/* FASTA */

dicknetherlands · andreasprlic · commit e97e2fee7319 · 2016-04-09T10:58:16.000-07:00
diff --git a/_wikis/BioJava3:HowTo.md b/_wikis/BioJava3:HowTo.md
@@ -139,10 +139,20 @@ The examples in this section require the biojava-fasta module. The
 examples that deal with converting to/from DNA sequences also require
 the biojava-dna module.
 
-At some point, convenience wrapper classes will be added to make the
-parsing process simpler for the most common use-cases.
+Convenience wrapper classes are provided to make the parsing process
+simpler for the most common use-cases.
 
-### Parsing a FASTA file
+### Parsing a FASTA file (the easy way)
+
+` ThingParser`<FASTA>` parser = ThingParserFactory.`  
+`   getReadParser(FASTA.format, new File("/path/to/my/fasta.fa"));`  
+` while (parser.hasNext()) {`  
+`   FASTA fasta = parser.next(); `  
+`   // fasta contains a complete FASTA record.`  
+` }`  
+` reader.close();`
+
+### Parsing a FASTA file (the hard way)
 
 ` FASTAReader reader = new FASTAFileReader(new File("/path/to/my/fasta.fa"));`  
 ` FASTABuilder builder = new FASTABuilder();`  
@@ -163,7 +173,14 @@ parsing process simpler for the most common use-cases.
 ` fasta.setDescription("My Description Line");`  
 ` fasta.setSequence(SymbolListFormatter.formatSymbols(mySeq));`
 
-### Writing a FASTA file
+### Writing a FASTA file (the easy way)
+
+` ThingParser`<FASTA>` parser = ThingParserFactory.`  
+`   getWriteParser(FASTA.format, new File("/path/to/my/fasta.fa"), fasta);`  
+` parser.parseAll();`  
+` writer.close();`
+
+### Writing a FASTA file (the hard way)
 
 ` FASTAEmitter emitter = new FASTAEmitter(fasta);`  
 ` FASTAWriter writer = new FASTAFileWriter(new File("/path/to/new/fasta.fa"));`  
diff --git a/_wikis/BioJava3:HowTo.mediawiki b/_wikis/BioJava3:HowTo.mediawiki
@@ -124,9 +124,19 @@ All the examples in this section require the biojava-dna module.
 
 The examples in this section require the biojava-fasta module. The examples that deal with converting to/from DNA sequences also require the biojava-dna module.
 
-At some point, convenience wrapper classes will be added to make the parsing process simpler for the most common use-cases.
+Convenience wrapper classes are provided to make the parsing process simpler for the most common use-cases.
 
-=== Parsing a FASTA file ===
+=== Parsing a FASTA file (the easy way) ===
+
+  ThingParser<FASTA> parser = ThingParserFactory.
+    getReadParser(FASTA.format, new File("/path/to/my/fasta.fa"));
+  while (parser.hasNext()) {
+    FASTA fasta = parser.next(); 
+    // fasta contains a complete FASTA record.
+  }
+  reader.close();
+
+=== Parsing a FASTA file (the hard way) ===
 
   FASTAReader reader = new FASTAFileReader(new File("/path/to/my/fasta.fa"));
   FASTABuilder builder = new FASTABuilder();
@@ -147,7 +157,14 @@ At some point, convenience wrapper classes will be added to make the parsing pro
   fasta.setDescription("My Description Line");
   fasta.setSequence(SymbolListFormatter.formatSymbols(mySeq));
 
-=== Writing a FASTA file ===
+=== Writing a FASTA file (the easy way) ===
+
+  ThingParser<FASTA> parser = ThingParserFactory.
+    getWriteParser(FASTA.format, new File("/path/to/my/fasta.fa"), fasta);
+  parser.parseAll();
+  writer.close();
+
+=== Writing a FASTA file (the hard way) ===
 
   FASTAEmitter emitter = new FASTAEmitter(fasta);
   FASTAWriter writer = new FASTAFileWriter(new File("/path/to/new/fasta.fa"));
