org.strbio.net
Class ProtParam

java.lang.Object
  extended by org.strbio.net.ProtParam

public class ProtParam
extends java.lang.Object

Class to access expasy.ch's ProtParam over the web.

  Version 1.1, 5/4/7 - parse out pI and molecular weight from results
  Version 1.0, 8/16/1 - original version
  

Version:
1.1, 5/4/7
Author:
JMC

Constructor Summary
ProtParam()
           
 
Method Summary
static java.lang.String getAnnot(Protein p, Printf outfile)
          gets annot for a protein... returns null error processing or reading sequence.
static java.lang.String getAnnot(java.lang.String seq, Printf outfile)
          gets annot for a protein... returns null error processing or reading sequence.
static java.lang.String getBody(java.lang.String raw)
          strip header and footer from raw output...
static java.lang.String getCheckedAnnot(Protein p, Printf outfile)
          gets raw annot for a protein... returns null error processing or reading sequence
static java.lang.String getCheckedAnnot(java.lang.String seq, Printf outfile)
          gets raw annot for a protein... returns null error processing or reading sequence
static double getMolecularWeight(java.lang.String raw)
          get molecular weight from raw output, or Double.NaN if not found
static double getPI(java.lang.String raw)
          get pI from raw output, or Double.NaN if not found
static java.lang.String getRawAnnot(java.lang.String sequence, Printf outfile)
          Query the server for annotation data
static java.lang.String getSequence(java.lang.String raw)
          get sequence given in raw output, or null if not found
static void main(java.lang.String[] argv)
          Looks up sequences in file
static void printRaw(java.lang.String sequence, Printf outfile)
          prints raw result of a search
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProtParam

public ProtParam()
Method Detail

getRawAnnot

public static java.lang.String getRawAnnot(java.lang.String sequence,
                                           Printf outfile)
Query the server for annotation data


printRaw

public static final void printRaw(java.lang.String sequence,
                                  Printf outfile)
prints raw result of a search


getPI

public static double getPI(java.lang.String raw)
get pI from raw output, or Double.NaN if not found


getMolecularWeight

public static double getMolecularWeight(java.lang.String raw)
get molecular weight from raw output, or Double.NaN if not found


getSequence

public static final java.lang.String getSequence(java.lang.String raw)
get sequence given in raw output, or null if not found


getBody

public static final java.lang.String getBody(java.lang.String raw)
strip header and footer from raw output... keeps everything from the "Number of amino acids:" line to the GRAVY line. If tags aren't found, returns the whole thing.


getCheckedAnnot

public static final java.lang.String getCheckedAnnot(java.lang.String seq,
                                                     Printf outfile)
gets raw annot for a protein... returns null error processing or reading sequence


getCheckedAnnot

public static final java.lang.String getCheckedAnnot(Protein p,
                                                     Printf outfile)
gets raw annot for a protein... returns null error processing or reading sequence


getAnnot

public static final java.lang.String getAnnot(java.lang.String seq,
                                              Printf outfile)
gets annot for a protein... returns null error processing or reading sequence. processes out html and header/footer


getAnnot

public static final java.lang.String getAnnot(Protein p,
                                              Printf outfile)
gets annot for a protein... returns null error processing or reading sequence. processes out html and header/footer


main

public static final void main(java.lang.String[] argv)
Looks up sequences in file