
+    this.setSeqs(parsedSeqs);
+  }
+
+  private GenBankVersion parseVersion(String line)
+  {
+    // VERSION U00096.2 GI:48994873
+    if (line.trim().equalsIgnoreCase("VERSION"))
+    {
+      return null;
+    }
+    else
+    {
+      GenBankVersion ver = new GenBankVersion();
+      String v = line.substring(11, line.indexOf(" ", 12)).trim();
+      ver.setVersion(v);
+      int posGI = line.indexOf("GI:", 11 + v.length());
+      if (posGI > -1)
+      {
+        ver.setGI(line.substring(posGI));
+      }
+      return ver;
+    }
+  }
+
+  private GenBankLocus parseLocus(String line)
+  {
+    GenBankLocus loc = new GenBankLocus();
+    Matcher mat = patLocus.matcher(line);
+    if (mat.find())
+    {
+      String name = mat.group(1);
+      String len = mat.group(2);
+      String strand = mat.group(3);
+      String mtype = mat.group(4);
+      String linear = mat.group(5);
+      String division = mat.group(6);
+      String date = mat.group(7);
+
+      loc.setName(name == null ? "" : name.trim());
+      loc.setSequenceLength(len == null ? 0 : Integer.parseInt(len));
+      loc.setStrand(strand == null ? "" : strand);
+      loc.setMoleculeType(mtype == null ? "" : mtype);
+      loc.setLinearSequence("linear".equals(linear));
+      loc.setDivision(division == null ? "" : division);
+      loc.setModificationDate(date == null ? "" : date);
+    }
+    return loc;
+  }
+
+  private GenBankSource parseSource(List<String> lines)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (String line : lines)
+    {
+      sb.append(line).append(newline);
+    }
+    // Source section
+    GenBankSource sou = new GenBankSource();
+    String aux = sb.toString().substring(11);
+    int fim1 = aux.indexOf("\n");
+    if (fim1 > -1)
+    {
+      sou.setSource(aux.substring(0, fim1));
+      int ini2 = aux.indexOf("ORGANISM");
+      if (ini2 > -1)
+      {
+        fim1 = aux.indexOf("\n", ini2 + 10);
+        if (fim1 > -1)
+        {
+          sou.setOrganism(aux.substring(ini2 + 10, fim1));
+          sou.setTaxonomic(aux.substring(fim1)
+                  .replaceAll("            ", "").replaceAll("\\s+", ""));
+        }
+        else
+        {
+          sou.setOrganism(aux);
+        }
+      }
+    }
+    else
+    {
+      sou.setSource(aux);
+    }
+    return sou;
+  }
+
+  /**
+   * Possible situations:
+   * 
+   * 467 Points to a single base in the presented sequence 340..565 Points to a
+   * continuous range of bases bounded by and including the starting and ending
+   * bases &lt;345..500 Indicates that the exact lower boundary point of a
+   * feature is unknown. The location begins at some base previous to the first
+   * base specified (which need not be contained in the presented sequence) and
+   * continues to and includes the ending base &lt;1..888 The feature starts
+   * before the first sequenced base and continues to and includes base 888
+   * 1..&gt;888 The feature starts at the first sequenced base and continues
+   * beyond base 888 102.110 Indicates that the exact location is unknown but
+   * that it is one of the bases between bases 102 and 110, inclusive 123^124
+   * Points to a site between bases 123 and 124 join(12..78,134..202) Regions 12
+   * to 78 and 134 to 202 should be joined to form one contiguous sequence
+   * complement(34..126) Start at the base complementary to 126 and finish at
+   * the base complementary to base 34 (the feature is on the strand
+   * complementary to the presented strand)
+   * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
+   * to 5163, then complements the joined segments (the feature is on the strand
+   * complementary to the presented strand)
+   * join(complement(4918..5163),complement(2691..4571)) Complements regions
+   * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
+   * feature is on the strand complementary to the presented strand)
+   * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
+   * this database) with primary accession number 'J00194'
+   * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
+   * with the region 100..202 of remote entry J00194
+   * 
+   * @param fea
+   * @param localiza
+   */
+  private GenBankLocation parserFeatureLocation(GenBankFeature fea,
+          String localiza)
+  {
+    // remove os espaços, quebra de linhas etc
+    String buf = localiza.replaceAll("\\s", "");
+
+    // checks if there is a comma present between ranges
+    // complement(100..110),complement(90..100)
+    char[] buf2 = buf.toCharArray();
+    int abertos = 0;
+    java.util.List<String> lista = new java.util.ArrayList<String>();
+    int pinicial = 0;
+    for (int i = 0; i < buf2.length; i++)
+    {
+      if (buf2[i] == '(')
+      {
+        abertos++;
+      }
+      else if (buf2[i] == ')')
+      {
+        abertos--;
+      }
+      else if (buf2[i] == ',' && abertos == 0)
+      {
+        lista.add(buf.substring(pinicial, i));
+        pinicial = i + 1;
+      }
+    }
+    if (lista.size() > 0)
+    {
+      lista.add(buf.substring(pinicial));
+      GenBankLocations um = new GenBankLocations();
+      um.setOperator(GenBankLocations.NONE);
+      for (String s : lista)
+      {
+        um.getUnits().add(parserFeatureLocation(fea, s));
+      }
+      fea.setLocation(um);
+      return um;
+    }
+
+    // trata as funcoes: complement(location,location...),
+    // join(location,location...), order(location,location...)
