ArrayListSequenceReader

java.lang.Object
- org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader<C>

Type Parameters:

C -

All Implemented Interfaces:

java.lang.Iterable<C>, Accessioned, Sequence<C>, SequenceReader<C>

Direct Known Subclasses:

ArrayListProxySequenceReader
```
public class ArrayListSequenceReader<C extends Compound>
extends java.lang.Object
implements SequenceReader<C>
```
Stores a Sequence as a collection of compounds in an ArrayList

Constructor Summary

Constructors
Constructor and Description
`ArrayListSequenceReader()`
`ArrayListSequenceReader(java.util.List<C> compounds, CompoundSet<C> compoundSet)`
`ArrayListSequenceReader(java.lang.String sequence, CompoundSet<C> compoundSet)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`countCompounds(C... compounds)` Returns the number of times we found a compound in the Sequence
`boolean`	`equals(java.lang.Object o)`
`AccessionID`	`getAccession()` Returns the AccessionID this location is currently bound with
`java.util.List<C>`	`getAsList()` Returns the Sequence as a List of compounds
`C`	`getCompoundAt(int position)` Returns the Compound at the given biological index
`CompoundSet<C>`	`getCompoundSet()` Gets the compound set used to back this Sequence
`int`	`getIndexOf(C compound)` Scans through the Sequence looking for the first occurrence of the given compound
`SequenceView<C>`	`getInverse()` Does the right thing to get the inverse of the current Sequence.
`int`	`getLastIndexOf(C compound)` Scans through the Sequence looking for the last occurrence of the given compound
`int`	`getLength()` Returns the length of the Sequence
`java.lang.String`	`getSequenceAsString()` Returns the String representation of the Sequence
`java.lang.String`	`getSequenceAsString(java.lang.Integer begin, java.lang.Integer end, Strand strand)`
`SequenceView<C>`	`getSubSequence(java.lang.Integer bioBegin, java.lang.Integer bioEnd)` Returns a portion of the sequence from the different positions.
`int`	`hashCode()`
`java.util.Iterator<C>`	`iterator()`
`void`	`setCompoundSet(CompoundSet<C> compoundSet)`
`void`	`setContents(java.util.List<C> list)`
`void`	`setContents(java.lang.String sequence)`

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - ArrayListSequenceReader
```
public ArrayListSequenceReader()
```
  - ArrayListSequenceReader
```
public ArrayListSequenceReader(java.util.List<C> compounds,
                               CompoundSet<C> compoundSet)
```
    Parameters:
    
    compounds -
    
    compoundSet -
  - ArrayListSequenceReader
```
public ArrayListSequenceReader(java.lang.String sequence,
                               CompoundSet<C> compoundSet)
                        throws CompoundNotFoundException
```
    Parameters:
    
    sequence -
    
    compoundSet -
    
    Throws:
    
    CompoundNotFoundException
- Method Detail
  - getSequenceAsString
```
public java.lang.String getSequenceAsString()
```
    Description copied from interface: Sequence
    
    Returns the String representation of the Sequence
    
    Specified by:
    
    getSequenceAsString in interface Sequence<C extends Compound>
    
    Returns:
  - getSequenceAsString
```
public java.lang.String getSequenceAsString(java.lang.Integer begin,
                                            java.lang.Integer end,
                                            Strand strand)
```
    Parameters:
    
    begin -
    
    end -
    
    strand -
    
    Returns:
  - getAsList
```
public java.util.List<C> getAsList()
```
    Description copied from interface: Sequence
    
    Returns the Sequence as a List of compounds
    
    Specified by:
    
    getAsList in interface Sequence<C extends Compound>
    
    Returns:
  - getCompoundAt
```
public C getCompoundAt(int position)
```
    Description copied from interface: Sequence
    
    Returns the Compound at the given biological index
    
    Specified by:
    
    getCompoundAt in interface Sequence<C extends Compound>
    
    Parameters:
    
    position -
    
    Returns:
  - getIndexOf
```
public int getIndexOf(C compound)
```
    Description copied from interface: Sequence
    
    Scans through the Sequence looking for the first occurrence of the given compound
    
    Specified by:
    
    getIndexOf in interface Sequence<C extends Compound>
    
    Parameters:
    
    compound -
    
    Returns:
  - getLastIndexOf
```
public int getLastIndexOf(C compound)
```
    Description copied from interface: Sequence
    
    Scans through the Sequence looking for the last occurrence of the given compound
    
    Specified by:
    
    getLastIndexOf in interface Sequence<C extends Compound>
    
    Parameters:
    
    compound -
    
    Returns:
  - getLength
```
public int getLength()
```
    Description copied from interface: Sequence
    
    Returns the length of the Sequence
    
    Specified by:
    
    getLength in interface Sequence<C extends Compound>
    
    Returns:
  - iterator
```
public java.util.Iterator<C> iterator()
```
    Specified by:
    
    iterator in interface java.lang.Iterable<C extends Compound>
    
    Returns:
  - setCompoundSet
```
public void setCompoundSet(CompoundSet<C> compoundSet)
```
    Specified by:
    
    setCompoundSet in interface SequenceReader<C extends Compound>
    
    Parameters:
    
    compoundSet -
  - getCompoundSet
```
public CompoundSet<C> getCompoundSet()
```
    Description copied from interface: Sequence
    
    Gets the compound set used to back this Sequence
    
    Specified by:
    
    getCompoundSet in interface Sequence<C extends Compound>
    
    Returns:
  - setContents
```
public void setContents(java.lang.String sequence)
                 throws CompoundNotFoundException
```
    Specified by:
    
    setContents in interface SequenceReader<C extends Compound>
    
    Parameters:
    
    sequence -
    
    Throws:
    
    CompoundNotFoundException
  - setContents
```
public void setContents(java.util.List<C> list)
```
    Parameters:
    
    list -
  - getSubSequence
```
public SequenceView<C> getSubSequence(java.lang.Integer bioBegin,
                                      java.lang.Integer bioEnd)
```
    Description copied from interface: Sequence
    
    Returns a portion of the sequence from the different positions. This is indexed from 1
    
    Specified by:
    
    getSubSequence in interface Sequence<C extends Compound>
    
    Parameters:
    
    bioBegin -
    
    bioEnd -
    
    Returns:
  - getAccession
```
public AccessionID getAccession()
```
    Description copied from interface: Accessioned
    
    Returns the AccessionID this location is currently bound with
    
    Specified by:
    
    getAccession in interface Accessioned
    
    Returns:
  - countCompounds
```
public int countCompounds(C... compounds)
```
    Description copied from interface: Sequence
    
    Returns the number of times we found a compound in the Sequence
    
    Specified by:
    
    countCompounds in interface Sequence<C extends Compound>
    
    Parameters:
    
    compounds -
    
    Returns:
  - getInverse
```
public SequenceView<C> getInverse()
```
    Description copied from interface: Sequence
    
    Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.
    
    Specified by:
    
    getInverse in interface Sequence<C extends Compound>
    
    Returns:
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object

Class ArrayListSequenceReader<C extends Compound>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

ArrayListSequenceReader

ArrayListSequenceReader

ArrayListSequenceReader

Method Detail

getSequenceAsString

getSequenceAsString

getAsList

getCompoundAt

getIndexOf

getLastIndexOf

getLength

iterator

setCompoundSet

getCompoundSet

setContents

setContents

getSubSequence

getAccession

countCompounds

getInverse

hashCode

equals