java.lang.Object
- org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet

All Implemented Interfaces:: CompoundSet<AminoAcidCompound>

public class ModifiedAminoAcidCompoundSet
extends java.lang.Object
implements CompoundSet<AminoAcidCompound>

Constructor Summary

Constructors
Constructor	Description
`ModifiedAminoAcidCompoundSet(java.util.List<AminoAcidComposition> aaList, java.util.Map<java.lang.Character,java.lang.Double> aaSymbol2MolecularWeight)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)`
`java.util.List<AminoAcidCompound>`	`getAllCompounds()`
`AminoAcidCompound`	`getCompoundForString(java.lang.String string)`	Return null if not recognised.
`java.util.Set<AminoAcidCompound>`	`getEquivalentCompounds(AminoAcidCompound compound)`
`int`	`getMaxSingleCompoundStringLength()`	Returns the maximum size of a compound String this set holds
`java.lang.String`	`getStringForCompound(AminoAcidCompound compound)`
`boolean`	`hasCompound(AminoAcidCompound compound)`
`boolean`	`isComplementable()`
`boolean`	`isCompoundStringLengthEqual()`	Returns true if all String representations of Compounds are of the same length.
`boolean`	`isValidSequence(Sequence<AminoAcidCompound> sequence)`

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

- Constructor Detail
  - ModifiedAminoAcidCompoundSet
```
public ModifiedAminoAcidCompoundSet(java.util.List<AminoAcidComposition> aaList,
                                    java.util.Map<java.lang.Character,java.lang.Double> aaSymbol2MolecularWeight)
```
- Method Detail
  - getMaxSingleCompoundStringLength
```
public int getMaxSingleCompoundStringLength()
```
    Description copied from interface: CompoundSet
    
    Returns the maximum size of a compound String this set holds
    
    Specified by:
    
    getMaxSingleCompoundStringLength in interface CompoundSet<AminoAcidCompound>
  - isCompoundStringLengthEqual
```
public boolean isCompoundStringLengthEqual()
```
    Description copied from interface: CompoundSet
    
    Returns true if all String representations of Compounds are of the same length.
    
    Specified by:
    
    isCompoundStringLengthEqual in interface CompoundSet<AminoAcidCompound>
  - getCompoundForString
```
public AminoAcidCompound getCompoundForString(java.lang.String string)
```
    Description copied from interface: CompoundSet
    
    Return null if not recognised. Throw IllegalArgumentException if string is longer than maximum allowed by CompoundSet.getStringForCompound(Compound).
    
    Specified by:
    
    getCompoundForString in interface CompoundSet<AminoAcidCompound>
  - getStringForCompound
```
public java.lang.String getStringForCompound(AminoAcidCompound compound)
```
    Specified by:
    
    getStringForCompound in interface CompoundSet<AminoAcidCompound>
  - compoundsEquivalent
```
public boolean compoundsEquivalent(AminoAcidCompound compoundOne,
                                   AminoAcidCompound compoundTwo)
```
    Specified by:
    
    compoundsEquivalent in interface CompoundSet<AminoAcidCompound>
  - getEquivalentCompounds
```
public java.util.Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
```
    Specified by:
    
    getEquivalentCompounds in interface CompoundSet<AminoAcidCompound>
  - hasCompound
```
public boolean hasCompound(AminoAcidCompound compound)
```
    Specified by:
    
    hasCompound in interface CompoundSet<AminoAcidCompound>
  - getAllCompounds
```
public java.util.List<AminoAcidCompound> getAllCompounds()
```
    Specified by:
    
    getAllCompounds in interface CompoundSet<AminoAcidCompound>
  - isComplementable
```
public boolean isComplementable()
```
    Specified by:
    
    isComplementable in interface CompoundSet<AminoAcidCompound>
  - isValidSequence
```
public boolean isValidSequence(Sequence<AminoAcidCompound> sequence)
```
    Specified by:
    
    isValidSequence in interface CompoundSet<AminoAcidCompound>

Class ModifiedAminoAcidCompoundSet

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ModifiedAminoAcidCompoundSet

Method Detail

getMaxSingleCompoundStringLength

isCompoundStringLengthEqual

getCompoundForString

getStringForCompound

compoundsEquivalent

getEquivalentCompounds

hasCompound

getAllCompounds

isComplementable

isValidSequence