PubMedLookup
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

addError(PubMedValidationErrors.codes) - Method in PubMedValidationErrors
Adds a Single Error Message.
Author - Class in edu.cornell.med.icb.ncbi.pubmed
Author() - Constructor in Author

B

BibTexFormatter - Class in edu.cornell.med.icb.ncbi.pubmed.formatters
Formatter to output a PubMedInfo as BibTeX.
BibTexFormatter(PubMedInfo) - Constructor in BibTexFormatter
Match for tex backspace.

C

cleanAccentsAndNewlines(String) - Method in PubMedInfoTool

D


E

EndNoteFormatter - Class in edu.cornell.med.icb.ncbi.pubmed.formatters
Formatter to output a PubMedInfo as EndNote.
EndNoteFormatter(PubMedInfo) - Constructor in EndNoteFormatter
Constructor.
equals(Object) - Method in Author
error(Log) - Method in PubMedValidationErrors
Prints all error messages to the passed logger.

F

fixBibTexString(String) - Method in BibTexFormatter
Fix an string for BibTeX export.
fixBibTexString(String) - Method in PubMedInfo
Fix an string for EndNote export.
fixEndNoteString(String) - Method in EndNoteFormatter
Fix an string for EndNote export.
fixEndNoteString(String) - Method in PubMedInfo
Fix an string for EndNote export.
format() - Method in BibTexFormatter
The PMI formatted as BibTeX.
format() - Method in EndNoteFormatter
The PMI formatted as EndNote.
format() - Method in JsonFormatter
The PMI formatted as JSON.
format() - Method in NcbiXmlFormatter
The PMI formatted as XML.
format() - Method in PubMedInfoFormatter
format() - Method in TaxInfoFormatter
format() - Method in XmlFormatter
The PMI formatted as XML.
formatText(TaxInfo) - Method in NcbiXmlFormatter
Take the PMI and format as JSON.
formatText(PubMedInfo) - Method in XmlFormatter
Take the PMI and format as JSON.

G

GeneticCode - Class in edu.cornell.med.icb.ncbi.tax
Taxonomy Genetic code.
GeneticCode(int, String) - Constructor in GeneticCode
Constructor.
getAbstractText() - Method in PubMedInfo
Get the abstractText.
getAffiliation() - Method in PubMedInfo
Get the affiliation.
getArticleTitle() - Method in PubMedInfo
Get the article title.
getArticleUri() - Method in PubMedInfo
Get the article uri.
getAuthors() - Method in PubMedInfo
Get the list of authors associated with the pubmed article.
getAuthorsShort() - Method in PubMedInfo
Get the list of authors associated with the pubmed article but format names like "Smith, Kevin Charles" as "Smith, KC".
getBibTexKey() - Method in PubMedInfo
Get the BibTex key.
getBibTexText() - Method in PubMedInfo
Get the BibTeX export text for the pubmed id.
getCitationHtml(int) - Method in PubMedInfo
Create the citation pre-formatting into HTML for the pubmed id.
getDateCreated() - Method in PubMedInfo
This returns a String and not a Date object as the PubMed Month field is a string and not an int, hence, string month to int month conversion must be done in order for this to work, and I don't know PubMed's String version of the months.
getDoi() - Method in PubMedInfo
Get the doi of the article, if it was set in the constructor (optional).
getEndNoteText() - Method in PubMedInfo
Get the EndNote export text for the pubmed id.
getErrorCodes() - Method in PubMedValidationErrors
Gets a Collection of Error Codes.
getErrorMessage(PubMedValidationErrors.codes) - Method in PubMedValidationErrors
Returns the error message linked to the error code.
getErrors() - Method in PubMedInfo
Get any validation errors associated with this reference.
getErrors() - Method in PubMedValidationErrors
Gets a Collection of Error Messages.
getFirstAuthorLastName() - Method in PubMedInfo
Get the list of authors associated with the pubmed article.
getId() - Method in GeneticCode
Get the genetic code id.
getIndexDocId() - Method in PubMedInfo
Set the related index document id, if any.
getJournalIssue() - Method in PubMedInfo
Get the journal issue.
getJournalTitle() - Method in PubMedInfo
Get the journal title.
getJournalVol() - Method in PubMedInfo
Get the journal volume.
getJsonText() - Method in PubMedInfo
Get the JSON (JavaScript Object Notation) text for the pubmed id.
getLastNameCommaFirstName() - Method in Author
getLastNameCommaInitials() - Method in Author
getLastNameFirstName() - Method in Author
getLastNameInitials() - Method in Author
getName() - Method in GeneticCode
Get the genetic code name.
getPages() - Method in PubMedInfo
Get the pages.
getPrettyPrintXml() - Method in PubMedInfo
Get if xml should be displayed with formatting for user consumption.
getPubMedID() - Method in PubMedInfo
Get the pubmed id.
getUniqueKey() - Method in PubMedInfo
Get the uniqueKey (notably for BibTeX export).
getXmlText() - Method in PubMedInfo
Get the xml text for the pubmed id.
getYearCreated() - Method in PubMedInfo
This returns a String of just the Year created.

