bioroot.antibody
Class AntibodyBase

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          bioroot.antibody.AntibodyBase

All Implemented Interfaces:

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

public class AntibodyBase

extends javax.servlet.http.HttpServlet

Author:

nix Contains static methods for Plasmids

See Also:

Serialized Form

Field Summary

static java.lang.String	antibodyPrepFeatureNames Used to see if any antibody preps are called for spreadsheet.
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 antibody Feature[].
static java.lang.String	useDilutionFeatureNames Used to see if any use dilutions are called for spreadsheet.

Constructor Summary

AntibodyBase()

Method Summary

static void	addPlasmid(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static void	addStrain(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static int	deleteAntibodyPrepIndex(AntibodyBean a, DBUtil bioRoot, java.util.HashMap m) Scans a hashmap for an antibody prep to delete returns the index number
static java.lang.String	deleteUseDilutionIndex(AntibodyBean a, DBUtil bioRoot, java.util.HashMap m) Scans a hashmap for a use dilution to delete returns the index string or null.
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.String	getAntibodyForm(AntibodyBean ab, DBUtil bioRoot, UserBean userBean) Returns an antibody form filled with the values in the bean.
static void	getAntibodyPrepForm(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int index)
static void	getAntibodyPrepForms(AntibodyBean ab, DBUtil bioRoot, java.lang.StringBuffer b)
static void	getAntibodyPrepReport(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int index, boolean commonForm)
static void	getAntibodyPrepReports(AntibodyBean ab, DBUtil bioRoot, java.lang.StringBuffer b, boolean commonForm)
static java.lang.String	getAntibodyReport(AntibodyBean ab, DBUtil bioRoot, UserBean user, boolean commonForm) Returns an antibody report filled with the values in the bean.
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 void	getUseDilutionForm(UseDilution u, java.lang.StringBuffer b, int index, int apbIndex, boolean lastForm) Returns a UseDilutionNotes where the names are apended with apbIndex.index ie 0.0, 0.1, 0.2,,1.0,1.1...
static void	getUseDilutionForms(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int apbIndex) Pumps out useDilution forms, should always have one with each Prep
static void	getUseDilutionReport(UseDilution u, java.lang.StringBuffer b, int index, int apbIndex)
static void	getUseDilutionReports(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int apbIndex, boolean commonForm) Pumps out useDilution reports
static int	newUseDilutionIndex(AntibodyBean a, DBUtil bioRoot, java.util.HashMap m) Scans a hashmap for a newUseDilution selection, returns the index number
static void	removePlasmid(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot)
static void	removeStrain(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot)
static java.lang.String	renameFile(java.lang.String oldFileName, java.lang.String directory) Copies an old file and renames it to tempRndmWrd_name.
static AntibodyBean[]	reverseAntibodyBeans(AntibodyBean[] beans) Reverses the order of an array of PlasmidBeans.
static Feature[][]	splitAntibodyFeatures(Feature[] all) Returns arrays of Features where the F[0] = antibody, F[1]=abPrep, F[2]=useDil specific features.
static java.lang.String	writeTempFile(java.lang.Object fileItemPoss, javax.servlet.http.HttpServletRequest request, java.lang.String directory) Looks for an uploaded file, writes it to the directory with a tempRNDMWord_FileName, will return the name, or null, or 'Too big'

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 antibody Feature[]. Watch order, stops when it finds a false. Be sure to reflect any changes here to the featureName Strings below.

antibodyPrepFeatureNames

public static final java.lang.String antibodyPrepFeatureNames

Used to see if any antibody preps are called for spreadsheet. Should match all of the feature names for antibodyPreps. Keep the last comma.

See Also:

Constant Field Values

useDilutionFeatureNames

public static final java.lang.String useDilutionFeatureNames

Used to see if any use dilutions are called for spreadsheet. Should match all of the feature names for use dilutions. Keep the last comma.

