@@ -21,7 +21,7 @@ your scala project. The easiest way to do this is to use Maven to build
2121your scala project and just add BioJava as a dependency. For instance,
2222add the following to the dependencies section of your pom.xml file.
2323
24- ``` xml
24+ ```
2525<dependency>
2626 <groupId>org.biojava</groupId>
2727 <artifactId>biojava3-core</artifactId>
@@ -40,7 +40,7 @@ Java classes can be imported and used in scala code without
4040modification. For instance, here is a scala version of
4141< BioJava:CookBook3:PSA_DNA > .
4242
43- ``` scala
43+ ```
4444/**
4545 * Demo of using BioJava from scala code. Performs a simple sequence alignment.
4646 *
@@ -99,7 +99,7 @@ First, include the ScaBio jars and dependencies in your classpath. If
9999using maven this is quite simple. Add the required packages to your
100100pom.xml:
101101
102- ``` xml
102+ ```
103103<dependency>
104104 <groupId>net.gumbix</groupId>
105105 <artifactId>scabio-demo</artifactId>
@@ -111,7 +111,7 @@ Scala objects and methods can now be used from Java code. To display
111111ScaBio's RNA secondary structure visualization too, for instance, just
112112call the appropriate method.
113113
114- ``` scala
114+ ```
115115public class RNAStruct2DViewer {
116116 public static void main(String[] args) {
117117 net.gumbix.bioinf.struct.RNAStruct2DViewer.main(args);
@@ -122,7 +122,7 @@ public class RNAStruct2DViewer {
122122Here is a more complex example to output the results of the RNA
123123secondary structure prediction in a simple text format.
124124
125- ``` scala
125+ ```
126126import java.util.List;
127127import net.gumbix.bioinf.struct.AbstractNussinov;
128128import net.gumbix.bioinf.struct.NussinovDecision;
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