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Fixing scala page formatting
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‎_wiki/Scala.md‎

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@@ -21,11 +21,13 @@ 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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<dependency>
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`    `<groupId>`org.biojava`</groupId>
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`    `<artifactId>`biojava3-core`</artifactId>
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`    `<version>`3.0.6`</version>
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    <groupId>org.biojava</groupId>
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    <artifactId>biojava3-core</artifactId>
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    <version>3.0.6</version>
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</dependency>
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```
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If you are using [SBT](http://www.scala-sbt.org/) to build your Scala
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project just add the following to your sbt file.
@@ -38,49 +40,51 @@ 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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`/**`
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` * Demo of using BioJava from scala code. Performs a simple sequence alignment.`
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` *`
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` * This shows off a few nice scala features, such as implicit methods`
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` */`
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```scala
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/**
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 * Demo of using BioJava from scala code. Performs a simple sequence alignment.
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 *
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 * This shows off a few nice scala features, such as implicit methods
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 */
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`import org.biojava3.alignment.{Alignments,SimpleGapPenalty,SubstitutionMatrixHelper}`
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`import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType.LOCAL`
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`import org.biojava3.core.sequence.DNASequence`
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`import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet`
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import org.biojava3.alignment.{Alignments,SimpleGapPenalty,SubstitutionMatrixHelper}
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType.LOCAL
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import org.biojava3.core.sequence.DNASequence
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import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
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`object PSA_DNA {`
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`  implicit def str2DNA(seq: String) = new DNASequence(seq,AmbiguityDNACompoundSet.getDNACompoundSet)`
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object PSA_DNA {
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  implicit def str2DNA(seq: String) = new DNASequence(seq,AmbiguityDNACompoundSet.getDNACompoundSet)
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`  def main(args: Array[String]) {`
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`    // Note implicit cast from strings to DNASequence`
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`    val target: DNASequence = "CACGTTTCTTGTGGCAGCTTAAGTTTGAATGTCATTTCTTCAATGGGACGGA"+`
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`      "GCGGGTGCGGTTGCTGGAAAGATGCATCTATAACCAAGAGGAGTCCGTGCGCTTCGACAGC"+`
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`      "GACGTGGGGGAGTACCGGGCGGTGACGGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACA"+`
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`      "GCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGCGGTGGACACCTACTGCAGACACAACTA"+`
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`      "CGGGGTTGGTGAGAGCTTCACAGTGCAGCGGCGAG"`
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  def main(args: Array[String]) {
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    // Note implicit cast from strings to DNASequence
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    val target: DNASequence = "CACGTTTCTTGTGGCAGCTTAAGTTTGAATGTCATTTCTTCAATGGGACGGA"+
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      "GCGGGTGCGGTTGCTGGAAAGATGCATCTATAACCAAGAGGAGTCCGTGCGCTTCGACAGC"+
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      "GACGTGGGGGAGTACCGGGCGGTGACGGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACA"+
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      "GCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGCGGTGGACACCTACTGCAGACACAACTA"+
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      "CGGGGTTGGTGAGAGCTTCACAGTGCAGCGGCGAG"
