bioroot
Class Search

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          bioroot.Search

All Implemented Interfaces:

java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig

public class Search

extends javax.servlet.http.HttpServlet

Author:

nix Search processing servlet

See Also:

Serialized Form

Constructor Summary

Search()

Method Summary

static java.lang.String	blastResultToHTML(BlastResult res)
static java.lang.String	checkPlasmidDBFile(DBUtil bioRoot) Looks for an upto date blast database file.
void	doGet(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
void	doPost(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
static java.lang.StringBuffer	makeBlastSummaryTable(BlastResult[] res) Returns a summary HTML table, hotlinked id, name, score, expect
static java.lang.String	makeHashSelectStatement(java.lang.String table, java.util.HashMap rowScore, UserBean userBean) Makes an SQL SELECT statement using a HashMap.
static java.lang.String	makeMultiFASTA(java.lang.String tableName, DBUtil bioRoot)

Methods inherited from class javax.servlet.http.HttpServlet

service

Methods inherited from class javax.servlet.GenericServlet

destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Search

public Search()

Method Detail

doGet

public void doGet(javax.servlet.http.HttpServletRequest request,
                  javax.servlet.http.HttpServletResponse response)
           throws javax.servlet.ServletException,
                  java.io.IOException

Throws:

javax.servlet.ServletException

java.io.IOException

doPost

public void doPost(javax.servlet.http.HttpServletRequest request,
                   javax.servlet.http.HttpServletResponse response)
            throws javax.servlet.ServletException,
                   java.io.IOException

Throws:

javax.servlet.ServletException

java.io.IOException

blastResultToHTML

public static java.lang.String blastResultToHTML(BlastResult res)

makeBlastSummaryTable

public static java.lang.StringBuffer makeBlastSummaryTable(BlastResult[] res)

Returns a summary HTML table, hotlinked id, name, score, expect

checkPlasmidDBFile

public static java.lang.String checkPlasmidDBFile(DBUtil bioRoot)
                                           throws java.lang.Exception

Looks for an upto date blast database file.

Throws:

java.lang.Exception

makeMultiFASTA

public static java.lang.String makeMultiFASTA(java.lang.String tableName,
                                              DBUtil bioRoot)

makeHashSelectStatement

public static java.lang.String makeHashSelectStatement(java.lang.String table,
                                                       java.util.HashMap rowScore,
                                                       UserBean userBean)

Makes an SQL SELECT statement using a HashMap. Retrieves all ids in keys