org.irisa.genouest.logol.utils
Class MySequence
java.lang.Object
org.irisa.genouest.logol.utils.MySequence
- All Implemented Interfaces:
- org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Sequence, org.biojava.bio.symbol.SymbolList, org.biojava.utils.Changeable
- Direct Known Subclasses:
- MyRevCompSequence
public class MySequence
- extends java.lang.Object
- implements org.biojava.bio.seq.Sequence
Simple Sequence implementation to fix memory issues with BioJava DNATools functions.
Implements minimum number of functions for sequence data manipulation (no symbols and features)
Fix : 1660
- Author:
- osallou
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
org.biojava.bio.Annotatable.AnnotationForwarder |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EDIT, EMPTY_LIST |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Method Summary |
void |
addChangeListener(org.biojava.utils.ChangeListener arg0)
|
void |
addChangeListener(org.biojava.utils.ChangeListener arg0,
org.biojava.utils.ChangeType arg1)
|
boolean |
containsFeature(org.biojava.bio.seq.Feature arg0)
|
int |
countFeatures()
|
org.biojava.bio.seq.Feature |
createFeature(org.biojava.bio.seq.Feature.Template arg0)
|
void |
edit(org.biojava.bio.symbol.Edit arg0)
|
java.util.Iterator<org.biojava.bio.seq.Feature> |
features()
|
org.biojava.bio.seq.FeatureHolder |
filter(org.biojava.bio.seq.FeatureFilter arg0)
|
org.biojava.bio.seq.FeatureHolder |
filter(org.biojava.bio.seq.FeatureFilter arg0,
boolean arg1)
|
org.biojava.bio.symbol.Alphabet |
getAlphabet()
|
org.biojava.bio.Annotation |
getAnnotation()
|
java.lang.String |
getContent()
|
java.lang.String |
getHeader()
|
java.lang.String |
getName()
|
org.biojava.bio.seq.FeatureFilter |
getSchema()
|
java.lang.String |
getURN()
|
boolean |
isUnchanging(org.biojava.utils.ChangeType arg0)
|
java.util.Iterator |
iterator()
|
int |
length()
|
void |
removeChangeListener(org.biojava.utils.ChangeListener arg0)
|
void |
removeChangeListener(org.biojava.utils.ChangeListener arg0,
org.biojava.utils.ChangeType arg1)
|
void |
removeFeature(org.biojava.bio.seq.Feature arg0)
|
java.lang.String |
seqString()
|
void |
setContent(java.lang.String content)
|
void |
setHeader(java.lang.String header)
|
void |
setPosition(long sequencePosition)
|
org.biojava.bio.symbol.SymbolList |
subList(int arg0,
int arg1)
|
java.lang.String |
subStr(int arg0,
int arg1)
|
org.biojava.bio.symbol.Symbol |
symbolAt(int arg0)
|
java.util.List |
toList()
|
static void |
writeFasta(java.io.BufferedOutputStream bos,
org.biojava.bio.seq.Sequence seq)
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MySequence
public MySequence()
MySequence
public MySequence(java.lang.String head,
java.lang.String data)
writeFasta
public static void writeFasta(java.io.BufferedOutputStream bos,
org.biojava.bio.seq.Sequence seq)
getContent
public java.lang.String getContent()
setContent
public void setContent(java.lang.String content)
getHeader
public java.lang.String getHeader()
setHeader
public void setHeader(java.lang.String header)
getName
public java.lang.String getName()
- Specified by:
getName
in interface org.biojava.bio.seq.Sequence
getURN
public java.lang.String getURN()
- Specified by:
getURN
in interface org.biojava.bio.seq.Sequence
edit
public void edit(org.biojava.bio.symbol.Edit arg0)
throws java.lang.IndexOutOfBoundsException,
org.biojava.bio.symbol.IllegalAlphabetException,
org.biojava.utils.ChangeVetoException
- Specified by:
edit
in interface org.biojava.bio.symbol.SymbolList
- Throws:
java.lang.IndexOutOfBoundsException
org.biojava.bio.symbol.IllegalAlphabetException
org.biojava.utils.ChangeVetoException
getAlphabet
public org.biojava.bio.symbol.Alphabet getAlphabet()
- Specified by:
getAlphabet
