UniProtEntry

java.lang.Object
- org.forester.ws.seqdb.UniProtEntry

All Implemented Interfaces:: SequenceDatabaseEntry

public final class UniProtEntry
extends java.lang.Object
implements SequenceDatabaseEntry

Field Summary

Fields
Modifier and Type	Field and Description
`static java.util.regex.Pattern`	`BindingDB_PATTERN`
`static java.util.regex.Pattern`	`CTD_PATTERN`
`static java.util.regex.Pattern`	`DrugBank_PATTERN`
`static java.util.regex.Pattern`	`GO_PATTERN`
`static java.util.regex.Pattern`	`HGNC_PATTERN`
`static java.util.regex.Pattern`	`KEGG_PATTERN`
`static java.util.regex.Pattern`	`MIM_PATTERN`
`static java.util.regex.Pattern`	`NCBI_TAXID_PATTERN`
`static java.util.regex.Pattern`	`NextBio_PATTERN`
`static java.util.regex.Pattern`	`Orphanet_PATTERN`
`static java.util.regex.Pattern`	`PDB_PATTERN`
`static java.util.regex.Pattern`	`PharmGKB_PATTERN`
`static java.util.regex.Pattern`	`Reactome_PATTERN`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.Object`	`clone()`
`static SequenceDatabaseEntry`	`createInstanceFromPlainText(java.util.List<java.lang.String> lines)`
`java.lang.String`	`getAccession()`
`java.util.SortedSet<Annotation>`	`getAnnotations()`
`java.lang.String`	`getChromosome()`
`java.util.SortedSet<Accession>`	`getCrossReferences()`
`java.lang.String`	`getGeneName()`
`java.util.SortedSet<GoTerm>`	`getGoTerms()`
`java.lang.String`	`getMap()`
`MolecularSequence`	`getMolecularSequence()`
`java.lang.String`	`getProvider()`
`java.lang.String`	`getSequenceName()`
`java.lang.String`	`getSequenceSymbol()`
`java.lang.String`	`getTaxonomyIdentifier()`
`java.lang.String`	`getTaxonomyScientificName()`
`boolean`	`isEmpty()`

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BindingDB_PATTERN

public static final java.util.regex.Pattern BindingDB_PATTERN

CTD_PATTERN

public static final java.util.regex.Pattern CTD_PATTERN

DrugBank_PATTERN

public static final java.util.regex.Pattern DrugBank_PATTERN

GO_PATTERN

public static final java.util.regex.Pattern GO_PATTERN

KEGG_PATTERN

public static final java.util.regex.Pattern KEGG_PATTERN

MIM_PATTERN

public static final java.util.regex.Pattern MIM_PATTERN

NextBio_PATTERN

public static final java.util.regex.Pattern NextBio_PATTERN

Orphanet_PATTERN

public static final java.util.regex.Pattern Orphanet_PATTERN

PDB_PATTERN

public static final java.util.regex.Pattern PDB_PATTERN

PharmGKB_PATTERN

public static final java.util.regex.Pattern PharmGKB_PATTERN

Reactome_PATTERN

public static final java.util.regex.Pattern Reactome_PATTERN

HGNC_PATTERN

public static final java.util.regex.Pattern HGNC_PATTERN

NCBI_TAXID_PATTERN

public static final java.util.regex.Pattern NCBI_TAXID_PATTERN

Method Detail
- clone
```
public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException
```
  Overrides:
  
  clone in class java.lang.Object
  
  Throws:
  
  java.lang.CloneNotSupportedException
- getAccession
```
public java.lang.String getAccession()
```
  Specified by:
  
  getAccession in interface SequenceDatabaseEntry
- getCrossReferences
```
public java.util.SortedSet<Accession> getCrossReferences()
```
  Specified by:
  
  getCrossReferences in interface SequenceDatabaseEntry
- getGeneName
```
public java.lang.String getGeneName()
```
  Specified by:
  
  getGeneName in interface SequenceDatabaseEntry
- getGoTerms
```
public java.util.SortedSet<GoTerm> getGoTerms()
```
  Specified by:
  
  getGoTerms in interface SequenceDatabaseEntry
- getProvider
```
public java.lang.String getProvider()
```
  Specified by:
  
  getProvider in interface SequenceDatabaseEntry
- getSequenceName
```
public java.lang.String getSequenceName()
```
  Specified by:
  
  getSequenceName in interface SequenceDatabaseEntry
- getSequenceSymbol
```
public java.lang.String getSequenceSymbol()
```
  Specified by:
  
  getSequenceSymbol in interface SequenceDatabaseEntry
- getTaxonomyIdentifier
```
public java.lang.String getTaxonomyIdentifier()
```
  Specified by:
  
  getTaxonomyIdentifier in interface SequenceDatabaseEntry
- getTaxonomyScientificName
```
public java.lang.String getTaxonomyScientificName()
```
  Specified by:
  
  getTaxonomyScientificName in interface SequenceDatabaseEntry
- isEmpty
```
public boolean isEmpty()
```
  Specified by:
  
  isEmpty in interface SequenceDatabaseEntry
- createInstanceFromPlainText
```
public static SequenceDatabaseEntry createInstanceFromPlainText(java.util.List<java.lang.String> lines)
```
- getAnnotations
```
public java.util.SortedSet<Annotation> getAnnotations()
```
  Specified by:
  
  getAnnotations in interface SequenceDatabaseEntry
- getMap
```
public java.lang.String getMap()
```
  Specified by:
  
  getMap in interface SequenceDatabaseEntry
- getChromosome
```
public java.lang.String getChromosome()
```
  Specified by:
  
  getChromosome in interface SequenceDatabaseEntry
- getMolecularSequence
```
public MolecularSequence getMolecularSequence()
```
  Specified by:
  
  getMolecularSequence in interface SequenceDatabaseEntry

Class UniProtEntry

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BindingDB_PATTERN

CTD_PATTERN

DrugBank_PATTERN

GO_PATTERN

KEGG_PATTERN

MIM_PATTERN

NextBio_PATTERN

Orphanet_PATTERN

PDB_PATTERN

PharmGKB_PATTERN

Reactome_PATTERN

HGNC_PATTERN

NCBI_TAXID_PATTERN

Method Detail

clone

getAccession

getCrossReferences

getGeneName

getGoTerms

getProvider

getSequenceName

getSequenceSymbol

getTaxonomyIdentifier

getTaxonomyScientificName

isEmpty

createInstanceFromPlainText

getAnnotations

getMap

getChromosome

getMolecularSequence