more on tokenization

Gwaldon · andreasprlic · commit c8067a242900 · 2016-04-09T10:59:13.000-07:00
diff --git a/_wikis/BioJava:Cookbook:Sequence.md b/_wikis/BioJava:Cookbook:Sequence.md
@@ -99,3 +99,22 @@ public class SymbolListToString {
 ` }`
 
 } </java>
+
+The above example uses the process of 'tokenization' to create the
+String, in this case hidden in the SeqString method. Different types of
+tokenization can be used to control the output String.
+
+<java>
+
+Alphabet alph; // An alphabet SymbolList sym; //A SymbolList
+
+SymbolTokenization tok= alph.getTokenization("token"); String output =
+tok.tokenizeSymbolList(sym)
+
+</java>
+
+Use "token" or "default" to represent nucleotides and amino acids in
+lower case single characters; use "alternate" to represent DNA in single
+capital letters and amino acids from the PROTEIN\_TERM alphabet in
+character triplets (e.g. Arg) (see
+[AlternateTokenization](http://www.biojava.org/docs/api1.8/org/biojava/bio/seq/io/AlternateTokenization.html)).
diff --git a/_wikis/BioJava:Cookbook:Sequence.mediawiki b/_wikis/BioJava:Cookbook:Sequence.mediawiki
@@ -76,4 +76,18 @@ public class SymbolListToString {
     String s = sl.seqString();
   }
 }
-</java>
+</java>
+
+The above example uses the process of 'tokenization' to create the String, in this case hidden in the SeqString method. Different types of tokenization can be used to control the output String.
+
+<java>
+
+Alphabet alph; // An alphabet
+SymbolList sym; //A SymbolList
+
+SymbolTokenization tok= alph.getTokenization("token");
+String output = tok.tokenizeSymbolList(sym)
+
+</java>
+
+Use "token" or "default" to represent nucleotides and amino acids in lower case single characters; use "alternate" to represent DNA in single capital letters and amino acids from the PROTEIN_TERM alphabet in character triplets (e.g. Arg) (see [http://www.biojava.org/docs/api1.8/org/biojava/bio/seq/io/AlternateTokenization.html AlternateTokenization]).
