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Merge pull request biojava#13 from roland-ewald/patch-1
Fix code snippet layout
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‎_wiki/BioJava_CookBook_Core_Overview.md‎

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@@ -72,10 +72,8 @@ We really want to make it easy to create a sequence and what could be
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easier than using a String.
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```java
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`           ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");`
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`           DNASequence dnaSequence = new DNASequence("ATCG");`
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           ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
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          DNASequence dnaSequence = new DNASequence("ATCG");
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```
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The storage of the sequence data is defined by the Sequence interface
@@ -110,8 +108,8 @@ some level of api changes as we improve the overall design.
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```java
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`           UniprotProxySequenceReader`<AminoAcidCompound>` uniprotSequence = new UniprotProxySequenceReader`<AminoAcidCompound>`("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet());`
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`           ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence);`
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           UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet());
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           ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence);
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```
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@@ -124,17 +122,15 @@ but is very specific to learning the location of the sequence data in
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the file.
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```java
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`           File file = new File(inputFile);`
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`           FastaReader`<ProteinSequence,AminoAcidCompound>` fastaProxyReader = new FastaReader`<ProteinSequence,AminoAcidCompound>`(file, new GenericFastaHeaderParser`<ProteinSequence,AminoAcidCompound>`(), new FileProxyProteinSequenceCreator(file, AminoAcidCompoundSet.getAminoAcidCompoundSet()));`
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`           LinkedHashMap`<String,ProteinSequence>` proteinProxySequences = fastaProxyReader.process();`
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`           for(String key : proteinProxySequences.keySet()){`
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`               ProteinSequence proteinSequence = proteinProxySequences.get(key);`
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`               System.out.println(key);`
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`               System.out.println(proteinSequence.toString());`
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`           }`
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           File file = new File(inputFile);
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           FastaReader<ProteinSequence,AminoAcidCompound> fastaProxyReader = new FastaReader<ProteinSequence,AminoAcidCompound>(file, new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), new FileProxyProteinSequenceCreator(file, AminoAcidCompoundSet.getAminoAcidCompoundSet()));
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           LinkedHashMap<String,ProteinSequence> proteinProxySequences = fastaProxyReader.process();
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           for(String key : proteinProxySequences.keySet()){
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               ProteinSequence proteinSequence = proteinProxySequences.get(key);
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               System.out.println(key);
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               System.out.println(proteinSequence.toString());
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           }
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```
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In the above example a FastaReader class is created where we abstract
@@ -171,10 +167,8 @@ code. The following code shows the use of FastaReaderHelper and
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FastaWriterHelper.
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```java
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`       LinkedHashMap`<String, DNASequence>` dnaSequences = FastaReaderHelper.readFastaDNASequence(new File("454Scaffolds.fna"));`
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`       FastaWriterHelper.writeNucleotideSequence(new File("454Scaffolds-1.fna"),dnaSequences.values());`
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       LinkedHashMap<String, DNASequence> dnaSequences = FastaReaderHelper.readFastaDNASequence(new File("454Scaffolds.fna"));
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       FastaWriterHelper.writeNucleotideSequence(new File("454Scaffolds-1.fna"),dnaSequences.values());
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```
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Working with Sequence Objects
@@ -204,17 +198,18 @@ Avoid using any kind of String method to do this since String operations
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are costly in BioJava (due to the String conversion that must be
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applied). Here is an example on how to do it for any Sequence object.
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```java List<Sequence<AminoAcidCompound>\> translations =
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```java
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List<Sequence<AminoAcidCompound>> translations =
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populateFromSomewhere(); Collections.sort(translations, new
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Comparator<Sequence<? extends Compound>\>() {
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`public int compare(Sequence`<? extends Compound>` o1, Sequence`<? extends Compound>` o2) {`
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`  Integer o1Length = o1.getLength();`
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`  Integer o2Length = o2.getLength();`
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`  return o1Length.compareTo(o2Length);`
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`}`
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}); ```
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Comparator<Sequence<? extends Compound>>() {
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public int compare(Sequence<? extends Compound> o1, Sequence<? extends Compound> o2) {
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  Integer o1Length = o1.getLength();
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  Integer o2Length = o2.getLength();
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  return o1Length.compareTo(o2Length);
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}
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});
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```
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Note our usage of the generic type to capture Sequence objects of any
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type since the assessment of length is something which can be applied to
@@ -241,9 +236,7 @@ non-ambiguity CompoundSets with Codon table 1 in Frame 1 in the forward
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orientation.