+    if (buf.contains("("))
+    {
+      GenBankLocations um = new GenBankLocations();
+      int ini = buf.indexOf("(");
+      int fim = buf.lastIndexOf(")");
+      String token = buf.substring(0, ini);
+      if ("complement".equalsIgnoreCase(token))
+      {
+        String inter = buf.substring(ini + 1, fim);
+        GenBankLocation interno = parserFeatureLocation(fea, inter);
+        interno.setComplement(true);
+        um.setOperator(GenBankLocations.COMPLEMENT);
+        um.getUnits().add(interno);
+        fea.setLocation(um);
+      }
+      else if ("join".equalsIgnoreCase(token))
+      {
+        String inter = buf.substring(ini + 1, fim);
+        GenBankLocation interno = parserFeatureLocation(fea, inter);
+        um.setOperator(GenBankLocations.JOIN);
+        um.getUnits().add(interno);
+        fea.setLocation(um);
+      }
+      else if ("order".equalsIgnoreCase(token))
+      {
+        String inter = buf.substring(ini + 1, fim);
+        GenBankLocation interno = parserFeatureLocation(fea, inter);
+        um.setOperator(GenBankLocations.ORDER);
+        um.getUnits().add(interno);
+        fea.setLocation(um);
+      }
+      else
+      {
+        log.log(Level.WARNING,
+                "Token desconhecido em location/features - {0}", token);
+        String inter = buf.substring(ini + 1, fim);
+        fea.setLocation(parserFeatureLocation(fea, inter));
+      }
+      return fea.getLocation();
+    }
+    else
+    {
+      // trata quando tiver uma lista de location
+      if (buf.contains(","))
+      {
+        String[] partes = buf.split(",");
+        GenBankLocations um = new GenBankLocations();
+        for (String p : partes)
+        {
+          um.getUnits().add(parserFeatureLocation(fea, p));
+        }
+        fea.setLocation(um);
+        return um;
+      }
+      else
+      {
+        // trata quando tiver range
+        if (buf.contains(".."))
+        {
+          String[] partes = buf.split("\\.\\.");
+          GenBankLocationRange range = new GenBankLocationRange();
+          if (buf.contains(":"))
+          {
+            for (int i = 0; i < partes.length; i++)
+            {
+              int pos = partes[i].indexOf(":");
+              if (pos > 0)
+              {
+                String entry = partes[i].substring(0, pos);
+                partes[i] = partes[i].substring(pos + 1);
+                range.setEntry(entry);
+              }
             }
+          }
+          GenBankLocationPoint gp0 = (GenBankLocationPoint) parserFeatureLocation(
+                  fea, partes[0]);
+          range.setStart(gp0);
+          GenBankLocationPoint gp1 = (GenBankLocationPoint) parserFeatureLocation(
+                  fea, partes[1]);
+          range.setEnd(gp1);
+          fea.setLocation(range);
+          return range;
         }
-        if (lista.size() > 0) {
-            lista.add(buf.substring(pinicial));
-            GenBankLocations um = new GenBankLocations();
-            um.setOperator(GenBankLocations.NONE);
-            for (String s : lista) {
-                um.getUnits().add(parserFeatureLocation(fea, s));
+        else
+        {
+          // trata um ponto
+          // possibilidades consideradas:
+          // 467
+          // 102.110
+          // 123^124
+          // <345
+          // >400
+          // 345>
+          // 400<
+          // ou uma combinacao dessas
+          GenBankLocationPoint gp = new GenBankLocationPoint();
+          if (buf.contains(":"))
+          {
+            int pos = buf.indexOf(":");
+            if (pos > 0)
+            {
+              String entry = buf.substring(0, pos);
+              buf = buf.substring(pos + 1);
+              gp.setEntry(entry);
             }
-            fea.setLocation(um);
-            return um;
-        }
-
-        // trata as funcoes: complement(location,location...),
-        // join(location,location...), order(location,location...)
