radaniba · November 29, 2012 16:53
diff --git a/parsefasta.html b/parsefasta.html
 #I found this stuff interesting to share, more on http://code.google.com/p/bio-js/

 #This is my attempt at a bioinformatics framework in JavaScript. I've noticed more and more bioinformatics interfaces going live online, and so we are in a kind of cloud-computing era in bioinformatics. For example, there are many sites out there which let a user paste FASTA sequences into a web form. Things like parsing FASTA files should be easy to do and should be object oriented. I have decided on using the existing framework PrototypeJS to facilitate the process and to ensure that the project is compatible with most operating systems and browsers. 

 #Example

 <html>
 <head>
  <title>Bio-JS Test</title>
  <script src='lib/prototype.js' type='text/javascript'></script>
  <script src='lib/Bio.js' type='text/javascript'></script>
  
  <!-- optional libraries -->
  <script src='lib/fauxconsole.js' type='text/javascript'></script>
  <!-- END optional libraries -->
  <script type='text/javascript'>
  <!--
  Event.observe(window,"load",function(){
    $$(".input").each(function(el){
      el.update(">sequence1 descr1\nAAAAATT\n>sequence2 blabla\nAAAAAAAA");
    });
  });
  function textareaToTextArea(){
    fastaSequenceInput=$('test1').select('.input')[0];
    fastaSequenceOutput=$('test1').select('.output')[0];
    
    seqin=new Bio.SeqIO.fasta(fastaSequenceInput,{
      html:false
    });
    seqout=new Bio.SeqIO.fasta(fastaSequenceOutput,{
      mode:"w",
      html:false
    });
    while(seq=seqin.next_seq()){
      seqout.write_seq(seq);
    }
  }
  function ioStringToTextArea(){
    IO=new Bio.IO.String();
    fastaSequenceInput=$('test2').select('.input')[0];
    fastaSequenceOutput=$('test2').select('.output')[0];
    
    // step 1: seqin to IO
    seqin=new Bio.SeqIO.fasta(fastaSequenceInput,{
      html:false
    });
    // seqout to the IO
    seqout=new Bio.SeqIO.fasta(IO,{
      mode:"w",
      html:false
    });
    while(seq=seqin.next_seq()){
      seqout.write_seq(seq);
    }
    
    // step 2: IO to textarea
    seqin=new Bio.SeqIO.fasta(IO,{
      html:false
    });
    seqout=new Bio.SeqIO.fasta(fastaSequenceOutput,{
      mode:"w",
      html:false
    });
    while(seq=seqin.next_seq()){
      seqout.write_seq(seq);
    }
  }
  //-->
  </script>
  <style type='text/css'>
    textarea.input,textarea.output{
      height:6em;
    }
  </style>
 </head>
 <body>
  <p>This is the demo page, which has clear source code for you to follow. Look at the <a href="doc/index.html">documentation</a> for details.</p>
  <table class="inputOutput">
    <tr>
      <th colspan="2">
        Input textarea to output textarea
      </th>
    </tr>
    <tr id='test1'>
      <td>
        <textarea class='input'></textarea>
      </td>
      <td>
        <textarea class='output'></textarea>
      </td>
    </tr>
    <tr>
      <td colspan="2" align='center'>
        <button onclick="javascript:textareaToTextArea();">Read/write</button>
      </td>
    </tr>
    <tr>
      <th colspan="2">
        IO::String to output textarea
      </th>
    </tr>
    <tr id='test2'>
      <td><textarea class='input'></textarea></td>
      <td><textarea class='output'></textarea></td>
    </tr>
    <tr>
      <td colspan="2" align='center'>
        <button onclick="javascript:ioStringToTextArea();">Read/write</button>
      </td>
    </tr>
  </table>
 </body>
 </html>
	#I found this stuff interesting to share, more on http://code.google.com/p/bio-js/

	#This is my attempt at a bioinformatics framework in JavaScript. I've noticed more and more bioinformatics interfaces going live online, and so we are in a kind of cloud-computing era in bioinformatics. For example, there are many sites out there which let a user paste FASTA sequences into a web form. Things like parsing FASTA files should be easy to do and should be object oriented. I have decided on using the existing framework PrototypeJS to facilitate the process and to ensure that the project is compatible with most operating systems and browsers.

	#Example

	<html>
	<head>
	<title>Bio-JS Test</title>
	<script src='lib/prototype.js' type='text/javascript'></script>
	<script src='lib/Bio.js' type='text/javascript'></script>

	<!-- optional libraries -->
	<script src='lib/fauxconsole.js' type='text/javascript'></script>
	<!-- END optional libraries -->
	<script type='text/javascript'>
	<!--
	Event.observe(window,"load",function(){
	$$(".input").each(function(el){
	el.update(">sequence1 descr1\nAAAAATT\n>sequence2 blabla\nAAAAAAAA");
	});
	});
	function textareaToTextArea(){
	fastaSequenceInput=$('test1').select('.input')[0];
	fastaSequenceOutput=$('test1').select('.output')[0];

	seqin=new Bio.SeqIO.fasta(fastaSequenceInput,{
	html:false
	});
	seqout=new Bio.SeqIO.fasta(fastaSequenceOutput,{
	mode:"w",
	html:false
	});
	while(seq=seqin.next_seq()){
	seqout.write_seq(seq);
	}
	}
	function ioStringToTextArea(){
	IO=new Bio.IO.String();
	fastaSequenceInput=$('test2').select('.input')[0];
	fastaSequenceOutput=$('test2').select('.output')[0];

	// step 1: seqin to IO
	seqin=new Bio.SeqIO.fasta(fastaSequenceInput,{
	html:false
	});
	// seqout to the IO
	seqout=new Bio.SeqIO.fasta(IO,{
	mode:"w",
	html:false
	});
	while(seq=seqin.next_seq()){
	seqout.write_seq(seq);
	}

	// step 2: IO to textarea
	seqin=new Bio.SeqIO.fasta(IO,{
	html:false
	});
	seqout=new Bio.SeqIO.fasta(fastaSequenceOutput,{
	mode:"w",
	html:false
	});
	while(seq=seqin.next_seq()){
	seqout.write_seq(seq);
	}
	}
	//-->
	</script>
	<style type='text/css'>
	textarea.input,textarea.output{
	height:6em;
	}
	</style>
	</head>
	<body>
	<p>This is the demo page, which has clear source code for you to follow. Look at the <a href="doc/index.html">documentation</a> for details.</p>
	<table class="inputOutput">
	<tr>
	<th colspan="2">
	Input textarea to output textarea
	</th>
	</tr>
	<tr id='test1'>
	<td>
	<textarea class='input'></textarea>
	</td>
	<td>
	<textarea class='output'></textarea>
	</td>
	</tr>
	<tr>
	<td colspan="2" align='center'>
	<button onclick="javascript:textareaToTextArea();">Read/write</button>
	</td>
	</tr>
	<tr>
	<th colspan="2">
	IO::String to output textarea
	</th>
	</tr>
	<tr id='test2'>
	<td><textarea class='input'></textarea></td>
	<td><textarea class='output'></textarea></td>
	</tr>
	<tr>
	<td colspan="2" align='center'>
	<button onclick="javascript:ioStringToTextArea();">Read/write</button>
	</td>
	</tr>
	</table>
	</body>
	</html>