jprotein.io.net
Class PsiBlastClientOld

java.lang.Object
  extended by jprotein.io.net.WebClient
      extended by jprotein.io.net.PsiBlastClientOld
All Implemented Interfaces:
Format

public class PsiBlastClientOld
extends WebClient
implements Format


Constructor Summary
PsiBlastClientOld(java.lang.String url, java.lang.String database, java.lang.String matrix, int maxResults, double eValue, int gap_exist, int gap_ext, int iteration)
           
 
Method Summary
 java.util.Vector getData()
           
 java.lang.String getDatabase()
           
 double getExpectedValue()
           
 java.lang.String getGapCosts()
           
 java.lang.String getMatrix()
           
 int getMaxResults()
           
 int getNumIteration()
           
 java.lang.String getPrevRID()
           
 java.lang.String getPsiThreshhold()
           
 Sequence getQuerySequence()
           
 java.lang.String getRTOE()
           
 java.util.Vector initData()
           
 java.util.Vector iterPutCommand()
           
 void parseGI(java.util.Vector buffer)
           
 java.util.Vector sendInitialPsiGetCommand()
           
 java.util.Vector sendIterPsiGetCommand()
           
 void sendPutCommand()
           
 void setDatabase(java.lang.String database)
           
 void setExpectedValue(double eValue)
           
 void setGapCosts(int gap_exist, int gap_ext)
           
 void setMatrix(java.lang.String matrix)
           
 void setMaxResults(int maxResults)
           
 void setNumIteration(int iteration)
           
 void setPrevRID(java.lang.String prevRID)
           
 void setQuerySequence(Sequence sequence)
           
 void setQuerySequence(java.lang.String sequence)
           
 void setRTOE(java.lang.String RTOE)
           
 
Methods inherited from class jprotein.io.net.WebClient
getURL, sendCommand, sendCommand, setURL
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PsiBlastClientOld

public PsiBlastClientOld(java.lang.String url,
                         java.lang.String database,
                         java.lang.String matrix,
                         int maxResults,
                         double eValue,
                         int gap_exist,
                         int gap_ext,
                         int iteration)
Method Detail

setDatabase

public void setDatabase(java.lang.String database)

setExpectedValue

public void setExpectedValue(double eValue)

setNumIteration

public void setNumIteration(int iteration)

getNumIteration

public int getNumIteration()

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)

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)

sendPutCommand

public void sendPutCommand()
                    throws java.lang.Exception
Throws:
java.lang.Exception

sendInitialPsiGetCommand

public java.util.Vector sendInitialPsiGetCommand()
                                          throws java.lang.Exception
Throws:
java.lang.Exception

sendIterPsiGetCommand

public java.util.Vector sendIterPsiGetCommand()
                                       throws java.lang.Exception
Throws:
java.lang.Exception

iterPutCommand

public java.util.Vector iterPutCommand()
                                throws java.lang.Exception
Throws:
java.lang.Exception