-        if (buf.contains("(")) {
-        	GenBankLocations um = new GenBankLocations();
-            int ini = buf.indexOf("(");
-            int fim = buf.lastIndexOf(")");
-            String token = buf.substring(0, ini);
-            if ("complement".equalsIgnoreCase(token)) {
-                String inter = buf.substring(ini + 1, fim);
-                GenBankLocation interno = parserFeatureLocation(fea, inter);
-                interno.setComplement(true);
-                um.setOperator(GenBankLocations.COMPLEMENT);
-                um.getUnits().add(interno);
-                fea.setLocation(um);
-            } else if ("join".equalsIgnoreCase(token)) {
-                String inter = buf.substring(ini + 1, fim);
-                GenBankLocation interno = parserFeatureLocation(fea, inter);
-                um.setOperator(GenBankLocations.JOIN);
-                um.getUnits().add(interno);
-                fea.setLocation(um);
-            } else if ("order".equalsIgnoreCase(token)) {
-                String inter = buf.substring(ini + 1, fim);
-                GenBankLocation interno = parserFeatureLocation(fea, inter);
-                um.setOperator(GenBankLocations.ORDER);
-                um.getUnits().add(interno);
-                fea.setLocation(um);
-            } else {
-                log.log(Level.WARNING, "Token desconhecido em location/features - {0}", token);
-                String inter = buf.substring(ini + 1, fim);
-                fea.setLocation(parserFeatureLocation(fea, inter));
+          }
+          int pos = 0;
+          // verifica os simb < e > antes do primeiro numero
+          if (buf.charAt(pos) == '<' || buf.charAt(pos) == '>')
+          {
+            gp.setPrefix(buf.charAt(pos));
+            pos++;
+          }
+          // pega o primeiro numero
+          int ini = pos;
+          while (pos < buf.length() && buf.charAt(pos) >= '0'
+                  && buf.charAt(pos) <= '9')
+          {
+            pos++;
+          }
+          if (buf.subSequence(ini, pos).length() < 1)
+          {
+            System.out.println(localiza);
+          }
+          int num = Integer.parseInt(buf.substring(ini, pos));
+          int num2 = num;
+          // o primeiro numero pode ser o unico numero
+          if (pos < buf.length())
+          {
+            // verifica se tem os sinais < e > apos o primeiro numero
+            if (buf.charAt(pos) == '<' || buf.charAt(pos) == '>')
+            {
+              if (buf.contains(".") || buf.contains("^"))
+              {
+                gp.setPrefix(buf.charAt(pos));
+              }
+              else
+              {
+                gp.setSufix(buf.charAt(pos));
+              }
+              pos++;
             }
-            return fea.getLocation();
-        } else {
-            // trata quando tiver uma lista de location
-            if (buf.contains(",")) {
-                String[] partes = buf.split(",");
-                GenBankLocations um = new GenBankLocations();
-                for (String p : partes) {
-                    um.getUnits().add(
-                            parserFeatureLocation(fea, p));
-                }
-                fea.setLocation(um);
-                return um;
-            } else {
-                // trata quando tiver range
-                if (buf.contains("..")) {
-                    String[] partes = buf.split("\\.\\.");
-                    GenBankLocationRange range = new GenBankLocationRange();
-                    if (buf.contains(":")) {
-                        for (int i = 0; i < partes.length; i++) {
-                            int pos = partes[i].indexOf(":");
-                            if (pos > 0) {
-                                String entry = partes[i].substring(0, pos);
-                                partes[i] = partes[i].substring(pos + 1);
-                                range.setEntry(entry);
-                            }
-                        }
-                    }
-                    GenBankLocationPoint gp0 = (GenBankLocationPoint) parserFeatureLocation(fea, partes[0]);
-                    range.setStart(gp0);
-                    GenBankLocationPoint gp1 = (GenBankLocationPoint) parserFeatureLocation(fea, partes[1]);
-                    range.setEnd(gp1);
-                    fea.setLocation(range);
-                    return range;
-                } else {
-                    // trata um ponto
-                    // possibilidades consideradas:
-                    //      467
