Runner
Class Settings

java.lang.Object
  Runner.Settings

public class Settings
extends java.lang.Object

Modify values in this file to change file locations or change categorization settings.
Notice that some settings are modified in the static initializer block, so be sure that your changes are not being overwritten there.

Author:

davidc

Constructor Summary

Settings()

Method Summary

static java.lang.String	getBackupFolder()
static java.lang.String	getCatDescription(int j)
static java.lang.String[]	getCatDescriptions()
static java.lang.String	getClusterIdxDesc()
static java.lang.String	getClusterOutputFolder()
static java.lang.String	getClusterSource()
static java.lang.String	getClusterTmpOutputFolder() Process in here and clean up in here Only when everything is successful should I delete the stuff
static java.lang.String	getCombineClusterSource() In case getClusterSource() returns abs, this should return art anyways since lots of papers with only an abstract aren't useful
static java.lang.String	getFoldImageSrc()
static java.lang.String	getFullTextURL(java.lang.String wbid)
static java.lang.String	getIntermediateFolder() Where the results of XMLToSentenceConverter, XMLToWordConverter, SentenceToWordConverter should go (same directory as TDB by default)
static java.lang.String	getKbFolder() This should be the only data needed when clustering general search results.
static java.lang.String	getListImageSrc()
static java.lang.String	getLocalOnlinePDFFolder()
static int	getNumCategories()
static java.lang.String	getOnlinePDFFolder()
static java.lang.String	getOpenImageSrc()
static java.lang.String	getOutputFolder()
static java.lang.String	getPMIDAccession(java.lang.String wbid) Looks in tdb/acc for the PMID accession number
static java.lang.String	getShortCatDescription(int j) Description that is compatible to fit within a URL e.g.
static java.lang.String	getSVMSource() Does SVM look at astract or article
static java.lang.String	getTDBFolder()
static java.lang.String	getTrainingFile() Since the training file is by default stored in the same directory where the stopwords, etc.
static boolean	isForceXMLParse()
static boolean	isVerbose()
static void	setCatDescriptions(java.lang.String[] catDescriptions)
static void	setCategories(java.lang.String[] cats)
static void	setForcexmlparse(boolean forcexmlparse)
static void	setIntermediateFolder(java.lang.String intermediateFolder)
static void	setKbFolder(java.lang.String kbFolder)
static void	setOutputFolder(java.lang.String outputFolder)
static void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Constructor Detail

Settings

public Settings()

Method Detail

getOnlinePDFFolder

public static java.lang.String getOnlinePDFFolder()

getTDBFolder

public static java.lang.String getTDBFolder()

getCatDescription

public static java.lang.String getCatDescription(int j)

Parameters:

j - Indexed from 1..n (instead of starting at 0)

Returns:

getShortCatDescription

public static java.lang.String getShortCatDescription(int j)

Description that is compatible to fit within a URL e.g. clusters/Genetics/...
(only alphanumeric characters allowed, should be kept short)

Parameters:

j - Indexed from 1..n (instead of starting at 0)

Returns:

getNumCategories

public static int getNumCategories()

getLocalOnlinePDFFolder

public static java.lang.String getLocalOnlinePDFFolder()

getOutputFolder

public static java.lang.String getOutputFolder()

getIntermediateFolder

public static java.lang.String getIntermediateFolder()

Where the results of XMLToSentenceConverter, XMLToWordConverter, SentenceToWordConverter should go (same directory as TDB by default)

Returns:

getClusterTmpOutputFolder

public static java.lang.String getClusterTmpOutputFolder()

Process in here and clean up in here
Only when everything is successful should I delete the stuff

Returns:

getClusterOutputFolder

public static java.lang.String getClusterOutputFolder()

getSVMSource

public static java.lang.String getSVMSource()

Does SVM look at astract or article

Returns:

getClusterSource

public static java.lang.String getClusterSource()

getCombineClusterSource

public static java.lang.String getCombineClusterSource()

In case getClusterSource() returns abs, this should return art anyways since lots of papers with only an abstract aren't useful

Returns:

isVerbose

public static boolean isVerbose()

getCatDescriptions

public static java.lang.String[] getCatDescriptions()

setVerbose

public static void setVerbose(boolean verbose)

getKbFolder

public static java.lang.String getKbFolder()

This should be the only data needed when clustering general search results. KBFolder includes the files for stopwords, verbs, names, useless words

Returns:

setKbFolder

public static void setKbFolder(java.lang.String kbFolder)

getClusterIdxDesc

public static java.lang.String getClusterIdxDesc()

getListImageSrc

public static java.lang.String getListImageSrc()

getFoldImageSrc

public static java.lang.String getFoldImageSrc()

getOpenImageSrc

public static java.lang.String getOpenImageSrc()

getBackupFolder

public static java.lang.String getBackupFolder()

getFullTextURL

public static java.lang.String getFullTextURL(java.lang.String wbid)

Parameters:

wbid - Must be the wbpaper used by both textpresso and wormbase

Returns:

getPMIDAccession

public static java.lang.String getPMIDAccession(java.lang.String wbid)
                                         throws java.io.IOException

Looks in tdb/acc for the PMID accession number

Parameters:

wbid -

Returns:

"" if the PMID was not found

Throws:

java.io.FileNotFoundException

java.io.IOException

getTrainingFile

public static java.lang.String getTrainingFile()

Since the training file is by default stored in the same directory where the stopwords, etc. are stored

Returns:

setCategories

public static void setCategories(java.lang.String[] cats)

setOutputFolder

public static void setOutputFolder(java.lang.String outputFolder)

setCatDescriptions

public static void setCatDescriptions(java.lang.String[] catDescriptions)

isForceXMLParse

public static boolean isForceXMLParse()

setForcexmlparse

public static void setForcexmlparse(boolean forcexmlparse)

setIntermediateFolder

public static void setIntermediateFolder(java.lang.String intermediateFolder)