BasicSequence

java.lang.Object
- org.forester.sequence.BasicSequence

All Implemented Interfaces:: MolecularSequence

public class BasicSequence
extends java.lang.Object
implements MolecularSequence

Nested Class Summary
- Nested classes/interfaces inherited from interface org.forester.sequence.MolecularSequence
  MolecularSequence.TYPE

Field Summary
- Fields inherited from interface org.forester.sequence.MolecularSequence
  AA_REGEXP, DNA_REGEXP, GAP, GAP_STR, RNA_REGEXP, TERMINATE, UNSPECIFIED_AA, UNSPECIFIED_NUC

Constructor Summary

Constructors
Constructor and Description
`BasicSequence(java.lang.String identifier, char[] mol_sequence, MolecularSequence.TYPE type)` Only use if you know what you are doing!
`BasicSequence(java.lang.String identifier, java.lang.String mol_sequence, MolecularSequence.TYPE type)` Only use if you know what you are doing!

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static MolecularSequence`	`copySequence(MolecularSequence seq)`
`static MolecularSequence`	`createAaSequence(java.lang.String identifier, java.lang.String mol_sequence)`
`static MolecularSequence`	`createDnaSequence(java.lang.String identifier, java.lang.String mol_sequence)`
`static MolecularSequence`	`createRnaSequence(java.lang.String identifier, java.lang.String mol_sequence)`
`boolean`	`equals(java.lang.Object obj)`
`java.lang.String`	`getIdentifier()`
`int`	`getLength()`
`char[]`	`getMolecularSequence()`
`java.lang.String`	`getMolecularSequenceAsString()`
`int`	`getNumberOfGapResidues()`
`char`	`getResidueAt(int position)`
`MolecularSequence.TYPE`	`getType()`
`int`	`hashCode()`
`boolean`	`isGapAt(int position)`
`void`	`setIdentifier(java.lang.String id)`
`java.lang.String`	`toString()`

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

Constructor Detail

BasicSequence

public BasicSequence(java.lang.String identifier,
                     java.lang.String mol_sequence,
                     MolecularSequence.TYPE type)

Only use if you know what you are doing!

BasicSequence

public BasicSequence(java.lang.String identifier,
                     char[] mol_sequence,
                     MolecularSequence.TYPE type)

Only use if you know what you are doing!

Method Detail

setIdentifier

public void setIdentifier(java.lang.String id)

getIdentifier
```
public java.lang.String getIdentifier()
```
Specified by:

getIdentifier in interface MolecularSequence

getLength
```
public int getLength()
```
Specified by:

getLength in interface MolecularSequence

getMolecularSequence
```
public char[] getMolecularSequence()
```
Specified by:

getMolecularSequence in interface MolecularSequence

getResidueAt
```
public char getResidueAt(int position)
```
Specified by:

getResidueAt in interface MolecularSequence

getType
```
public MolecularSequence.TYPE getType()
```
Specified by:

getType in interface MolecularSequence

getNumberOfGapResidues
```
public int getNumberOfGapResidues()
```
Specified by:

getNumberOfGapResidues in interface MolecularSequence

equals

public boolean equals(java.lang.Object obj)

Overrides:: equals in class java.lang.Object

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class java.lang.Object

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object

copySequence

public static MolecularSequence copySequence(MolecularSequence seq)

createAaSequence

public static MolecularSequence createAaSequence(java.lang.String identifier,
                                                 java.lang.String mol_sequence)

createDnaSequence

public static MolecularSequence createDnaSequence(java.lang.String identifier,
                                                  java.lang.String mol_sequence)

createRnaSequence

public static MolecularSequence createRnaSequence(java.lang.String identifier,
                                                  java.lang.String mol_sequence)

getMolecularSequenceAsString
```
public java.lang.String getMolecularSequenceAsString()
```
Specified by:

getMolecularSequenceAsString in interface MolecularSequence

isGapAt
```
public boolean isGapAt(int position)
```
Specified by:

isGapAt in interface MolecularSequence

Class BasicSequence

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.sequence.MolecularSequence

Field Summary

Fields inherited from interface org.forester.sequence.MolecularSequence

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicSequence

BasicSequence

Method Detail

setIdentifier

getIdentifier

getLength

getMolecularSequence

getResidueAt

getType

getNumberOfGapResidues

equals

hashCode

toString

copySequence

createAaSequence

createDnaSequence

createRnaSequence

getMolecularSequenceAsString

isGapAt