See Also:

Constant Field Values

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

AntibodyBase

public AntibodyBase()

Method Detail

splitAntibodyFeatures

public static Feature[][] splitAntibodyFeatures(Feature[] all)

Returns arrays of Features where the F[0] = antibody, F[1]=abPrep, F[2]=useDil specific features. For displaying in the Antibody View Preferences

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

addStrain

public static void addStrain(AntibodyBean bean,
                             java.util.HashMap nameValue,
                             DBUtil bioRoot,
                             UserBean userBean)

removeStrain

public static void removeStrain(AntibodyBean bean,
                                java.util.HashMap nameValue,
                                DBUtil bioRoot)

addPlasmid

public static void addPlasmid(AntibodyBean bean,
                              java.util.HashMap nameValue,
                              DBUtil bioRoot,
                              UserBean userBean)

removePlasmid

public static void removePlasmid(AntibodyBean bean,
                                 java.util.HashMap nameValue,
                                 DBUtil bioRoot)

deleteUseDilutionIndex

public static java.lang.String deleteUseDilutionIndex(AntibodyBean a,
                                                      DBUtil bioRoot,
                                                      java.util.HashMap m)

Scans a hashmap for a use dilution to delete returns the index string or null.

deleteAntibodyPrepIndex

public static int deleteAntibodyPrepIndex(AntibodyBean a,
                                          DBUtil bioRoot,
                                          java.util.HashMap m)

Scans a hashmap for an antibody prep to delete returns the index number

newUseDilutionIndex

public static int newUseDilutionIndex(AntibodyBean a,
                                      DBUtil bioRoot,
                                      java.util.HashMap m)

Scans a hashmap for a newUseDilution selection, returns the index number

reverseAntibodyBeans

public static AntibodyBean[] reverseAntibodyBeans(AntibodyBean[] beans)

Reverses the order of an array of PlasmidBeans.

getAntibodyForm

public static java.lang.String getAntibodyForm(AntibodyBean ab,
                                               DBUtil bioRoot,
                                               UserBean userBean)

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

" and start and stop HTML stuff

getAntibodyPrepForms

public static void getAntibodyPrepForms(AntibodyBean ab,
                                        DBUtil bioRoot,
                                        java.lang.StringBuffer b)

getAntibodyPrepForm

public static void getAntibodyPrepForm(AntibodyPrep a,
                                       DBUtil bioRoot,
                                       java.lang.StringBuffer b,
                                       int index)

getUseDilutionForms

public static void getUseDilutionForms(AntibodyPrep a,
                                       DBUtil bioRoot,
                                       java.lang.StringBuffer b,
                                       int apbIndex)

Pumps out useDilution forms, should always have one with each Prep

getUseDilutionForm

public static void getUseDilutionForm(UseDilution u,
                                      java.lang.StringBuffer b,
                                      int index,
                                      int apbIndex,
                                      boolean lastForm)

Returns a UseDilutionNotes where the names are apended with apbIndex.index ie 0.0, 0.1, 0.2,,1.0,1.1...

getAntibodyReport

public static java.lang.String getAntibodyReport(AntibodyBean ab,
                                                 DBUtil bioRoot,
                                                 UserBean user,
                                                 boolean commonForm)

Returns an antibody report filled with the values in the bean.

getAntibodyPrepReports

public static void getAntibodyPrepReports(AntibodyBean ab,
                                          DBUtil bioRoot,
                                          java.lang.StringBuffer b,
                                          boolean commonForm)

getAntibodyPrepReport

public static void getAntibodyPrepReport(AntibodyPrep a,
                                         DBUtil bioRoot,
                                         java.lang.StringBuffer b,
                                         int index,
                                         boolean commonForm)

getUseDilutionReports

public static void getUseDilutionReports(AntibodyPrep a,
                                         DBUtil bioRoot,
                                         java.lang.StringBuffer b,
                                         int apbIndex,
                                         boolean commonForm)

Pumps out useDilution reports

getUseDilutionReport

public static void getUseDilutionReport(UseDilution u,
                                        java.lang.StringBuffer b,
                                        int index,
                                        int apbIndex)

writeTempFile

public static java.lang.String writeTempFile(java.lang.Object fileItemPoss,
                                             javax.servlet.http.HttpServletRequest request,
                                             java.lang.String directory)

Looks for an uploaded file, writes it to the directory with a tempRNDMWord_FileName, will return the name, or null, or 'Too big'

renameFile

public static java.lang.String renameFile(java.lang.String oldFileName,
                                          java.lang.String directory)

Copies an old file and renames it to tempRndmWrd_name. Returns null problems.