bioroot.plasmid
Class PlasmidBean

java.lang.Object
  extended bybioroot.ReagentBean
      extended bybioroot.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)