jprotein.io.net
Class PsiBlastClient

java.lang.Object
  extended by jprotein.io.net.WebClient
      extended by 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)
           
 
Method Summary
 java.util.Vector getData()
           
 java.lang.String getDatabase()
           
 double getExpectedValue()
           
 java.lang.String getFormat()
           
 java.lang.String getGapCosts()
           
 java.lang.String getMatrix()
           
 int getMaxIteration()
           
 int getMaxResults()
           
 int getNumAlignments()
           
 int getNumDescriptions()
           
 java.lang.String getPrevRID()
           
 java.lang.String getPsiThreshhold()
           
 Sequence getQuerySequence()
           
 java.lang.String getRTOE()
           
 java.util.Vector initData()
           
 java.util.Vector iteratePsiPutCommand()
           
 void parseGI(java.util.Vector buffer)
           
 void parsePGR(java.util.Vector buffer)
           
 void sendInitialPsiPutCommand()
           
 java.util.Vector sendPsiGetCommand()
           
 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 setMaxIteration(int maxIteration)
           
 void setMaxResults(int maxResults)
           
 void setPrevRID(java.lang.String prevRID)
           
 void setQuerySequence(Sequence sequence)
           
 void setQuerySequence(java.lang.String sequence)
           
 void setRetrieveMode(boolean retrieveMode)
           
 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

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)
Method Detail

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