@@ -21,7 +21,7 @@ your scala project. The easiest way to do this is to use Maven to build
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your scala project and just add BioJava as a dependency. For instance,
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add the following to the dependencies section of your pom.xml file.
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- ``` xml
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+ ```
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-core</artifactId>
@@ -40,7 +40,7 @@ Java classes can be imported and used in scala code without
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modification. For instance, here is a scala version of
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< BioJava:CookBook3:PSA_DNA > .
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- ``` scala
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+ ```
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/**
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* Demo of using BioJava from scala code. Performs a simple sequence alignment.
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*
@@ -99,7 +99,7 @@ First, include the ScaBio jars and dependencies in your classpath. If
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using maven this is quite simple. Add the required packages to your
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pom.xml:
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- ``` xml
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+ ```
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<dependency>
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<groupId>net.gumbix</groupId>
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<artifactId>scabio-demo</artifactId>
@@ -111,7 +111,7 @@ Scala objects and methods can now be used from Java code. To display
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ScaBio's RNA secondary structure visualization too, for instance, just
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call the appropriate method.
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- ``` scala
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+ ```
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public class RNAStruct2DViewer {
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public static void main(String[] args) {
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net.gumbix.bioinf.struct.RNAStruct2DViewer.main(args);
@@ -122,7 +122,7 @@ public class RNAStruct2DViewer {
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Here is a more complex example to output the results of the RNA
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secondary structure prediction in a simple text format.
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- ``` scala
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+ ```
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import java.util.List;
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import net.gumbix.bioinf.struct.AbstractNussinov;
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import net.gumbix.bioinf.struct.NussinovDecision;
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