-                    //      102.110
-                    //      123^124
-                    //      <345
-                    //      >400
-                    //      345>
-                    //      400<
-                    //      ou uma combinacao dessas
-                	GenBankLocationPoint gp = new GenBankLocationPoint();
-                    if (buf.contains(":")) {
-                        int pos = buf.indexOf(":");
-                        if (pos > 0) {
-                            String entry = buf.substring(0, pos);
-                            buf = buf.substring(pos + 1);
-                            gp.setEntry(entry);
-                        }
-                    }
-                    int pos = 0;
-                    // verifica os simb < e > antes do primeiro numero
-                    if (buf.charAt(pos) == '<' || buf.charAt(pos) == '>') {
-                        gp.setPrefix(buf.charAt(pos));
-                        pos++;
-                    }
-                    // pega o primeiro numero
-                    int ini = pos;
-                    while (pos < buf.length() && buf.charAt(pos) >= '0'
-                            && buf.charAt(pos) <= '9') {
-                        pos++;
-                    }
-                    if (buf.subSequence(ini, pos).length() < 1) {
-                        System.out.println(localiza);
-                    }
-                    int num = Integer.parseInt(buf.substring(ini, pos));
-                    int num2 = num;
-                    // o primeiro numero pode ser o unico numero
-                    if (pos < buf.length()) {
-                        // verifica se tem os sinais < e > apos o primeiro numero
-                        if (buf.charAt(pos) == '<' || buf.charAt(pos) == '>') {
-                            if (buf.contains(".") || buf.contains("^")) {
-                                gp.setPrefix(buf.charAt(pos));
-                            } else {
-                                gp.setSufix(buf.charAt(pos));
-                            }
-                            pos++;
-                        }
-
-                        // verifica a separacao dos numeros . ou ^
-                        if (pos < buf.length()
-                                && (buf.charAt(pos) == '.' || buf.charAt(pos) == '^')) {
-                            // separação localizada, possibilidade de mais numero
-                            gp.setSymbol(buf.charAt(pos));
-                            pos++;
-
-                            // verifica os simb < e > antes do segundo numero
-                            if (buf.charAt(pos) == '<' || buf.charAt(pos) == '>') {
-                                gp.setSufix(buf.charAt(pos));
-                                pos++;
-                            }
-
-                            // pega o segundo numero
-                            ini = pos;
-                            while (pos < buf.length() && buf.charAt(pos) >= '0'
-                                    && buf.charAt(pos) <= '9') {
-                                pos++;
-                            }
-                            num2 = Integer.parseInt(buf.substring(ini, pos));
-
-                            // verifica os simb < e > após o segundo numero
-                            if (pos < buf.length() && (buf.charAt(pos) == '<' || buf.charAt(pos) == '>')) {
-                                gp.setSufix(buf.charAt(pos));
-                                pos++;
-                            }
-                        }
-                    }
-                    gp.setMin(num);
-                    gp.setMax(num2);
-                    fea.setLocation(gp);
-                    return gp;
-                }
+
+            // verifica a separacao dos numeros . ou ^
+            if (pos < buf.length()
+                    && (buf.charAt(pos) == '.' || buf.charAt(pos) == '^'))
+            {
+              // separação localizada, possibilidade de mais numero
+              gp.setSymbol(buf.charAt(pos));
+              pos++;
+
+              // verifica os simb < e > antes do segundo numero
+              if (buf.charAt(pos) == '<' || buf.charAt(pos) == '>')
+              {
+                gp.setSufix(buf.charAt(pos));
+                pos++;
+              }
+
+              // pega o segundo numero
+              ini = pos;
+              while (pos < buf.length() && buf.charAt(pos) >= '0'
+                      && buf.charAt(pos) <= '9')
+              {
+                pos++;
+              }