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`    val query: DNASequence = "ACGAGTGCGTGTTTTCCCGCCTGGTCCCCAGGCCCCCTTTCCGTCCTCAGGAA"+`
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`      "GACAGAGGAGGAGCCCCTCGGGCTGCAGGTGGTGGGCGTTGCGGCGGCGGCCGGTTAAGGT"+`
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`      "TCCCAGTGCCCGCACCCGGCCCACGGGAGCCCCGGACTGGCGGCGTCACTGTCAGTGTCTT"+`
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`      "CTCAGGAGGCCGCCTGTGTGACTGGATCGTTCGTGTCCCCACAGCACGTTTCTTGGAGTAC"+`
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`      "TCTACGTCTGAGTGTCATTTCTTCAATGGGACGGAGCGGGTGCGGTTCCTGGACAGATACT"+`
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`      "TCCATAACCAGGAGGAGAACGTGCGCTTCGACAGCGACGTGGGGGAGTTCCGGGCGGTGAC"+`
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`      "GGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGACATCCTGGAAGACGAG"+`
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`      "CGGGCCGCGGTGGACACCTACTGCAGACACAACTACGGGGTTGTGAGAGCTTCACCGTGCA"+`
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`      "GCGGCGAGACGCACTCGT"`
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    val query: DNASequence = "ACGAGTGCGTGTTTTCCCGCCTGGTCCCCAGGCCCCCTTTCCGTCCTCAGGAA"+
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      "GACAGAGGAGGAGCCCCTCGGGCTGCAGGTGGTGGGCGTTGCGGCGGCGGCCGGTTAAGGT"+
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      "TCCCAGTGCCCGCACCCGGCCCACGGGAGCCCCGGACTGGCGGCGTCACTGTCAGTGTCTT"+
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      "CTCAGGAGGCCGCCTGTGTGACTGGATCGTTCGTGTCCCCACAGCACGTTTCTTGGAGTAC"+
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      "TCTACGTCTGAGTGTCATTTCTTCAATGGGACGGAGCGGGTGCGGTTCCTGGACAGATACT"+
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      "TCCATAACCAGGAGGAGAACGTGCGCTTCGACAGCGACGTGGGGGAGTTCCGGGCGGTGAC"+
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      "GGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGACATCCTGGAAGACGAG"+
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      "CGGGCCGCGGTGGACACCTACTGCAGACACAACTACGGGGTTGTGAGAGCTTCACCGTGCA"+
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      "GCGGCGAGACGCACTCGT"
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73-
`    val matrix = SubstitutionMatrixHelper.getNuc4_4()`
76+
    val matrix = SubstitutionMatrixHelper.getNuc4_4()
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`    val gapP = new SimpleGapPenalty()`
76-
`    gapP.setOpenPenalty(5)`
77-
`    gapP.setExtensionPenalty(2)`
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    val gapP = new SimpleGapPenalty()
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    gapP.setOpenPenalty(5)
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    gapP.setExtensionPenalty(2)
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79-
`    val psa = Alignments.getPairwiseAlignment(query, target, LOCAL, gapP, matrix)`
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    val psa = Alignments.getPairwiseAlignment(query, target, LOCAL, gapP, matrix)
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81-
`    println(psa)`
82-
`  }`
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`}`
84+
    println(psa)
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  }
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}
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```
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Including ScaBio code in Java
8690
-----------------------------
@@ -94,78 +98,85 @@ present in BioJava.
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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:
97-
101+
```xml
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<dependency>
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`    `<groupId>`net.gumbix`</groupId>
100-
`    `<artifactId>`scabio-demo`</artifactId>
101-
`    `<version>`0.1-SNAPSHOT`</version>
103+
    <groupId>net.gumbix</groupId>
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    <artifactId>scabio-demo</artifactId>
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    <version>0.1-SNAPSHOT</version>
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</dependency>
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```
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104109
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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108-
`public class RNAStruct2DViewer {`
109-
`   public static void main(String[] args) {`
110-
`       net.gumbix.bioinf.struct.RNAStruct2DViewer.main(args);`
111-
`   }`
112-
`}`
113+
```scala
114+
public class RNAStruct2DViewer {
115+
   public static void main(String[] args) {
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       net.gumbix.bioinf.struct.RNAStruct2DViewer.main(args);
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   }
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}
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```
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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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`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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`import net.gumbix.bioinf.struct.NussinovEnergy;`
