public class SequenceBasedComparison
extends java.lang.Object
Constructor and Description |
---|
SequenceBasedComparison()
Empty constructor
|
SequenceBasedComparison(org.apache.logging.log4j.Logger log4j_)
Enables logging capabilites along with creation of a SequenceBasedComparison instance
|
Modifier and Type | Method and Description |
---|---|
int |
getGapExt() |
int |
getGapOpen() |
java.lang.String |
getPidMethod() |
org.biojava.nbio.core.sequence.ProteinSequence |
getProtSeqTarget(java.lang.String targetAsString)
Method is necessary for determination that the target sequence causes the exception.
|
java.lang.String |
getSubstMatrixID() |
java.util.HashMap<java.lang.String,java.lang.String> |
pairwiseSequenceComp(java.lang.String queryAsString,
java.lang.String targetAsString)
The method performs a pairwise sequence based comparison.
|
void |
setGapExt(int gapExt_) |
void |
setGapOpen(int gapOpen_) |
void |
setLog4j(org.apache.logging.log4j.Logger log4j_) |
void |
setPidMethod(java.lang.String pidMethod_)
Setter and getter
|
void |
setSubstMatrixID(java.lang.String substMatrixID_) |
public SequenceBasedComparison()
public SequenceBasedComparison(org.apache.logging.log4j.Logger log4j_)
public java.util.HashMap<java.lang.String,java.lang.String> pairwiseSequenceComp(java.lang.String queryAsString, java.lang.String targetAsString) throws EmptySequenceException, org.biojava.nbio.core.exceptions.CompoundNotFoundException, NoPercentIdentityValueComputedException
queryAsString
- targetAsString
- EmptySequenceException
org.biojava.nbio.core.exceptions.CompoundNotFoundException
NoPercentIdentityValueComputedException
public org.biojava.nbio.core.sequence.ProteinSequence getProtSeqTarget(java.lang.String targetAsString) throws org.biojava.nbio.core.exceptions.CompoundNotFoundException
targetAsString
- org.biojava.nbio.core.exceptions.CompoundNotFoundException
public void setPidMethod(java.lang.String pidMethod_)
public java.lang.String getPidMethod()
public void setSubstMatrixID(java.lang.String substMatrixID_)
public java.lang.String getSubstMatrixID()
public void setGapOpen(int gapOpen_)
public int getGapOpen()
public void setGapExt(int gapExt_)
public int getGapExt()
public void setLog4j(org.apache.logging.log4j.Logger log4j_)