edu.iastate.jtm.jmed
Class PubMedFetcher

java.lang.Object
  edu.iastate.jtm.jmed.PubMedFetcher

public class PubMedFetcher
extends java.lang.Object

Retrive abstracts from Medline given a list of PMIDs or last query's history.

Author:

Jing Ding

Field Summary

static Limits	GET_FASTA
static Limits	GET_XML

Constructor Summary

PubMedFetcher()
Create a new instance of PubMedFetcher with default buffer size.

PubMedFetcher(int size)
Create a new instance of PubMedFetcher with specified buffer size.

PubMedFetcher(MedlineParser pmp)
Create a new instance of PubMedFetcher with default buffer size and a specified MedlineParser.

PubMedFetcher(java.lang.String tool, java.lang.String email)
Create a new instance of PubMedFetcher with a tool name and email address.

Method Summary

void	fetchFasta(java.io.File gifile, java.io.File outfile)
void	fetchPlain(java.io.File listfile, java.io.File outDir) Fetch abstracts given PMIDs in a file.
void	fetchPlain(java.io.File listfile, java.lang.String outDir, int size) Fetch abstracts given a PMID file.
void	fetchPlain(Limits history, java.io.File outDir) Fetch abstracts given a query history.
void	fetchPlain(Limits history, java.lang.String outDir, int size) Fetch abstracts given a query history.
void	fetchPlain(java.lang.String[] pmidList, int listSize, java.io.File outDir) Fetch abstracts given a list of PMIDs.
void	fetchPlain(java.lang.String[] pmidList, int listSize, java.lang.String outDir, int size) Fetch abstracts given a list of PMIDs.
java.io.InputStream	fetchStream(Limits limits) Retrieve abstracts from query history.
java.io.InputStream	fetchStream(java.lang.String[] pmids)
java.io.InputStream	fetchStream(java.lang.String[] pmids, int offset, int count)
java.io.InputStream	fetchStream(java.lang.String[] pmids, int offset, int count, Limits limits)
java.io.InputStream	fetchStream(java.lang.String[] pmids, Limits limits)
void	fetchXml(java.io.File listfile, java.io.File output, boolean compress) Fetch abstracts given PMIDs in a file.
void	fetchXml(java.io.File listfile, java.lang.String output, int size, boolean compress) Fetch abstracts given a PMID file.
void	fetchXml(Limits history, java.io.File output, boolean compress) Fetch abstracts given a query history.
void	fetchXml(Limits history, java.lang.String output, int size, boolean compress) Fetch abstracts given a query history.
void	fetchXml(java.lang.String[] pmidList, int listSize, java.io.File output, boolean compress) Fetch abstracts given a list of PMIDs.
void	fetchXml(java.lang.String[] pmidList, int listSize, java.lang.String output, int size, boolean compress) Fetch abstracts given a list of PMIDs.
static java.lang.String[]	getPmidFromFile(java.lang.String pfile) Read PMID list from a file.
static void	main(java.lang.String[] args)
void	outputStream(java.io.InputStream stream, java.io.Writer writer)
void	setDatabase(int db)
void	setParser(MedlineParser p) Set the fetcher's parser.
void	setVerbose(boolean v) Set verbose mode.

Methods inherited from class java.lang.Object

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

Field Detail

GET_XML

public static final Limits GET_XML

GET_FASTA

public static final Limits GET_FASTA

Constructor Detail

PubMedFetcher

public PubMedFetcher()

Create a new instance of PubMedFetcher with default buffer size.

PubMedFetcher

public PubMedFetcher(int size)

Create a new instance of PubMedFetcher with specified buffer size.

Parameters:

size - buffer size

PubMedFetcher

public PubMedFetcher(MedlineParser pmp)

Create a new instance of PubMedFetcher with default buffer size and a specified MedlineParser.