in interface org.biojava.bio.symbol.SymbolList
iterator
public java.util.Iterator iterator()
- Specified by:
iterator
in interface org.biojava.bio.symbol.SymbolList
length
public int length()
- Specified by:
length
in interface org.biojava.bio.symbol.SymbolList
seqString
public java.lang.String seqString()
- Specified by:
seqString
in interface org.biojava.bio.symbol.SymbolList
subList
public org.biojava.bio.symbol.SymbolList subList(int arg0,
int arg1)
throws java.lang.IndexOutOfBoundsException
- Specified by:
subList
in interface org.biojava.bio.symbol.SymbolList
- Throws:
java.lang.IndexOutOfBoundsException
subStr
public java.lang.String subStr(int arg0,
int arg1)
throws java.lang.IndexOutOfBoundsException
- Specified by:
subStr
in interface org.biojava.bio.symbol.SymbolList
- Throws:
java.lang.IndexOutOfBoundsException
symbolAt
public org.biojava.bio.symbol.Symbol symbolAt(int arg0)
throws java.lang.IndexOutOfBoundsException
- Specified by:
symbolAt
in interface org.biojava.bio.symbol.SymbolList
- Throws:
java.lang.IndexOutOfBoundsException
toList
public java.util.List toList()
- Specified by:
toList
in interface org.biojava.bio.symbol.SymbolList
addChangeListener
public void addChangeListener(org.biojava.utils.ChangeListener arg0)
- Specified by:
addChangeListener
in interface org.biojava.utils.Changeable
addChangeListener
public void addChangeListener(org.biojava.utils.ChangeListener arg0,
org.biojava.utils.ChangeType arg1)
- Specified by:
addChangeListener
in interface org.biojava.utils.Changeable
isUnchanging
public boolean isUnchanging(org.biojava.utils.ChangeType arg0)
- Specified by:
isUnchanging
in interface org.biojava.utils.Changeable
removeChangeListener
public void removeChangeListener(org.biojava.utils.ChangeListener arg0)
- Specified by:
removeChangeListener
in interface org.biojava.utils.Changeable
removeChangeListener
public void removeChangeListener(org.biojava.utils.ChangeListener arg0,
org.biojava.utils.ChangeType arg1)
- Specified by:
removeChangeListener
in interface org.biojava.utils.Changeable
containsFeature
public boolean containsFeature(org.biojava.bio.seq.Feature arg0)
- Specified by:
containsFeature
in interface org.biojava.bio.seq.FeatureHolder
countFeatures
public int countFeatures()
- Specified by:
countFeatures
in interface org.biojava.bio.seq.FeatureHolder
createFeature
public org.biojava.bio.seq.Feature createFeature(org.biojava.bio.seq.Feature.Template arg0)
throws org.biojava.bio.BioException,
org.biojava.utils.ChangeVetoException
- Specified by:
createFeature
in interface org.biojava.bio.seq.FeatureHolder
- Throws:
org.biojava.bio.BioException
org.biojava.utils.ChangeVetoException
features
public java.util.Iterator<org.biojava.bio.seq.Feature> features()
- Specified by:
features
in interface org.biojava.bio.seq.FeatureHolder
filter
public org.biojava.bio.seq.FeatureHolder filter(org.biojava.bio.seq.FeatureFilter arg0)
- Specified by:
filter
in interface org.biojava.bio.seq.FeatureHolder
filter
public org.biojava.bio.seq.FeatureHolder filter(org.biojava.bio.seq.FeatureFilter arg0,
boolean arg1)
- Specified by:
filter
in interface org.biojava.bio.seq.FeatureHolder
getSchema
public org.biojava.bio.seq.FeatureFilter getSchema()
- Specified by:
getSchema
in interface org.biojava.bio.seq.FeatureHolder
removeFeature
public void removeFeature(org.biojava.bio.seq.Feature arg0)
throws org.biojava.utils.ChangeVetoException,
org.biojava.bio.BioException
- Specified by:
removeFeature
in interface org.biojava.bio.seq.FeatureHolder
- Throws:
org.biojava.utils.ChangeVetoException
org.biojava.bio.BioException
getAnnotation
public org.biojava.bio.Annotation getAnnotation()
- Specified by:
getAnnotation
in interface org.biojava.bio.Annotatable
setPosition
public void setPosition(long sequencePosition)