H

hasErrors() - Method in PubMedValidationErrors
Indicates if any errors have been recorded.
hashCode(Object) - Method in Author
hasName() - Method in Author

I

isEmpty() - Method in PubMedInfo
Set if the object is empty (just a pmid).

J

JsonFormatter - Class in edu.cornell.med.icb.ncbi.pubmed.formatters
Formatter to output a PubMedInfo as JSON.
JsonFormatter(PubMedInfo) - Constructor in JsonFormatter
Constructor.
jsonQuote(String) - Method in JsonFormatter
Produce a string in double quotes with backslash sequences in all the right places.
jsonQuote(String) - Method in PubMedInfo
Produce a string in double quotes with backslash sequences in all the right places.

K


L


M

main(String[]) - Method in PubMedInfo
Main method for command line interface.
main(String[]) - Method in PubMedInfoTool
Main method for command line interface.
MAMMALIA_FAMILY_TAX_ID - Field in TaxInfoTool
The Tax id for Mammalia.
MAX_AUTHORS - Field in PubMedInfo
The maximum number of authors to display in the citation as formatted HTML.
MAX_NCBI_RETRIES - Field in PubMedInfoTool
Number of times to try to retrieve xml data from NCBI.

N

NcbiXmlFormatter - Class in edu.cornell.med.icb.ncbi.tax.formatters
Formatter to output a TaxInfo as XML.
NcbiXmlFormatter(TaxInfo, boolean) - Constructor in NcbiXmlFormatter
ncbiXmlUrlForPmid(String, int) - Method in PubMedInfoTool
URL for NCBI XML for details on a specified PMID.
NEWLINE_PATTERN - Field in PubMedInfoTool
Match for newline.
NON_ALPHA_NUM_PATTERN - Field in PubMedInfoTool
Match for non alpha numeric.