+              num2 = Integer.parseInt(buf.substring(ini, pos));
+
+              // verifica os simb < e > após o segundo numero
+              if (pos < buf.length()
+                      && (buf.charAt(pos) == '<' || buf.charAt(pos) == '>'))
+              {
+                gp.setSufix(buf.charAt(pos));
+                pos++;
+              }
             }
+          }
+          gp.setMin(num);
+          gp.setMax(num2);
+          fea.setLocation(gp);
+          return gp;
         }
+      }
+    }
+  }
+
+  private int[] parseReferenceDescriptor(String descriptor)
+  {
+    // 1 (bases 1 to 1609)
+    int[] resultado = new int[3];
+    descriptor = descriptor.replace("(bases", ",").replace("to", ",")
+            .replace(")", "");
+    String[] args = descriptor.split(",");
+    resultado[0] = Integer.parseInt(args[0].trim());
+    resultado[1] = Integer.parseInt(args[1].trim());
+    resultado[2] = Integer.parseInt(args[2].trim());
+    return resultado;
+  }
+
+  private String processReferenceLine(String line, String component)
+  {
+    int init = line.indexOf(component);
+    if (init != -1)
+    {
+      line = line.replace(component, "");
+    }
+    return line;
+  }
+
+  private String processHeaderLine(String line, String header)
+  {
+    int init = line.indexOf(header);
+    if (init != -1)
+    {
+      line = line.replace(header, "");
     }
-    
-    private int[] parseReferenceDescriptor(String descriptor){
-    	// 1 (bases 1 to 1609) 
-    	int[] resultado = new int[3];
-    	descriptor = descriptor.replace("(bases", ",").replace("to", ",").replace(")", "");
-    	String[] args = descriptor.split(",");
-    	resultado[0] = Integer.parseInt(args[0].trim());
-    	resultado[1] = Integer.parseInt(args[1].trim());
-    	resultado[2] = Integer.parseInt(args[2].trim());
-    	return resultado;
+    return line;
+  }
+
+  private GenBankSequence processSequenceLine(String line)
+  {
+    GenBankSequence gbs = new GenBankSequence();
+    line = ltrim(line);
+    String[] args = line.split(" ");
+    gbs.setId(Integer.parseInt(args[0]));
+    int len = args.length - 1;
+    Vector<String> seqs = new Vector<String>();
+    for (int i = 0; i < len; i++)
+      seqs.add(args[i + 1]);
+    gbs.setSequences(seqs);
+    return gbs;
+  }
+
+  private String processCommentLine(String line)
+  {
+    int init = line.indexOf("COMMENT");
+    if (init != -1)
+    {
+      line = line.replace("COMMENT", "");
+    }
+    return line;
+  }
+
+  public String rtrim(String s)
+  {
+    int i = s.length() - 1;
+    while (i >= 0 && Character.isWhitespace(s.charAt(i)))
+    {
+      i--;
     }
-	private String processReferenceLine(String line, String component){
-		int init = line.indexOf(component);
-		if (init!=-1){
-			 line = line.replace(component,"");
-		}
-		return line;
-	}
-	private String processHeaderLine(String line, String header){
-		int init = line.indexOf(header);
-		if (init!=-1){
-			 line = line.replace(header,"");
-		}
-		return line;
-	}
-
-	private GenBankSequence processSequenceLine(String line) {
-		GenBankSequence gbs = new GenBankSequence();
-		line = ltrim(line);
-		String[] args = line.split(" ");
-		gbs.setId(Integer.parseInt(args[0]));
-		int len = args.length-1;
-		Vector<String> seqs = new Vector<String>();
-		for (int i=0;i<len;i++)
-			seqs.add(args[i+1]);
-		gbs.setSequences(seqs);
-		return gbs;
-	}
-
-	private String processCommentLine(String line){
-		int init = line.indexOf("COMMENT");
-		if (init!=-1){
-			 line = line.replace("COMMENT","");
-		}
-		return line;
-	}
-    public String rtrim(String s) {
-        int i = s.length()-1;
-        while (i >= 0 && Character.isWhitespace(s.charAt(i))) {
-            i--;
-        }
-        return s.substring(0,i+1);
+    return s.substring(0, i + 1);
+  }
+
+  public String ltrim(String s)
+  {
+    int i = 0;
+    while (i < s.length() && Character.isWhitespace(s.charAt(i)))
+    {
+      i++;
     }
+    return s.substring(i);
+  }
 
-    public String ltrim(String s) {
-        int i = 0;
-        while (i < s.length() && Character.isWhitespace(s.charAt(i))) {
-            i++;
-        }
-        return s.substring(i);
-    }	
-
-    public String print(){
-    	StringBuffer out = new StringBuffer();
-    	for (SequenceI seq: this.getSeqs()){
-    		SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
-			boolean featureLinePrinted = false;
-    		for(SequenceFeature sf:seqFeatures){
-    			if(sf.getType().equals("LOCUS")){
-    				out.append(sf.getDescription()).append(newline);    				
