'STRAP:multiple sequence alignments '

charite.christo.strap
Class StrapProtein2BiojavaSequence

java.lang.Object
  extended by 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 Class Summary
 
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
 
Field Summary
 
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
 
Constructor Summary
StrapProtein2BiojavaSequence(StrapProtein p)
           
 
Method Summary
 void addChangeListener(org.biojava.utils.ChangeListener cl)
           
 void addChangeListener(org.biojava.utils.ChangeListener cl, org.biojava.utils.ChangeType ct)
           
 boolean containsFeature(org.biojava.bio.seq.Feature f)
           
 int countFeatures()
           
 org.biojava.bio.seq.Feature createFeature(org.biojava.bio.seq.Feature.Template ft)
           
 void edit(org.biojava.bio.symbol.Edit ed)
           
 Iterator features()
           
 org.biojava.bio.seq.FeatureHolder filter(org.biojava.bio.seq.FeatureFilter ft)
           
 org.biojava.bio.seq.FeatureHolder filter(org.biojava.bio.seq.FeatureFilter ft, boolean b)
           
 org.biojava.bio.symbol.Alphabet getAlphabet()
           
 org.biojava.bio.Annotation getAnnotation()
           
 String getName()
           
 org.biojava.bio.seq.FeatureFilter getSchema()
           
 String getURN()
           
 boolean isUnchanging(org.biojava.utils.ChangeType ct)
           
 Iterator iterator()
           
 int length()
           
 void removeChangeListener(org.biojava.utils.ChangeListener cl)
           
 void removeChangeListener(org.biojava.utils.ChangeListener cl, org.biojava.utils.ChangeType ct)
           
 void removeFeature(org.biojava.bio.seq.Feature f)
           
 String seqString()
           
 org.biojava.bio.seq.GappedSequence sequence()
           
 org.biojava.bio.symbol.SymbolList subList(int from, int to)
           
 String subStr(int from, int to)
           
 org.biojava.bio.symbol.Symbol symbolAt(int idx)
           
 List toList()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

StrapProtein2BiojavaSequence

public StrapProtein2BiojavaSequence(StrapProtein p)
Method Detail

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

'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, StrapProtein and StrapEvent.'