public class Header
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable
Modifier and Type | Class and Description |
---|---|
static class |
Header.DatabaseType
A list of the database types.
|
Modifier and Type | Method and Description |
---|---|
void |
addAddendum(java.lang.String aAddendum)
This method allows the addition of an addendum to the list.
|
java.lang.Object |
clone()
This method provides a deep copy of the Header instance.
|
java.lang.String |
getAbbreviatedFASTAHeader()
This method returns an abbreviated version of the Header, suitable for
inclusion in FASTA formatted files.
|
java.lang.String |
getAbbreviatedFASTAHeaderWithAddenda()
This method returns an abbreviated version of the Header, suitable for
inclusion in FASTA formatted files.
|
java.lang.String |
getAccession() |
java.lang.String |
getAddenda()
This method allows the caller to retrieve all addenda for the current
header, or 'null' if there aren't any.
|
java.lang.String |
getCoreHeader()
This method reports on the core information for the header, which is
comprised of the ID and the accession String:
|
Header.DatabaseType |
getDatabaseType() |
java.lang.String |
getDescription() |
int |
getEndLocation()
This method reports on the end index of the header.
|
java.lang.String |
getForeignAccession() |
java.lang.String |
getForeignDescription() |
java.lang.String |
getForeignID() |
java.lang.String |
getFullHeaderWithAddenda()
This method reports on the full header, with the addenda (if present).
|
java.lang.String |
getGeneName() |
java.lang.String |
getID() |
java.lang.String |
getProteinEvidence() |
java.lang.String |
getRest() |
int |
getScore()
This method will attribute a score to the current header, based on the
following scoring list: SwissProt : 4 IPI, SwissProt
reference : 3 IPI, TrEMBL or REFSEQ_NP reference : 2
IPI, without SwissProt, TrEMBL or REFSEQ_NP reference : 1
NCBI, SwissProt reference : 2 NCBI, other reference : 1
Unknown header format : 0
|
int |
getStartLocation()
This method reports on the start index of the header.
|
java.lang.String |
getTaxonomy() |
boolean |
hasAddenda()
This method reports on the presence of addenda for this header.
|
static Header |
parseFromFASTA(java.lang.String aFASTAHeader)
Factory method that constructs a Header instance based on a FASTA header
line.
|
void |
setAccession(java.lang.String aAccession) |
void |
setDatabaseType(Header.DatabaseType aDatabaseType) |
void |
setDescription(java.lang.String aDescription) |
void |
setForeignAccession(java.lang.String aForeignAccession) |
void |
setForeignDescription(java.lang.String aForeignDescription) |
void |
setForeignID(java.lang.String aForeignID) |
void |
setGeneName(java.lang.String aGeneName) |
void |
setID(java.lang.String aID) |
void |
setLocation(int aStart,
int aEnd)
This method allows the caller to add information to the header about
location of the sequence in a certain master sequence.
|
void |
setProteinEvidence(java.lang.String aProteinEvidence) |
void |
setRest(java.lang.String aRest) |
void |
setTaxonomy(java.lang.String aTaxonomy) |
java.lang.String |
toString()
This method reports on the entire header.
|
public static Header parseFromFASTA(java.lang.String aFASTAHeader) throws java.lang.StringIndexOutOfBoundsException
aFASTAHeader
- the String with the original FASTA header line.java.lang.StringIndexOutOfBoundsException
- thrown if issues occur during the
parsingpublic java.lang.String getID()
public void setID(java.lang.String aID)
public java.lang.String getForeignID()
public void setForeignID(java.lang.String aForeignID)
public java.lang.String getAccession()
public void setAccession(java.lang.String aAccession)
public Header.DatabaseType getDatabaseType()
public void setDatabaseType(Header.DatabaseType aDatabaseType)
public java.lang.String getForeignAccession()
public void setForeignAccession(java.lang.String aForeignAccession)
public java.lang.String getDescription()
public void setDescription(java.lang.String aDescription)
public java.lang.String getGeneName()
public void setGeneName(java.lang.String aGeneName)
public java.lang.String getProteinEvidence()
public void setProteinEvidence(java.lang.String aProteinEvidence)
public java.lang.String getTaxonomy()
public void setTaxonomy(java.lang.String aTaxonomy)
public java.lang.String getForeignDescription()
public void setForeignDescription(java.lang.String aForeignDescription)
public java.lang.String getRest()
public void setRest(java.lang.String aRest)
public java.lang.String getAbbreviatedFASTAHeader()
>[ID]|[accession_string]|([foreign_ID]|[foreign_accession_string]|[foreign_description] )[description]
public java.lang.String toString()
toString
in class java.lang.Object
public int getScore()
public java.lang.String getCoreHeader()
[ID]|[accession_string]This is mostly useful for appending this core as an addendum to another header.
public void addAddendum(java.lang.String aAddendum)
aAddendum
- String with the addendum, facultatively preceded by
'^A'.public java.lang.String getAddenda()
public boolean hasAddenda()
public java.lang.String getFullHeaderWithAddenda()
public java.lang.String getAbbreviatedFASTAHeaderWithAddenda()
>[ID]|[accession_string]|([foreign_ID]|[foreign_accession_string]|[foreign_description] )[description]([addenda])Note that the output of this method is identical to that of the getAbbreviatedFASTAHeader() if no addenda are present.
public void setLocation(int aStart, int aEnd)
[id]|[accession_string] ([startindex]-[endindex])|...Please note the following:
aStart
- int with the startindex.aEnd
- int with the endindex.public int getStartLocation()
public int getEndLocation()
public java.lang.Object clone()
clone
in class java.lang.Object
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