-    			}else if (sf.getType().equals("DEFINITION")){
-    				out.append("DEFINITION  ").append(sf.getDescription()).append(newline);    				
-    			}else if (sf.getType().equals("VERSION")){
-    				out.append("VERSION     ").append(sf.getDescription()).append(newline);    				
-    			}else if (sf.getType().equals("ACCESSION")){
-    				out.append("ACCESSION  ").append(sf.getDescription()).append(newline);
-    			}else if (sf.getType().equals("DBLINK")){
-    				out.append("DBLINK ").append(sf.getDescription()).append(newline);
-    			}else if (sf.getType().equals("KEYWORDS")){
-    				out.append("KEYWORDS  ").append(sf.getDescription()).append(newline);    				
-    			}else if (sf.getType().equals("SOURCE")){
-    				out.append("SOURCE      ").append(sf.getDescription()).append(newline);
-    			}else if (sf.getType().equals("REFERENCE")){
-    				out.append(sf.getDescription()).append(newline);
-    			}else if (sf.getType().equals("COMMENT")){
-    				out.append("COMMENT     ").append(sf.getDescription()).append(newline);    				
-    			}else if (sf.getType().equals("BASE COUNT")){
-    				out.append("BASE COUNT     ").append(sf.getDescription()).append(newline);    				
-    			}else{
-    				if (!featureLinePrinted){
-    					out.append("FEATURES             Location/Qualifiers").append(newline);
-    					featureLinePrinted = true;
-    				}
-    				out.append("     ").append(sf.getType()).append("          ").append(sf.getBegin()).append("..").append(sf.getEnd()).append(newline);
-    				Hashtable<String,String> qualifiers = sf.otherDetails;
-    				if (qualifiers!=null){
-	    				Enumeration<String> keys = qualifiers.keys();
-	    				while (keys.hasMoreElements()){
-	    					String key = keys.nextElement();
-	    					String value = qualifiers.get(key);
-	    					if (value!=null){
-	    						out.append("                     /").append(key).append("=").append(value).append(newline);
-	    					}
-	    				}
-    				}
-    			}
-    		}
-			out.append("ORIGIN").append(newline);
-			//We have to divide sequence in groups of 6x10 chars
-			String sequenceString = seq.getSequenceAsString();
-			int howManyGroups = (int) Math.floor(sequenceString.length()/60);
-			for (int i=0;i<=howManyGroups;i++){
-				String sequenceSegment = sequenceString.substring(i*60,Math.min((i+1)*60, sequenceString.length()));
-				 if ((!"".equals(sequenceSegment) && (sequenceSegment!=null) && (sequenceSegment.length()>0))){
-						out.append("        ").append(60*i+1).append(" ");
-				 }
-				int segmentLength = sequenceSegment.length();
-				if (segmentLength>=10){
-					out.append(sequenceSegment.substring(0,10)).append(" ");
-					if (segmentLength>=20){
-						out.append(sequenceSegment.substring(10,20)).append(" ");					
-						if (segmentLength>=30){
-							out.append(sequenceSegment.substring(20,30)).append(" ");					
-							if (segmentLength>=40){
-								out.append(sequenceSegment.substring(30,40)).append(" ");					
-								if (segmentLength>=50){
-									out.append(sequenceSegment.substring(40,50)).append(" ");	
-									if (segmentLength<=60){
-										out.append(sequenceSegment.substring(50,sequenceSegment.length()));
-									}
-								}else{
-									out.append(sequenceSegment.substring(40,sequenceSegment.length()));
-								}
-							}else{
-								out.append(sequenceSegment.substring(30,sequenceSegment.length()));
-							}
-						}else{
-							out.append(sequenceSegment.substring(20,sequenceSegment.length()));
-						}
-					}else{
-						out.append(sequenceSegment.substring(10,sequenceSegment.length()));
-					}
-				} else if ((!"".equals(sequenceSegment) && (sequenceSegment!=null) && (sequenceSegment.length()>0))){
-					out.append(sequenceSegment);
-				}
-				out.append(newline);
-			}
-			out.append("//");
-    	}
-    	return out.toString();
+  public String print()
+  {
+    StringBuffer out = new StringBuffer();
+    for (SequenceI seq : this.getSeqs())
+    {
+      SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
+      boolean featureLinePrinted = false;
+      for (SequenceFeature sf : seqFeatures)
+      {
+        if (sf.getType().equals("LOCUS"))
+        {
+          out.append(sf.getDescription()).append(newline);
+        }
+        else if (sf.getType().equals("DEFINITION"))
+        {
+          out.append("DEFINITION  ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else if (sf.getType().equals("VERSION"))
+        {
+          out.append("VERSION     ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else if (sf.getType().equals("ACCESSION"))
