bioroot.plasmid
Class PlasmidBean

java.lang.Object
  bioroot.ReagentBean
      bioroot.plasmid.PlasmidBean

All Implemented Interfaces:

java.lang.Comparable

public class PlasmidBean

extends ReagentBean

Author:

nix Container for holding plasmid information

Field Summary

Fields inherited from class bioroot.ReagentBean

log

Constructor Summary

PlasmidBean()

PlasmidBean(int id, DBUtil bioRoot)

PlasmidBean(java.sql.ResultSet results)

PlasmidBean(java.lang.String[] cells, IdNameMatch[] genes, IdNameMatch[] organisms, IdNameMatch[] markerIDMatch, UserBean userBean, DBUtil bioRoot)
For bulk file upload should be 16 cells 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Name Alias Source Recipients Reference Gene Organism Markers StrainIds Location Concentration Volume Purification Availability Visibility Notes Sequence

Method Summary

int	compareTo(java.lang.Object obj)
java.lang.String	getConcentration()
java.lang.String	getFileName()
int	getGeneId()
java.lang.String	getGeneName(DBUtil bioRoot)
java.lang.String	getHotLinkedOligos() Returns HTML for of oligoMatches for display.
java.lang.String	getHotLinkedStrains(DBUtil bioRoot) Returns HTML strain names for display.
int	getLength()
java.lang.String[]	getMarkers(DBUtil bioRoot)
OligoMatch[]	getOligoMatches()
java.lang.String	getPlainTextOligos() Returns plain text of oligoMatches for archive.
java.lang.String	getPlainTextStrain() Returns plain text of strain ids for archive.
java.lang.String	getPurification()
java.lang.String	getRecipients()
java.lang.String	getRestrictionCutSites(Enzyme[] enzymes)
java.lang.String	getSequence()
java.lang.String	getSource()
java.lang.String[]	getStrainConcats(DBUtil bioRoot) Returns an array of id: strainName, or empty String[]{""} if there are none.
java.lang.String	getVolume()
boolean	isBlasted()
boolean	isPlasmidNameUnique(DBUtil bioRoot) checks to see if plasmid name is unique within labgroup, assumes a connection has been made
void	loadPlasmidBean(java.sql.ResultSet results)
boolean	saveMarkers(DBUtil bioRoot, boolean deleteOld)
boolean	saveStrainIds(DBUtil bioRoot, boolean deleteOld) Can delete old strainIds from PlasmidStrain table, and add new entries if any are present in the strainConcats.
void	setBlasted(boolean blasted)
void	setConcentration(java.lang.String ngUl)
void	setFileName(java.lang.String fileName)
void	setGeneId(int i)
void	setGeneName(java.lang.String string)
void	setMarkers(java.lang.String[] markers)
void	setOligoMatches(OligoMatch[] oligoMatches)
void	setPurification(java.lang.String string)
void	setRecipients(java.lang.String string)
void	setSequence(java.lang.String string)
void	setSource(java.lang.String source)
void	setStrainConcats(java.lang.String[] strainConcats)
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, 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

PlasmidBean

public PlasmidBean()

PlasmidBean

public PlasmidBean(int id,
                   DBUtil bioRoot)

PlasmidBean

public PlasmidBean(java.sql.ResultSet results)

PlasmidBean

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

For bulk file upload should be 16 cells 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Name Alias Source Recipients Reference Gene Organism Markers StrainIds Location Concentration Volume Purification Availability Visibility Notes Sequence

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

Overrides:

compareTo in class ReagentBean

getLength

public int getLength()

getRestrictionCutSites

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

getGeneName

public java.lang.String getGeneName(DBUtil bioRoot)

getMarkers

public java.lang.String[] getMarkers(DBUtil bioRoot)

setMarkers

public void setMarkers(java.lang.String[] markers)

saveMarkers

public boolean saveMarkers(DBUtil bioRoot,
                           boolean deleteOld)

getHotLinkedOligos

public java.lang.String getHotLinkedOligos()

Returns HTML for of oligoMatches for display.

getPlainTextOligos

public java.lang.String getPlainTextOligos()

Returns plain text of oligoMatches for archive.

setStrainConcats

public void setStrainConcats(java.lang.String[] strainConcats)

getStrainConcats

public java.lang.String[] getStrainConcats(DBUtil bioRoot)

Returns an array of id: strainName, or empty String[]{""} if there are none.

saveStrainIds

public boolean saveStrainIds(DBUtil bioRoot,
                             boolean deleteOld)

Can delete old strainIds from PlasmidStrain table, and add new entries if any are present in the strainConcats.

getHotLinkedStrains

public java.lang.String getHotLinkedStrains(DBUtil bioRoot)

Returns HTML strain names for display.

getPlainTextStrain

public java.lang.String getPlainTextStrain()

Returns plain text of strain ids for archive.

loadPlasmidBean

public void loadPlasmidBean(java.sql.ResultSet results)

submitNew

public boolean submitNew(DBUtil bioRoot)

updateOld

public boolean updateOld(DBUtil bioRoot,
                         UserBean submitter)

isPlasmidNameUnique

public boolean isPlasmidNameUnique(DBUtil bioRoot)

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

getPurification

public java.lang.String getPurification()

getSequence

public java.lang.String getSequence()

getVolume

public java.lang.String getVolume()

setGeneName

public void setGeneName(java.lang.String string)

setGeneId

public void setGeneId(int i)

setPurification

public void setPurification(java.lang.String string)

setSequence

public void setSequence(java.lang.String string)

setVolume

public void setVolume(java.lang.String d)

getGeneId

public int getGeneId()

getFileName

public java.lang.String getFileName()

setFileName

public void setFileName(java.lang.String fileName)

getConcentration

public java.lang.String getConcentration()

setConcentration

public void setConcentration(java.lang.String ngUl)

getSource

public java.lang.String getSource()

setSource

public void setSource(java.lang.String source)

setOligoMatches

public void setOligoMatches(OligoMatch[] oligoMatches)

getOligoMatches

public OligoMatch[] getOligoMatches()

isBlasted

public boolean isBlasted()

setBlasted

public void setBlasted(boolean blasted)

getRecipients

public java.lang.String getRecipients()

setRecipients

public void setRecipients(java.lang.String string)