Initial Commit.

pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>rnafold4j</groupId>
+  <artifactId>rnafold4j</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+	<build>
+		<plugins>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<version>2.6</version>
+				<executions>
+					<execution>
+						<id>RNAFold4J</id>
+						<configuration>
+							<appendAssemblyId>false</appendAssemblyId>
+							<finalName>rnafold4j</finalName>
+							<descriptorRefs>
+								<descriptorRef>jar-with-dependencies</descriptorRef>
+							</descriptorRefs>
+							<archive>
+								<manifest>
+									<mainClass>rnafold4j.RNAFold</mainClass>
+								</manifest>
+							</archive>
+						</configuration>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>commons-lang</groupId>
+			<artifactId>commons-lang</artifactId>
+			<version>2.6</version>
+		</dependency>	
+	</dependencies>  
+
+
+
+</project>

src/main/java/rnafold4j/BondT.java

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+/**
+ * 
+ */
+package rnafold4j;
+
+/**
+ * @author Jan Hoinka
+ *
+ * RNAFold4j is a port of RNAFold to Java. RNAFold is implemented and developed by Ivo L Hofacker et al.
+ * as part of the ViennaRNA package v 1.8.5. All intellectual credits of this work 
+ * go to the original authors and the Institute for Theoretical Chemistry of the 
+ * University of Vienna. My only contribution is the adaptation of the C source code to Java.
+ */
+public class BondT {
+	public int i;
+	public int j;
+}

src/main/java/rnafold4j/CentroidData.java

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+/**
+ * 
+ */
+package rnafold4j;
+
+/**
+ * @author Jan Hoinka
+ *
+ * RNAFold4j is a port of RNAFold to Java. RNAFold is implemented and developed by Ivo L Hofacker et al.
+ * as part of the ViennaRNA package v 1.8.5. All intellectual credits of this work 
+ * go to the original authors and the Institute for Theoretical Chemistry of the 
+ * University of Vienna. My only contribution is the adaptation of the C source code to Java.
+ */
+public class CentroidData {
+
+	public byte[] structure;
+	public double distance;
+
+}

src/main/java/rnafold4j/EnergyConst.java

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+/**
+ * 
+ */
+package rnafold4j;
+
+/**
+ * @author Jan Hoinka
+ *
+ * RNAFold4j is a port of RNAFold to Java. RNAFold is implemented and developed by Ivo L Hofacker et al.
+ * as part of the ViennaRNA package v 1.8.5. All intellectual credits of this work 
+ * go to the original authors and the Institute for Theoretical Chemistry of the 
+ * University of Vienna. My only contribution is the adaptation of the C source code to Java.
+ * 
+ * energy constants, formerly defined in
+ *           energy_par.h
+ *
+ * customized for use with RNAedit by
+ * S.Kopp, IMB-Jena, Germany, Mar 1996
+ */
+
+
+public final class EnergyConst {
+	static double GASCONST = 1.98717;  /* in [cal/K] */
+	static double K0 =  273.15;
+	static int INF = 1000000;
+	static int FORBIDDEN = 9999;
+	static int BONUS = 10000;
+	static int NBPAIRS = 7;
+	static int TURN = 3;
+	static int MAXLOOP = 30;
+}