+        {
+          out.append("ACCESSION  ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else if (sf.getType().equals("DBLINK"))
+        {
+          out.append("DBLINK ").append(sf.getDescription()).append(newline);
+        }
+        else if (sf.getType().equals("KEYWORDS"))
+        {
+          out.append("KEYWORDS  ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else if (sf.getType().equals("SOURCE"))
+        {
+          out.append("SOURCE      ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else if (sf.getType().equals("REFERENCE"))
+        {
+          out.append(sf.getDescription()).append(newline);
+        }
+        else if (sf.getType().equals("COMMENT"))
+        {
+          out.append("COMMENT     ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else if (sf.getType().equals("BASE COUNT"))
+        {
+          out.append("BASE COUNT     ").append(sf.getDescription())
+                  .append(newline);
+        }
+        else
+        {
+          if (!featureLinePrinted)
+          {
+            out.append("FEATURES             Location/Qualifiers").append(
+                    newline);
+            featureLinePrinted = true;
+          }
+          out.append("     ").append(sf.getType()).append("          ")
+                  .append(sf.getBegin()).append("..").append(sf.getEnd())
+                  .append(newline);
+          Hashtable<String, String> qualifiers = sf.otherDetails;
+          if (qualifiers != null)
+          {
+            Enumeration<String> keys = qualifiers.keys();
+            while (keys.hasMoreElements())
+            {
+              String key = keys.nextElement();
+              String value = qualifiers.get(key);
+              if (value != null)
+              {
+                out.append("                     /").append(key)
+                        .append("=").append(value).append(newline);
+              }
+            }
+          }
+        }
+      }
+      out.append("ORIGIN").append(newline);
+      // We have to divide sequence in groups of 6x10 chars
+      String sequenceString = seq.getSequenceAsString();
+      int howManyGroups = (int) Math.floor(sequenceString.length() / 60);
+      for (int i = 0; i <= howManyGroups; i++)
+      {
+        String sequenceSegment = sequenceString.substring(i * 60,
+                Math.min((i + 1) * 60, sequenceString.length()));
+        if ((!"".equals(sequenceSegment) && (sequenceSegment != null) && (sequenceSegment
+                .length() > 0)))
+        {
+          out.append("        ").append(60 * i + 1).append(" ");
+        }
+        int segmentLength = sequenceSegment.length();
+        if (segmentLength >= 10)
+        {
+          out.append(sequenceSegment.substring(0, 10)).append(" ");
+          if (segmentLength >= 20)
+          {
+            out.append(sequenceSegment.substring(10, 20)).append(" ");
+            if (segmentLength >= 30)
+            {
+              out.append(sequenceSegment.substring(20, 30)).append(" ");
+              if (segmentLength >= 40)
+              {
+                out.append(sequenceSegment.substring(30, 40)).append(" ");
+                if (segmentLength >= 50)
+                {
+                  out.append(sequenceSegment.substring(40, 50)).append(" ");
+                  if (segmentLength <= 60)
+                  {
+                    out.append(sequenceSegment.substring(50,
+                            sequenceSegment.length()));
+                  }
+                }
+                else
+                {
+                  out.append(sequenceSegment.substring(40,
+                          sequenceSegment.length()));
+                }
+              }
+              else
+              {
+                out.append(sequenceSegment.substring(30,
+                        sequenceSegment.length()));
+              }
+            }
+            else
+            {
+              out.append(sequenceSegment.substring(20,
+                      sequenceSegment.length()));
+            }
+          }
+          else
+          {
+            out.append(sequenceSegment.substring(10,
+                    sequenceSegment.length()));
+          }
+        }
+        else if ((!"".equals(sequenceSegment) && (sequenceSegment != null) && (sequenceSegment
+                .length() > 0)))
+        {
+          out.append(sequenceSegment);
+        }
+        out.append(newline);
+      }
+      out.append("//");
     }
+    return out.toString();
+  }
 }