charite.christo.strap
Class StrapProtein2BiojavaSequence
java.lang.Object
charite.christo.strap.StrapProtein2BiojavaSequence
- 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
public class StrapProtein2BiojavaSequence
- extends Object
- implements org.biojava.bio.seq.Sequence, org.biojava.bio.symbol.SymbolList
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 |
StrapProtein2BiojavaSequence
public StrapProtein2BiojavaSequence(StrapProtein p)
sequence
public org.biojava.bio.seq.GappedSequence sequence()
getAnnotation
public org.biojava.bio.Annotation getAnnotation()
- Specified by:
getAnnotation
in interface org.biojava.bio.Annotatable
isUnchanging
public boolean isUnchanging(org.biojava.utils.ChangeType ct)
- Specified by:
isUnchanging
in interface org.biojava.utils.Changeable
removeChangeListener
public void removeChangeListener(org.biojava.utils.ChangeListener cl,
org.biojava.utils.ChangeType ct)
- Specified by:
removeChangeListener
in interface org.biojava.utils.Changeable
removeChangeListener
public void removeChangeListener(org.biojava.utils.ChangeListener cl)
- Specified by:
removeChangeListener
in interface org.biojava.utils.Changeable
addChangeListener
public void addChangeListener(org.biojava.utils.ChangeListener cl,
org.biojava.utils.ChangeType ct)
- Specified by:
addChangeListener
in interface org.biojava.utils.Changeable
addChangeListener
public void addChangeListener(org.biojava.utils.ChangeListener cl)
- Specified by:
addChangeListener
in interface org.biojava.utils.Changeable
getSchema
public org.biojava.bio.seq.FeatureFilter getSchema()
- Specified by:
getSchema
in interface org.biojava.bio.seq.FeatureHolder
containsFeature
public boolean containsFeature(org.biojava.bio.seq.Feature f)
- Specified by:
containsFeature
in interface org.biojava.bio.seq.FeatureHolder
removeFeature
public void removeFeature(org.biojava.bio.seq.Feature f)
throws org.biojava.bio.BioException,
org.biojava.utils.ChangeVetoException
- Specified by:
removeFeature
in interface org.biojava.bio.seq.FeatureHolder
- Throws:
org.biojava.bio.BioException
org.biojava.utils.ChangeVetoException
createFeature
public org.biojava.bio.seq.Feature createFeature(org.biojava.bio.seq.Feature.Template ft)
throws org.biojava.utils.ChangeVetoException,
org.biojava.bio.BioException
- Specified by:
createFeature
in interface org.biojava.bio.seq.FeatureHolder
- Throws:
org.biojava.utils.ChangeVetoException
org.biojava.bio.BioException
filter
public org.biojava.bio.seq.FeatureHolder filter(org.biojava.bio.seq.FeatureFilter ft)
- Specified by:
filter
in interface org.biojava.bio.seq.FeatureHolder
filter
public org.biojava.bio.seq.FeatureHolder filter(org.biojava.bio.seq.FeatureFilter ft,
boolean b)
- Specified by:
filter
in interface org.biojava.bio.seq.FeatureHolder
features
public Iterator features()
- Specified by:
features
in interface org.biojava.bio.seq.FeatureHolder
countFeatures
public int countFeatures()
- Specified by:
countFeatures
in interface org.biojava.bio.seq.FeatureHolder
edit
public void edit(org.biojava.bio.symbol.Edit ed)
throws org.biojava.utils.ChangeVetoException,
org.biojava.bio.symbol.IllegalAlphabetException,
IndexOutOfBoundsException
- Specified by:
edit
in interface org.biojava.bio.symbol.SymbolList
- Throws:
org.biojava.utils.ChangeVetoException
org.biojava.bio.symbol.IllegalAlphabetException
IndexOutOfBoundsException
subStr
public String subStr(int from,
int to)
throws IndexOutOfBoundsException
- Specified by:
subStr
in interface org.biojava.bio.symbol.SymbolList
- Throws:
IndexOutOfBoundsException
seqString
public String seqString()
- Specified by:
seqString
in interface org.biojava.bio.symbol.SymbolList
subList
public org.biojava.bio.symbol.SymbolList subList(int from,
int to)
throws IndexOutOfBoundsException
- Specified by:
subList
in interface org.biojava.bio.symbol.SymbolList
- Throws:
IndexOutOfBoundsException
iterator
public Iterator iterator()
- Specified by:
iterator
in interface org.biojava.bio.symbol.SymbolList
toList
public List toList()
- Specified by:
toList
in interface org.biojava.bio.symbol.SymbolList
symbolAt
public org.biojava.bio.symbol.Symbol symbolAt(int idx)
throws IndexOutOfBoundsException
- Specified by:
symbolAt
in interface org.biojava.bio.symbol.SymbolList
- Throws:
IndexOutOfBoundsException
length
public int length()
- Specified by:
length
in interface org.biojava.bio.symbol.SymbolList
getAlphabet
public org.biojava.bio.symbol.Alphabet getAlphabet()
- Specified by:
getAlphabet
in interface org.biojava.bio.symbol.SymbolList
getName
public String getName()
- Specified by:
getName
in interface org.biojava.bio.seq.Sequence
getURN
public String getURN()
- Specified by:
getURN
in interface org.biojava.bio.seq.Sequence
'The most important classes are StrapAlign, StrapProtein and StrapEvent.'