bioroot.plasmid
Class PlasmidBase

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          bioroot.plasmid.PlasmidBase

All Implemented Interfaces:

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

public class PlasmidBase

extends javax.servlet.http.HttpServlet

Author:

nix Contains static methods for Plasmids

See Also:

Serialized Form

Field Summary

static java.lang.String[]	searchHeadings Use to make a hash of column heading in which to search, name then the actual search column name.
static java.lang.String[]	stringFeatures Use to make a default plasmid Feature[].

Constructor Summary

PlasmidBase()

Method Summary

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 void	findOligoMatches(UserBean user, PlasmidBean[] plasmids, DBUtil bioRoot) Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user.
static void	findOligos(UserBean user, PlasmidBean[] plasmids, DBUtil bioRoot) Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user.
static void	findOligos(UserBean user, PlasmidBean plasmid, DBUtil bioRoot) Uses Blast to find oligo matches to a plasmid from all the oligos in a labgroup visible to the user.
static java.lang.String	getPlasmidForm(PlasmidBean ob, DBUtil bioRoot, UserBean userBean) Returns a plasmid form filled with the values in the bean.
static java.lang.String	getPlasmidReport(PlasmidBean pb, DBUtil bioRoot, UserBean userBean, boolean commonForm) Returns an plasmid report.
static java.lang.String[]	getSearchColumnNames() Returns a list of the search column names used in an SQL statment , ie Oligo.name, 1/2 the searchHash.
static java.util.LinkedHashMap	getSearchHash()
static java.lang.String[]	getSearchNames()
static java.lang.String	makeOligoConcat(BlastMatcher[] oligos) Converts a BlastMatcher[] to a concat of oligo sequences and NNNNNNNNNN spacers.
static PlasmidBean[]	reversePlasmidBeans(PlasmidBean[] beans) Reverses the order of an array of PlasmidBeans.

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

Field Detail

stringFeatures

public static java.lang.String[] stringFeatures

Use to make a default plasmid Feature[]. Watch order, stops when it finds a false.

searchHeadings

public static final java.lang.String[] searchHeadings

Use to make a hash of column heading in which to search, name then the actual search column name.

Constructor Detail

PlasmidBase

public PlasmidBase()

Method Detail

getSearchHash

public static java.util.LinkedHashMap getSearchHash()

getSearchNames

public static java.lang.String[] getSearchNames()

getSearchColumnNames

public static java.lang.String[] getSearchColumnNames()

Returns a list of the search column names used in an SQL statment , ie Oligo.name, 1/2 the searchHash.

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

reversePlasmidBeans

public static PlasmidBean[] reversePlasmidBeans(PlasmidBean[] beans)

Reverses the order of an array of PlasmidBeans.

getPlasmidReport

public static java.lang.String getPlasmidReport(PlasmidBean pb,
                                                DBUtil bioRoot,
                                                UserBean userBean,
                                                boolean commonForm)

Returns an plasmid report.

getPlasmidForm

public static java.lang.String getPlasmidForm(PlasmidBean ob,
                                              DBUtil bioRoot,
                                              UserBean userBean)

Returns a plasmid form filled with the values in the bean. Must add a form entry. ie + "

" and start and stop HTML stuff

findOligos

public static void findOligos(UserBean user,
                              PlasmidBean plasmid,
                              DBUtil bioRoot)

Uses Blast to find oligo matches to a plasmid from all the oligos in a labgroup visible to the user. Will only attempt a BLAST if PlasmidBean.blasted == false.

findOligos

public static void findOligos(UserBean user,
                              PlasmidBean[] plasmids,
                              DBUtil bioRoot)

Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user. Will not search if PlasmidBean.blasted = true.

findOligoMatches

public static void findOligoMatches(UserBean user,
                                    PlasmidBean[] plasmids,
                                    DBUtil bioRoot)

Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user. Will search everything irregardles of PlasmidBean.blasted flag. Avoid calling this method directly. Use findOligos method instead!

makeOligoConcat

public static java.lang.String makeOligoConcat(BlastMatcher[] oligos)

Converts a BlastMatcher[] to a concat of oligo sequences and NNNNNNNNNN spacers. Updates array with bp coordinates for positions of the oligo in the concat.