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```java
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` ProteinSequence protein = new DNASequence("ATG").getRNASequence().getProteinSequence();`
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ProteinSequence protein = new DNASequence("ATG").getRNASequence().getProteinSequence();
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```
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### Translating in a Different Frame
@@ -257,11 +250,9 @@ object when we request the RNA. Multiple frames of translations are
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possible but see later on.
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```java
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` DNASequence dna = new DNASequence("AATG");`
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` RNASequence rna = dna.getRNASequence(Frame.TWO);`
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` ProteinSequence protein = rna.getProteinSequence();`
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DNASequence dna = new DNASequence("AATG");
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RNASequence rna = dna.getRNASequence(Frame.TWO);
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ProteinSequence protein = rna.getProteinSequence();
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```
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### Translating in Multiple Frames
@@ -273,10 +264,11 @@ translation in. The following example attempts to translate a sequence
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in all three forward frames. The code returns a map of the results keyed
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by their frame.
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```java TranscriptionEngine te = TranscriptionEngine.getDefault();
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```java
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TranscriptionEngine te = TranscriptionEngine.getDefault();
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Frame[] frames = Frame.getForwardFrames();
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Map<Frame, Sequence<AminoAcidCompound>\> results =
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te.multipleFrameTranslation(dna, frames); ```
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Map<Frame, Sequence<AminoAcidCompound>> results = te.multipleFrameTranslation(dna, frames);
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```
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Using this we can replicate the functionality found in EMBOSS' transeq
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package.
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- Convert any initiating amino acid which is not methionine into one
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- Trim stops
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```java TranscriptionEngine.Builder b = new
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TranscriptionEngine.Builder(); b.table(11).initMet(true).trimStop(true);
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TranscriptionEngine engine = b.build(); ```
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```java
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TranscriptionEngine.Builder b = new TranscriptionEngine.Builder();
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b.table(11).initMet(true).trimStop(true);
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TranscriptionEngine engine = b.build();
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```
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This can be handed to the translation methods like so:
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```java
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` DNASequence dna = new DNASequence("ATG");`
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` RNASequence rna = dna.getRNASequence(engine);`
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` ProteinSequence protein = rna.getProteinSequence(engine);`
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DNASequence dna = new DNASequence("ATG");
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RNASequence rna = dna.getRNASequence(engine);
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ProteinSequence protein = rna.getProteinSequence(engine);
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```
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The translation can be started from the TranscriptionEngine directly
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except this results in more general objects (you will get back objects
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which implement the Sequence interface and not the true object type).
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```java
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` DNASequence dna = new DNASequence("ATG");`
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` TranscriptionEngine engine = TranscriptionEngine.getDefault(); //Get the default engine`
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` Sequence`<NucleotideCompound>` rna = engine.getDnaRnaTranslator().createSequence(dna);`
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` Sequence`<AminoAcidCompound>` protein = engine.getRnaAminoAcidTranslator().createSequence(rna);`
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` `
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` //Or to jump to it straight away use this method (coming soon)`
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` Sequence`<AminoAcidCompound>` protein = engine.translate(dna);`
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DNASequence dna = new DNASequence("ATG");
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TranscriptionEngine engine = TranscriptionEngine.getDefault(); //Get the default engine
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Sequence<NucleotideCompound> rna = engine.getDnaRnaTranslator().createSequence(dna);
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Sequence<AminoAcidCompound> protein = engine.getRnaAminoAcidTranslator().createSequence(rna);
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//Or to jump to it straight away use this method (coming soon)
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Sequence<AminoAcidCompound> protein = engine.translate(dna);
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```
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### Codon Tables

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