<%@ page import="java.io.*,java.util.*,java.net.*,javax.servlet.http.*,javax.servlet.jsp.*" %>
<%@ page import="iubio.readseq.*,iubio.bioseq.*" %>
<%! ///////////// static/global code //////////////////
// readseq.jsp
// using http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq.jar
// readseq-2.1.23 patched to work inside servlets (ClassLoader issue)
String TEST_SEQ="http://iubio.bio.indiana.edu/soft/molbio/readseq/java/test-seq.gb";
String HOME_URL="http://iubio.bio.indiana.edu/soft/molbio/readseq/java/";
BioseqRecord testSeq() throws Exception
{
Bioseq seq = new Bioseq( "ccggagtgaggagcaacatgaactacgtgggactgggacttatcattgtgctgagctgcc");
BasicBioseqDoc seqdoc= new BasicBioseqDoc("DMU57488");
seqdoc.addDocField( seqdoc.kAccession, "U57488");
seqdoc.addComment("Just a test sequence");
seqdoc.addDate( new Date("February 11, 1997"));
seqdoc.addSequenceStats( seq);
seqdoc.addFeature("gene", new SeqRange("18..1684"));
seqdoc.addFeatureNote("symbol", "est-6");
seqdoc.addFeature("intron", new SeqRange("1405..1455"));
BioseqRecord seqrec= new BioseqRecord( seq, seqdoc);
return seqrec;
}
String selectFormat(String param, String current)
{
boolean isout= (!param.startsWith("in"));
StringBuffer sb= new StringBuffer();
sb.append("\n");
return sb.toString();
}
boolean nullstr(String s) { return (s==null||s.trim().length()==0||"null".equals(s)); }
Object writeSeq(Object seqrec, String format, JspWriter out) throws Exception
{
//ByteArrayOutputStream os= new ByteArrayOutputStream();
try {
BioseqWriterIface writer= BioseqFormats.newWriter(
BioseqFormats.getFormatId(format) // "GenBank" "EMBL" "fasta" "XML"
);
writer.setOutput( out) ; //writer.setOutput( os) ;
writer.writeHeader();
if(seqrec instanceof List)
for (int i=0, ns= ((List)seqrec).size(); i
ReadSeq
<%= Readseq.version %>
<%
String self_url= request.getRequestURI();
String format= request.getParameter("format"); if(nullstr(format)) format="EMBL";
String input = request.getParameter("in"); if(nullstr(input)) input="";
%>
Example:
readseq.jsp?format=embl&in=<%= TEST_SEQ %>
Using software from <%= HOME_URL %>
Reformat:
<%
ArrayList seqlist= new ArrayList();
if (nullstr(input)) seqlist.add( testSeq() );
else {
Readseq rd= new Readseq();
String seqname= rd.setInputObject( input );
if ( rd.isKnownFormat() && rd.readInit() ) {
while (rd.readNext()) seqlist.add( rd.nextSeq() );
}
}
%>
<%= writeSeq( seqlist, format, out)%>