O


P

parse() - Method in PubMedInfoParser
Parse the XML PubMedInfo data retrieved from NCBI (or local file) given a XOM Document.
parse() - Method in TaxInfoParser
Given a XOM document, retrieve a list of TaxInfo.
partOfFamily(Integer) - Method in TaxInfo
Given the taxIdToFind (a tax-id), return true if taxIdToFind is the taxId of this object or one of the TaxInfo objects in lineage.
printAll() - Method in PubMedInfo
Print the description of the current PubMed Info to System.out.
pubmedIdFromDoi(String, String) - Method in PubMedInfo
Obtain the pmid from a doi.
pubmedIdFromDOI(String, String) - Method in PubMedInfoTool
Obtain the pmid from a doi.
PubMedInfo - Class in edu.cornell.med.icb.pubmed
------------------------------------------------------------------ This class is deprecated!!
PubMedInfo(String, String, String, boolean) - Constructor in PubMedInfo
Constructor that extracts creates an empty PubMedInfo.
pubMedInfoFactoryDOI(String, String, boolean) - Method in PubMedInfoTool
Create a PubMedInfo.
pubMedInfoFactoryPMID(String, int, boolean) - Method in PubMedInfoTool
Create a PubMedInfo.
pubMedInfoFactoryXMLFile(File) - Method in PubMedInfoTool
Create a PubMedInfo using data from a the specified XML file in the same format for PubMedInfo that NCBI provides.
pubMedInfoFactoryXMLFileDOI(File, String) - Method in PubMedInfoTool
Create a PubMedInfo using data from a the specified XML file in the same format for PubMedInfo that NCBI provides.
PubMedInfoFormatter - Interface in edu.cornell.med.icb.ncbi.pubmed.formatters
Interface for PubMedInfo formatting classes.
PubMedInfoParser - Class in edu.cornell.med.icb.ncbi.pubmed
Class to parse NCBI Pub Med Info XML Files.
PubMedInfoParser(File) - Constructor in PubMedInfoParser
Create a PubMedInfo using data from a the specified XML file in the same format for PubMedInfo that NCBI provides.
PubMedInfoTool - Class in edu.cornell.med.icb.ncbi.pubmed
Describe class here.
pubmedUriFromPmid(long) - Method in PubMedInfo
Obtain the pubmed uri from a long pmid.
pubmedUriFromPmid(int) - Method in PubMedInfoTool
Obtain the pubmed uri from a long pmid.
PubMedValidationErrors - Class in edu.cornell.med.icb.pubmed
Encapsulates all validation errors for a specific SigPath Submission.
PubMedValidationErrors.codes - Enum in edu.cornell.med.icb.pubmed
List of possible validation error codes.
PubMedValidationErrors() - Constructor in PubMedValidationErrors
Constructor.

Q


R

readXmlFromUrlWithRetries(File, int) - Method in XmlSlurperHelper
resolveBibTexKeys(Map) - Method in PubMedInfo
Step through each PubMedInfo in the HashMap and set the bibTexKey so if the first author's last name/year is unique in the Map the key will be set to first authors lastname + year, otherwise it will append "a", "b", "c", etc. to the key.
resolveUniqueKeys(HashMap) - Method in PubMedInfoTool
Step through each PubMedInfo in the HashMap and set the uniqueKey so if the first author's last name/year is unique in the Map the key will be set to first authors lastname + year, otherwise it will append "a", "b", "c", etc. to the key.

S

setIndexDocId(int) - Method in PubMedInfo
Set the related index document id, if any.
setLineage(List) - Method in TaxInfo
Set the taxonomy lineage.
setPrettyPrintXml(boolean) - Method in PubMedInfo
Set if xml should be displayed with formatting for user consumption.
SLEEP_TIME_AFTER_FAIL - Field in PubMedInfoTool
Time to sleep before trying to get data from NCBI again after failure..

T

TaxInfo - Class in edu.cornell.med.icb.ncbi.tax
Class that contains information about a NCBI Taxonomy ID and retailed details.
TaxInfo() - Constructor in TaxInfo
Create an empty TaxInfo object, just specifying a tool.
taxInfoFactory(File) - Method in TaxInfoTool
Retrieve a list of TaxInfo from a local XML file.
TaxInfoFormatter - Interface in edu.cornell.med.icb.ncbi.tax.formatters
Interface for TaxInfo data formatters.
TaxInfoParser - Class in edu.cornell.med.icb.ncbi.tax
Class to parse NCBI Taxonomy Info XML Files.
TaxInfoParser(File) - Constructor in TaxInfoParser
Retrieve a list of TaxInfo from a local XML file.
TaxInfoTool - Class in edu.cornell.med.icb.ncbi.tax
Class that connects to the NCBI database at http://www.ncbi.nlm.nih.gov and retrieves taxonomy information given one or more taxonomy ids (comma separated) or retrieves taxonomy information from a given XML file.
toString() - Method in Author
toString() - Method in GeneticCode
Convert this object to a human readable string.
toString() - Method in PubMedInfo
toString() - Method in PubMedValidationErrors
Converts all error messages to a single String with errors messages delimited by line breaks.
toString() - Method in TaxInfo
ToString value of the current object.

U


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W


X

XmlFormatter - Class in edu.cornell.med.icb.ncbi.pubmed.formatters
Formatter to output a PubMedInfo as XML.
XmlFormatter(PubMedInfo, boolean) - Constructor in XmlFormatter
XmlSlurperHelper - Class in edu.cornell.med.icb.xml
Some XOM helper methods.

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