Fixing badly formatted page after automatic conversion

Author: josemduarte

_wikis/BioJava:CookBook3:MSA.md

@@ -5,8 +5,8 @@ title: BioJava:CookBook3:MSA
 How to create a Multiple Sequence Alignment in BioJava
 ======================================================
 
-<java>
 
+```java
 package org.biojava.nbio.alignment;
 
 import java.net.URL; import java.util.ArrayList; import java.util.List;
@@ -20,32 +20,32 @@ org.biojava.nbio.core.util.ConcurrencyTools;
 
 public class CookbookMSA {
 
-`   public static void main(String[] args) {`  
-`       String[] ids = new String[] {"Q21691", "A8WS47", "O48771"};`  
-`       try {`  
-`           multipleSequenceAlignment(ids);`  
-`       } catch (Exception e){`  
-`           e.printStackTrace();`  
-`       }`  
-`   }`
-
-`   private static void multipleSequenceAlignment(String[] ids) throws Exception {`  
-`       List`<ProteinSequence>` lst = new ArrayList`<ProteinSequence>`();`  
-`       for (String id : ids) {`  
-`           lst.add(getSequenceForId(id));`  
-`       }`  
-`       Profile`<ProteinSequence, AminoAcidCompound>` profile = Alignments.getMultipleSequenceAlignment(lst);`  
-`       System.out.printf("Clustalw:%n%s%n", profile);`  
-`       ConcurrencyTools.shutdown();`  
-`   }`
-
-`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`  
-`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`  
-`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`  
-`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`  
-`       return seq;`  
-`   }`
+   public static void main(String[] args) {  
+       String[] ids = new String[] {"Q21691", "A8WS47", "O48771"};  
+       try {  
+           multipleSequenceAlignment(ids);  
+       } catch (Exception e){  
+           e.printStackTrace();  
+       }  
+   }
+
+   private static void multipleSequenceAlignment(String[] ids) throws Exception {  
+       List<ProteinSequence> lst = new ArrayList<ProteinSequence>();  
+       for (String id : ids) {  
+           lst.add(getSequenceForId(id));  
+       }  
+       Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(lst);  
+       System.out.printf("Clustalw:%n%s%n", profile);  
+       ConcurrencyTools.shutdown();  
+   }
+
+   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {  
+       URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));  
+       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);  
+       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());  
+       return seq;  
+   }
 
 }
 
-</java>
+```