bioroot.oligo
Class OligoBean

java.lang.Object
  bioroot.ReagentBean
      bioroot.oligo.OligoBean

All Implemented Interfaces:

java.lang.Comparable

public class OligoBean

extends ReagentBean

Author:

nix Container for holding oligo information

Field Summary

Fields inherited from class bioroot.ReagentBean

log

Constructor Summary

OligoBean()

OligoBean(int id, DBUtil bioRoot)

OligoBean(java.sql.ResultSet results)

OligoBean(java.lang.String[] cells, IdNameMatch[] genes, IdNameMatch[] organisms, UserBean userBean, DBUtil bioRoot)
For bulk file upload should be 17? cells Name, Alias Oligo Sequence, Matching Gene Sequence, uM Stock Concentration, ng/uL Stock Concentration, Volume(uL), Purification, 0 1 2 3 4 5 6 7 Modifications, Orientation, Type, Storage Location, Availibility, Visibility, Handling Instructions, Target Gene Name, Organism, Notes 8 9 10 11 12 13 14 15 16 17

Method Summary

double	getBasicTm(java.lang.String seq)
java.lang.String	getConcentration()
java.lang.String	getConcentrationUnits()
double	getGC(java.lang.String seq)
int	getGeneId()
java.lang.String	getGeneName(DBUtil bioRoot)
java.lang.String	getGeneSequence()
java.lang.String	getHandlingInstructions()
int	getLength()
java.lang.String	getModifications()
double	getMW(java.lang.String seq)
double	getNearestNbrTm(java.lang.String seq) Returns -1 if non GATC's are found.
double	getNgUl()
java.lang.String	getOrientation()
java.lang.String	getPurification()
java.lang.String	getRestrictionCutSites(Enzyme[] enzymes)
java.lang.String	getSequence()
java.lang.String	getType()
double	getUM()
java.lang.String	getUMNgUl()
java.lang.String	getVolume()
boolean	isOligoNameUnique(DBUtil bioRoot) checks to see if oligo name is unique within labgroup, assumes a connection has been made
void	loadOligoBean(java.sql.ResultSet results)
void	setConcentration(java.lang.String d)
void	setConcentrationUnits(java.lang.String string)
void	setGeneId(int i)
void	setGeneName(java.lang.String string)
void	setGeneSequence(java.lang.String string)
void	setHandlingInstructions(java.lang.String string)
void	setModifications(java.lang.String string)
void	setNgUl(double d)
void	setOrientation(java.lang.String string)
void	setPurification(java.lang.String string)
void	setSequence(java.lang.String string)
void	setType(java.lang.String string)
void	setUM(double d)
void	setVolume(java.lang.String d)
boolean	submitNew(DBUtil bioRoot)
boolean	updateOld(DBUtil bioRoot, UserBean submitter)

Methods inherited from class bioroot.ReagentBean

appendMessages, canModifyAll, canModifyCommon, canView, compareTo, getAlias, getAvailability, getComments, getEditHistory, getGenericVisibility, getId, getLabGroupId, getLabGroupName, getLastUser, getLocation, getMessages, getName, getNotes, getOrderBy, getOrganismId, getOrganismName, getOrganization, getOwnerId, getOwnerName, getReference, getVisibility, isComplete, isReagentNameUnique, loadReagentBean, setAlias, setAvailability, setComments, setComplete, setEditHistory, setId, setLabGroupId, setLabGroupName, setLastUser, setLocation, setMessages, setName, setNotes, setOrderBy, setOrganismId, setOrganismName, setOwnerId, setOwnerName, setReference, setVisibility, updateCommonAccessFields

Methods inherited from class java.lang.Object

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

Constructor Detail

OligoBean

public OligoBean()

OligoBean

public OligoBean(int id,
                 DBUtil bioRoot)

OligoBean

public OligoBean(java.sql.ResultSet results)

OligoBean

public OligoBean(java.lang.String[] cells,
                 IdNameMatch[] genes,
                 IdNameMatch[] organisms,
                 UserBean userBean,
                 DBUtil bioRoot)

For bulk file upload should be 17? cells Name, Alias Oligo Sequence, Matching Gene Sequence, uM Stock Concentration, ng/uL Stock Concentration, Volume(uL), Purification, 0 1 2 3 4 5 6 7 Modifications, Orientation, Type, Storage Location, Availibility, Visibility, Handling Instructions, Target Gene Name, Organism, Notes 8 9 10 11 12 13 14 15 16 17

Method Detail

getMW

public double getMW(java.lang.String seq)

getGC

public double getGC(java.lang.String seq)

getLength

public int getLength()

getRestrictionCutSites

public java.lang.String getRestrictionCutSites(Enzyme[] enzymes)

getBasicTm

public double getBasicTm(java.lang.String seq)

getNearestNbrTm

public double getNearestNbrTm(java.lang.String seq)

Returns -1 if non GATC's are found.

getGeneName

public java.lang.String getGeneName(DBUtil bioRoot)

getGeneId

public int getGeneId()

getUMNgUl

public java.lang.String getUMNgUl()

getConcentrationUnits

public java.lang.String getConcentrationUnits()

setConcentrationUnits

public void setConcentrationUnits(java.lang.String string)

getConcentration

public java.lang.String getConcentration()

setConcentration

public void setConcentration(java.lang.String d)

getUM

public double getUM()

setNgUl

public void setNgUl(double d)

getNgUl

public double getNgUl()

setUM

public void setUM(double d)

loadOligoBean

public void loadOligoBean(java.sql.ResultSet results)

submitNew

public boolean submitNew(DBUtil bioRoot)

updateOld

public boolean updateOld(DBUtil bioRoot,
                         UserBean submitter)

isOligoNameUnique

public boolean isOligoNameUnique(DBUtil bioRoot)

checks to see if oligo name is unique within labgroup, assumes a connection has been made

getGeneSequence

public java.lang.String getGeneSequence()

getHandlingInstructions

public java.lang.String getHandlingInstructions()

getModifications

public java.lang.String getModifications()

getOrientation

public java.lang.String getOrientation()

getPurification

public java.lang.String getPurification()

getSequence

public java.lang.String getSequence()

getType

public java.lang.String getType()

getVolume

public java.lang.String getVolume()

setGeneName

public void setGeneName(java.lang.String string)

setGeneSequence

public void setGeneSequence(java.lang.String string)

setHandlingInstructions

public void setHandlingInstructions(java.lang.String string)

setModifications

public void setModifications(java.lang.String string)

setGeneId

public void setGeneId(int i)

setOrientation

public void setOrientation(java.lang.String string)

setPurification

public void setPurification(java.lang.String string)

setSequence

public void setSequence(java.lang.String string)

setType

public void setType(java.lang.String string)

setVolume

public void setVolume(java.lang.String d)