Parameters:

pmp - MedlineParser

PubMedFetcher

public PubMedFetcher(java.lang.String tool,
                     java.lang.String email)

Create a new instance of PubMedFetcher with a tool name and email address. They are useful for PubMed's statistics, have no effect on fetching abstracts.

Parameters:

tool - applicaiton name

email - email address

Method Detail

setDatabase

public void setDatabase(int db)

setParser

public void setParser(MedlineParser p)

Set the fetcher's parser.

Parameters:

p - the parser

setVerbose

public void setVerbose(boolean v)

Set verbose mode.

Parameters:

v - whether or not show more info

getPmidFromFile

public static java.lang.String[] getPmidFromFile(java.lang.String pfile)
                                          throws java.io.IOException

Read PMID list from a file.

Parameters:

pfile - the PMID file.

Returns:

the array of PMIDs.

Throws:

java.io.IOException

fetchXml

public void fetchXml(java.io.File listfile,
                     java.io.File output,
                     boolean compress)
              throws java.io.IOException,
                     org.dom4j.DocumentException

Fetch abstracts given PMIDs in a file. Write output to a file in XML format.

Parameters:

listfile - input PMID file

output - output file

compress - compress output files

Throws:

java.io.IOException

org.dom4j.DocumentException

fetchXml

public void fetchXml(java.io.File listfile,
                     java.lang.String output,
                     int size,
                     boolean compress)
              throws java.io.IOException,
                     org.dom4j.DocumentException

Fetch abstracts given a PMID file. Write output to multiple files in XML format.

Parameters:

listfile - the PMID file

output - prefix of output files

size - number of abstracts per file

compress - compress output files

Throws:

java.io.IOException

org.dom4j.DocumentException

fetchXml

public void fetchXml(java.lang.String[] pmidList,
                     int listSize,
                     java.io.File output,
                     boolean compress)
              throws java.io.IOException,
                     org.dom4j.DocumentException

Fetch abstracts given a list of PMIDs. Write output to a file in XML format.

Parameters:

pmidList - the array of PMIDs

listSize - effective size of the array (may smaller than its actual size)

output - output file

compress - compress output files

Throws:

java.io.IOException

org.dom4j.DocumentException

fetchXml

public void fetchXml(java.lang.String[] pmidList,
                     int listSize,
                     java.lang.String output,
                     int size,
                     boolean compress)
              throws java.io.IOException,
                     org.dom4j.DocumentException

Fetch abstracts given a list of PMIDs. Write output to multiple files in XML format

Parameters:

pmidList - the list of PMIDs

listSize - effective size of the list (may be smaller than its actual size)

output - prefix of output files

size - number of abstracts per file

compress - compress output files

Throws:

java.io.IOException

org.dom4j.DocumentException

fetchXml

public void fetchXml(Limits history,
                     java.io.File output,
                     boolean compress)
              throws org.xml.sax.SAXException,
                     java.io.IOException

Fetch abstracts given a query history. Write them to a file in XML format.

Parameters:

history - the query history

output - the output file

compress - compress output files

Throws:

org.xml.sax.SAXException

java.io.IOException

fetchXml

public void fetchXml(Limits history,
                     java.lang.String output,
                     int size,
                     boolean compress)
              throws org.xml.sax.SAXException,
                     org.dom4j.DocumentException,
                     java.io.IOException

Fetch abstracts given a query history. Write output to multiple files in XML format.

Parameters:

history - the query history

output - prefix of output files

size - number of abstracts per file

compress - compress output files

Throws:

org.xml.sax.SAXException

org.dom4j.DocumentException

java.io.IOException

fetchPlain

public void fetchPlain(java.io.File listfile,
                       java.io.File outDir)
                throws java.io.IOException,
                       org.dom4j.DocumentException,
                       org.xml.sax.SAXException

Fetch abstracts given PMIDs in a file. Write them to a directory in plain text format.

