org.strbio.net
Class FruitFly

java.lang.Object
  org.strbio.net.FruitFly

public class FruitFly
extends java.lang.Object

Class to access fruitfly.org over the web.

  Version 1.2, 3/13/1 - uses IO.getURLData
  Version 1.1, 3/5/1 - added getRawAnnotSlow
  Version 1.0, 1/16/1 - original version
  

Version:

1.2, 3/13/1

Author:

JMC

Constructor Summary

FruitFly()

Method Summary

static java.lang.String	getArm(java.lang.String rawdata) Return the arm from a search, or null if not there.
static int	getCG(java.lang.String rawdata) returns cg from query, if found, or -1 if not found.
static int[]	getCGOptions(java.lang.String rawdata) returns multiple CG options from query.
static java.lang.String	getCytogenetic(java.lang.String rawdata) Return the cytogenetic position from a search, or null if not there.
static int	getFBan(java.lang.String rawdata) Return the FBan (annotation number) from a search, or -1 if not there.
static int	getFBgn(java.lang.String rawdata) Return the FBgn (gene number) from a search, or -1 if not there.
static java.lang.String	getRawAnnot(int release, java.lang.String geneName, Printf outfile) Query the server for annotation data
static java.lang.String	getRawAnnot(java.lang.String geneName, Printf outfile) Query the server for annotation data
static java.lang.String	getRawAnnotSlow(int release, java.lang.String geneName, Printf outfile) Query the server for annotation data
static boolean	isArmUnknown(java.lang.String rawdata) Is there an annotation of unknown Arm?
static void	main(java.lang.String[] argv) Looks up something in entrez.
static void	printRaw(java.lang.String geneName, Printf outfile) prints raw result of a flybase search

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FruitFly

public FruitFly()

Method Detail

getRawAnnot

public static java.lang.String getRawAnnot(int release,
                                           java.lang.String geneName,
                                           Printf outfile)

Query the server for annotation data

getRawAnnotSlow

public static java.lang.String getRawAnnotSlow(int release,
                                               java.lang.String geneName,
                                               Printf outfile)

Query the server for annotation data

getRawAnnot

public static java.lang.String getRawAnnot(java.lang.String geneName,
                                           Printf outfile)

Query the server for annotation data

getCG

public static final int getCG(java.lang.String rawdata)

returns cg from query, if found, or -1 if not found.

getCGOptions

public static final int[] getCGOptions(java.lang.String rawdata)

returns multiple CG options from query. Null if none are found. If found, returns array of cg, then accession number of scaffold (AExxxxxx), then transcript (AA) length; 3 integers per answer.

getCytogenetic

public static final java.lang.String getCytogenetic(java.lang.String rawdata)

Return the cytogenetic position from a search, or null if not there.

getFBgn

public static final int getFBgn(java.lang.String rawdata)

Return the FBgn (gene number) from a search, or -1 if not there.

getFBan

public static final int getFBan(java.lang.String rawdata)

Return the FBan (annotation number) from a search, or -1 if not there.

getArm

public static final java.lang.String getArm(java.lang.String rawdata)

Return the arm from a search, or null if not there.

isArmUnknown

public static final boolean isArmUnknown(java.lang.String rawdata)

Is there an annotation of unknown Arm?

printRaw

public static final void printRaw(java.lang.String geneName,
                                  Printf outfile)

prints raw result of a flybase search

main

public static final void main(java.lang.String[] argv)

Looks up something in entrez.