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`import net.gumbix.bioinf.struct.NussinovState;`
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`import net.gumbix.dynpro.Idx;`
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`import net.gumbix.dynpro.PathEntry;`
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`import scala.collection.JavaConversions;`
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```scala
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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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import net.gumbix.bioinf.struct.NussinovEnergy;
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import net.gumbix.bioinf.struct.NussinovState;
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import net.gumbix.dynpro.Idx;
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import net.gumbix.dynpro.PathEntry;
132+
import scala.collection.JavaConversions;
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126-
`public class RNAStructPredictor {`
127-
`   public static void main(String[] args) {`
128-
`       String s = "UGGGAAGGUUUUGGAACCC";`
129-
`       AbstractNussinov dp = new NussinovEnergy(s);`
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`       Idx idx = new Idx(0, dp.n()-1);`
131-
`       scala.collection.immutable.List`<PathEntry<NussinovDecision>`> solution = dp.solution(idx);`
134+
public class RNAStructPredictor {
135+
   public static void main(String[] args) {
136+
       String s = "UGGGAAGGUUUUGGAACCC";
137+
       AbstractNussinov dp = new NussinovEnergy(s);
138+
       Idx idx = new Idx(0, dp.n()-1);
139+
       scala.collection.immutable.List<PathEntry<NussinovDecision>> solution = dp.solution(idx);
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133-
`       String topology = rnaTopologyString(solution, dp.n());`
141+
       String topology = rnaTopologyString(solution, dp.n());
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135-
`       System.out.println(s);`
136-
`       System.out.println(topology);`
137-
`   }`
143+
       System.out.println(s);
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       System.out.println(topology);
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   }
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139-
`   /**`
140-
`    * Get a topology string for the given RNA secondary structure prediction`
141-
`    * @param s The solved RNA secondary structure from ScaBio`
142-
`    * @return A string of '(', ')', and '-' giving the paired RNA residues`
143-
`    */`
144-
`   public static String rnaTopologyString(scala.collection.immutable.List`<PathEntry<NussinovDecision>`> s,int len) {`
145-
`       //Wrap scala list as a Java collection for ease of use`
146-
`       List`<PathEntry<NussinovDecision>`> solution = JavaConversions.seqAsJavaList(s);`
147+
   /**
148+
    * Get a topology string for the given RNA secondary structure prediction
149+
    * @param s The solved RNA secondary structure from ScaBio
150+
    * @return A string of '(', ')', and '-' giving the paired RNA residues
151+
    */
152+
   public static String rnaTopologyString(scala.collection.immutable.List<PathEntry<NussinovDecision>> s,int len) {
153+
       //Wrap scala list as a Java collection for ease of use
154+
       List<PathEntry<NussinovDecision>> solution = JavaConversions.seqAsJavaList(s);
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148-
`       // All nucleotides are initially unpaired`
149-
`       StringBuffer str = new StringBuffer(len);`
150-
`       for(int i=0;i`<len;i++) {
156+
       // All nucleotides are initially unpaired
157+
       StringBuffer str = new StringBuffer(len);
158+
       for(int i=0;i<len;i++) {
151159
str.append('-');
152160
}
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154162
// Assign parentheses for paired nucleotides
155-
for(PathEntry<NussinovDecision>` entry : solution) {`
156-
`           NussinovDecision decision = entry.decision();`
157-
`           if( decision.move() == NussinovState.PAIR() ) { // focus on nucleotide pairs`
158-
`               Idx pair = decision.idx(); // stores indices of the bound pair`
159-
`               str.setCharAt(pair.i(), '(');`
160-
`               str.setCharAt(pair.j(), ')');`
161-
`           }`
162-
`       }`
163+
for(PathEntry<NussinovDecision> entry : solution) {
164+
           NussinovDecision decision = entry.decision();
165+
           if( decision.move() == NussinovState.PAIR() ) { // focus on nucleotide pairs
166+
               Idx pair = decision.idx(); // stores indices of the bound pair
167+
               str.setCharAt(pair.i(), '(');
168+
               str.setCharAt(pair.j(), ')');
169+
           }
170+
       }
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164-
`       return str.toString();`
165-
`   }`
166-
`}`
172+
       return str.toString();
173+
   }
174+
}
175+
```
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168177
Running the code produces the following output:
169178

170-
`UGGGAAGGUUUUGGAACCC`
171-
`-(((((--))((--)))))`
179+
```
180+
UGGGAAGGUUUUGGAACCC
181+
-(((((--))((--)))))
182+
```

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