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FASTAParser.java

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+
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Reads a multiple FASTA file containing DNA sequences in FASTA format
+ * and stores the entries as FASTAEntry objects.
+ * 
+ * @author Alexander Herbig
+ *
+ */
+public class FASTAParser 
+{
+	/**
+	 * Reads a multiple FASTA file containing DNA sequences in FASTA format.
+	 * @param br	the BufferedReader which reads from the multiple FASTA file
+	 * @return	a list containing the resulting FASTAEntry objects
+	 * @throws Exception
+	 */
+	public static Map<String,String> parseDNA(String filename) throws Exception
+	{
+		BufferedReader br = new BufferedReader(new FileReader(filename));
+
+		Map<String,String> fastaEntries = new HashMap<String, String>();
+
+		String tmpID;
+		StringBuffer tmpSeqString = new StringBuffer();
+		String tmpLine = br.readLine();
+
+		//jump to first header line
+		while(tmpLine!=null&&(tmpLine.charAt(0)!='>' || tmpLine.length()==0))
+		{
+			tmpLine=br.readLine();
+		}
+		tmpID=tmpLine;
+
+		tmpLine=br.readLine();
+		while(tmpLine!=null)
+		{
+			if(tmpLine.length()!=0)
+			{
+				if(tmpLine.charAt(0)=='>')
+				{
+					fastaEntries.put(toID(tmpID), tmpSeqString.toString());
+
+					tmpSeqString = new StringBuffer();
+
+					tmpID = tmpLine;
+				}
+				else
+				{
+					tmpSeqString.append(tmpLine);
+				}
+			}
+			tmpLine = br.readLine();
+		}
+		fastaEntries.put(toID(tmpID), tmpSeqString.toString());
+
+		br.close();
+
+		return fastaEntries;
+	}
+
+	private static String toID(String fastaID)
+	{
+		return(fastaID.substring(1));
+	}
+
+}

FASTAWriter.java

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+
+import java.io.BufferedWriter;
+
+/**
+ * Writes a list of sequences to a file in FASTA format.
+ * 
+ * @author Alexander Herbig
+ *
+ */
+public class FASTAWriter 
+{
+	/**
+	 * Writes a list of sequences to a file in FASTA format.
+	 * 
+	 * @param bw	the BufferedWriter writing the FASTA file
+	 * @param fastaEntries	list of FASTAEntry objects holding the sequences 
+	 * 						which are written to the FASTA file
+	 * @throws Exception
+	 */
+	public static void write(BufferedWriter bw, String genomeID, String sequence) throws Exception
+	{	
+		int charsInLine;
+		String tmpSeqString;
+
+		tmpSeqString=sequence;
+		bw.write(">"+genomeID);
+		bw.newLine();
+
+		charsInLine=0;
+		for(int i=0; i<tmpSeqString.length();i++)
+		{
+			bw.write(tmpSeqString.charAt(i));
+			charsInLine++;
+
+			if(charsInLine==60)
+			{
+				bw.newLine();
+				charsInLine=0;
+			}
+		}
+		if(charsInLine!=0)
+		{
+			bw.newLine();
+		}
+
+		bw.flush();
+	}
+}

Gene.java

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+/**
+ * 
+ * @author Alexander Herbig
+ *
+ */
+public class Gene
+{
+	public String name;
+	public String anno;
+
+	public int start;
+	public int end;
+	public char strand;
+	public String idAsParent;
+
+
+	public Gene(String name, String anno, int start, int end, char strand, String idAsParent) {
+		super();
+		this.name = name;
+		this.anno = anno;
+		this.start = start;
+		this.end = end;
+		this.strand = strand;
+		this.idAsParent = idAsParent;
+	}
+
+	public Gene(String name, String anno)
+	{
+		super();
+		this.name = name;
+		this.anno = anno;
+	}
+
+	public Gene(String name, String anno, int length)
+	{
+		this(name,anno);
+	}
+
+	public int length()
+	{
+		return Math.abs(end-start)+1;
+	}
+}