jprotein.io.net
Class PsiBlastClient
java.lang.Object
jprotein.io.net.WebClient
jprotein.io.net.PsiBlastClient
- All Implemented Interfaces:
- Format
public class PsiBlastClient
- extends WebClient
- implements Format
Constructor Summary |
PsiBlastClient(java.lang.String url,
java.lang.String database,
java.lang.String matrix,
int maxResults,
double eValue,
int gap_exist,
int gap_ext,
int maxIteration)
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PsiBlastClient
public PsiBlastClient(java.lang.String url,
java.lang.String database,
java.lang.String matrix,
int maxResults,
double eValue,
int gap_exist,
int gap_ext,
int maxIteration)
setDatabase
public void setDatabase(java.lang.String database)
setExpectedValue
public void setExpectedValue(double eValue)
setMaxIteration
public void setMaxIteration(int maxIteration)
getMaxIteration
public int getMaxIteration()
setGapCosts
public void setGapCosts(int gap_exist,
int gap_ext)
setMatrix
public void setMatrix(java.lang.String matrix)
setMaxResults
public void setMaxResults(int maxResults)
setQuerySequence
public void setQuerySequence(Sequence sequence)
setQuerySequence
public void setQuerySequence(java.lang.String sequence)
getDatabase
public java.lang.String getDatabase()
getExpectedValue
public double getExpectedValue()
getGapCosts
public java.lang.String getGapCosts()
getMatrix
public java.lang.String getMatrix()
getMaxResults
public int getMaxResults()
setPrevRID
public void setPrevRID(java.lang.String prevRID)
getPrevRID
public java.lang.String getPrevRID()
getPsiThreshhold
public java.lang.String getPsiThreshhold()
getRTOE
public java.lang.String getRTOE()
setRTOE
public void setRTOE(java.lang.String RTOE)
setRetrieveMode
public void setRetrieveMode(boolean retrieveMode)
getFormat
public java.lang.String getFormat()
getNumDescriptions
public int getNumDescriptions()
getNumAlignments
public int getNumAlignments()
getQuerySequence
public Sequence getQuerySequence()
getData
public java.util.Vector getData()
- Specified by:
getData
in interface Format
initData
public java.util.Vector initData()
parseGI
public void parseGI(java.util.Vector buffer)
parsePGR
public void parsePGR(java.util.Vector buffer)
sendInitialPsiPutCommand
public void sendInitialPsiPutCommand()
throws java.lang.Exception
- Throws:
java.lang.Exception
iteratePsiPutCommand
public java.util.Vector iteratePsiPutCommand()
throws java.lang.Exception
- Throws:
java.lang.Exception
sendPsiGetCommand
public java.util.Vector sendPsiGetCommand()
throws java.lang.Exception
- Throws:
java.lang.Exception