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apollo.dataadapter.organism
Class FlyNameAdapter  

java.lang.Object
  apollo.dataadapter.organism.FlyNameAdapter

All Implemented Interfaces:

ApolloNameAdapterI

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public class FlyNameAdapter

extends java.lang.Object

implements ApolloNameAdapterI

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Field Summary
private  apollo.datamodel.CurationSet	curationSet
private static int	exonNumber
private static int	geneNumber
private static java.lang.String[]	suffixes
private static int	transcriptNumber

 

Constructor Summary

FlyNameAdapter()

 

Method Summary
java.lang.String	generateId(apollo.datamodel.SeqFeatureI feature)
java.lang.String	generateName(apollo.datamodel.SeqFeatureI feature)
java.lang.String	generateURL(apollo.datamodel.Gene g)
private  java.lang.String	getCG(java.lang.String name, java.lang.String prefix)
java.lang.String	getDisplayName(apollo.datamodel.SeqFeatureI sf)
private  java.lang.String	getGeneName(apollo.datamodel.Gene feature)
java.lang.String	getHeader(apollo.datamodel.SeqFeatureI sf)
private  java.lang.String	getId(java.lang.Class featureClass, int start, java.lang.String prefix, java.lang.String suffix)
private  int	getNameCount(java.lang.Class featureClass, int start, java.lang.String prefix)
java.lang.String	getShortName(apollo.datamodel.SeqFeatureI sf)
java.lang.String	getTitle(apollo.datamodel.CurationSet curation)           generate a title for this curation
private  java.lang.String	getTransName(apollo.datamodel.Transcript feature)
boolean	nameIsId(apollo.datamodel.SeqFeatureI feature)
void	removeCurationSet()
java.lang.String	selectMergeName(apollo.datamodel.Gene feature1, apollo.datamodel.Gene feature2)
void	setCurationSet(apollo.datamodel.CurationSet set)
void	setName(apollo.datamodel.SeqFeatureI sf, java.lang.String name)
private  boolean	suffixInUse(java.util.Vector transcripts, java.lang.String suffix, int t_index)

 

Methods inherited from class java.lang.Object

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

 

Field Detail

geneNumber

private static int geneNumber

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transcriptNumber

private static int transcriptNumber

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exonNumber

private static int exonNumber

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curationSet

private apollo.datamodel.CurationSet curationSet

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suffixes

private static java.lang.String[] suffixes

Constructor Detail

FlyNameAdapter

public FlyNameAdapter()

Method Detail

generateName

public java.lang.String generateName(apollo.datamodel.SeqFeatureI feature)

Specified by:

generateName in interface ApolloNameAdapterI

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generateId

public java.lang.String generateId(apollo.datamodel.SeqFeatureI feature)

Specified by:

generateId in interface ApolloNameAdapterI

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getDisplayName

public java.lang.String getDisplayName(apollo.datamodel.SeqFeatureI sf)

Specified by:

getDisplayName in interface ApolloNameAdapterI

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getShortName

public java.lang.String getShortName(apollo.datamodel.SeqFeatureI sf)

Specified by:

getShortName in interface ApolloNameAdapterI

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setName

public void setName(apollo.datamodel.SeqFeatureI sf,
                    java.lang.String name)

Specified by:

setName in interface ApolloNameAdapterI

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getHeader

public java.lang.String getHeader(apollo.datamodel.SeqFeatureI sf)

Specified by:

getHeader in interface ApolloNameAdapterI

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nameIsId

public boolean nameIsId(apollo.datamodel.SeqFeatureI feature)

Specified by:

nameIsId in interface ApolloNameAdapterI

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getId

private java.lang.String getId(java.lang.Class featureClass,
                               int start,
                               java.lang.String prefix,
                               java.lang.String suffix)

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getNameCount

private int getNameCount(java.lang.Class featureClass,
                         int start,
                         java.lang.String prefix)

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getGeneName

private java.lang.String getGeneName(apollo.datamodel.Gene feature)

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getTransName

private java.lang.String getTransName(apollo.datamodel.Transcript feature)

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generateURL

public java.lang.String generateURL(apollo.datamodel.Gene g)

Specified by:

generateURL in interface ApolloNameAdapterI

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getCG

private java.lang.String getCG(java.lang.String name,
                               java.lang.String prefix)

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suffixInUse

private boolean suffixInUse(java.util.Vector transcripts,
                            java.lang.String suffix,
                            int t_index)

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setCurationSet

public void setCurationSet(apollo.datamodel.CurationSet set)

Specified by:

setCurationSet in interface ApolloNameAdapterI

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removeCurationSet

public void removeCurationSet()

Specified by:

removeCurationSet in interface ApolloNameAdapterI

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selectMergeName

public java.lang.String selectMergeName(apollo.datamodel.Gene feature1,
                                        apollo.datamodel.Gene feature2)

Specified by:

selectMergeName in interface ApolloNameAdapterI

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getTitle

public java.lang.String getTitle(apollo.datamodel.CurationSet curation)

Description copied from interface: ApolloNameAdapterI

generate a title for this curation

Specified by:

getTitle in interface ApolloNameAdapterI

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> apollo >> dataadapter >> [ organism overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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