Parameters:

listfile - the input file of PMIDs

outDir - output directory

Throws:

java.io.IOException

org.dom4j.DocumentException

org.xml.sax.SAXException

fetchPlain

public void fetchPlain(java.io.File listfile,
                       java.lang.String outDir,
                       int size)
                throws java.io.IOException,
                       org.dom4j.DocumentException,
                       org.xml.sax.SAXException

Fetch abstracts given a PMID file. Write output to multiple directories in plain text format.

Parameters:

listfile - the PMID file

outDir - prefix of output directories

size - number of abstracts per directory

Throws:

java.io.IOException

org.dom4j.DocumentException

org.xml.sax.SAXException

fetchPlain

public void fetchPlain(java.lang.String[] pmidList,
                       int listSize,
                       java.io.File outDir)
                throws java.io.IOException,
                       org.dom4j.DocumentException,
                       org.xml.sax.SAXException

Fetch abstracts given a list of PMIDs. Write them to a directory in plain text format.

Parameters:

pmidList - the list of PMIDs

listSize - effective size of the PMID array (may be smaller than its actual size

outDir - output directory

Throws:

java.io.IOException

org.dom4j.DocumentException

org.xml.sax.SAXException

fetchPlain

public void fetchPlain(java.lang.String[] pmidList,
                       int listSize,
                       java.lang.String outDir,
                       int size)
                throws java.io.IOException,
                       org.dom4j.DocumentException,
                       org.xml.sax.SAXException

Fetch abstracts given a list of PMIDs. Write output to multiple directories in plain text format.

Parameters:

pmidList - the list of PMIDs

listSize - effective list size (may be smaller than its actual size)

outDir - prefix of output directories

size - number of abstracts per directory

Throws:

java.io.IOException

org.dom4j.DocumentException

org.xml.sax.SAXException

fetchPlain

public void fetchPlain(Limits history,
                       java.io.File outDir)
                throws org.xml.sax.SAXException,
                       org.dom4j.DocumentException,
                       java.io.IOException

Fetch abstracts given a query history. Write them to a directory in plain text format.

Parameters:

history - the query history

outDir - output directory

Throws:

org.xml.sax.SAXException

org.dom4j.DocumentException

java.io.IOException

fetchPlain

public void fetchPlain(Limits history,
                       java.lang.String outDir,
                       int size)
                throws org.dom4j.DocumentException,
                       java.io.IOException,
                       org.xml.sax.SAXException

Fetch abstracts given a query history. Write them to multiple directories in plain text format.

Parameters:

history - the query history

outDir - prefix of output directories

size - number of abstracts per directory

Throws:

org.dom4j.DocumentException

java.io.IOException

org.xml.sax.SAXException

fetchFasta

public void fetchFasta(java.io.File gifile,
                       java.io.File outfile)
                throws java.io.IOException

Throws:

java.io.IOException

fetchStream

public java.io.InputStream fetchStream(java.lang.String[] pmids,
                                       Limits limits)
                                throws java.io.IOException

Throws:

java.io.IOException

fetchStream

public java.io.InputStream fetchStream(java.lang.String[] pmids)
                                throws java.io.IOException

Throws:

java.io.IOException

fetchStream

public java.io.InputStream fetchStream(java.lang.String[] pmids,
                                       int offset,
                                       int count)
                                throws java.io.IOException

Throws:

java.io.IOException

fetchStream

public java.io.InputStream fetchStream(java.lang.String[] pmids,
                                       int offset,
                                       int count,
                                       Limits limits)
                                throws java.io.IOException

Throws:

java.io.IOException

fetchStream

public java.io.InputStream fetchStream(Limits limits)
                                throws java.io.IOException

Retrieve abstracts from query history. No limit on number of abstracts.

Parameters:

limits - containing query history.

ps - output destination (may be null).

Returns:

stream containing the retrieved abstracts. Null if already written to ps.

Throws:

java.io.IOException

outputStream

public void outputStream(java.io.InputStream stream,
                         java.io.Writer writer)
                  throws java.io.IOException

Throws:

java.io.IOException

main

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

Parameters:

args - the command line arguments