org.openscience.nmrshiftdb.util
Class SubmittingData

java.lang.Object
  org.openscience.nmrshiftdb.util.SubmittingData

All Implemented Interfaces:

java.io.Serializable

public class SubmittingData
extends java.lang.Object
implements java.io.Serializable

This class is used for holding the data of a molecule and an assigned spectrum in the session while the user is doing the sumbmit

Author:

shk3

See Also:

Serialized Form

Field Summary

org.apache.torque.om.NumberKey	accept
(package private) java.lang.String	autonomeName
(package private) java.lang.String	casNumber
(package private) java.lang.String	chemName
(package private) DBSpectrumType	choosenSpectrumType
(package private) java.lang.String	comment
(package private) java.util.List<DBConditionType>	conditions
int	coordinatesetid3
java.lang.String[][]	couplings
int[]	dbatoms
private int	dbmol
(package private) boolean	doubleBondConfiguration
(package private) int	editSpectrum
boolean	enterconstants
private int	existingMoleculeId
(package private) java.util.ArrayList	existingMoleculeKeywords
(package private) java.util.ArrayList	existingSpectrumKeywords
int	fullfillsOrder
(package private) java.util.Map	identifiers
boolean	isChiralProv
(package private) boolean[]	isDoubleBondSpecified
(package private) java.lang.String	keepAssignmentEntries
(package private) int	level
(package private) java.util.List	literature
java.lang.String	literaturecomplete
int	literatureForIdentifiers
java.lang.String	literatureOld
(package private) char	measuredOrCalculated
org.openscience.cdk.interfaces.IMolecule	molcoord
(package private) java.lang.String	molecule
(package private) java.lang.String	moleculeKeywords
(package private) java.lang.String	moleculeLinks
private org.openscience.cdk.interfaces.IMolecule	moleculeWith3d
(package private) org.openscience.cdk.interfaces.IMolecule	molWithH
(package private) org.openscience.cdk.interfaces.IMolecule	molWithHCount
java.util.Map	multis
java.util.Map	newAtomNumbersMap
boolean	norenumber
boolean	noreview
(package private) java.lang.String	path
DBRawFile	rawfile
java.lang.String	reviewFlag
java.util.ArrayList	reviews
private org.openscience.cdk.interfaces.IRingSet	ringSet
java.lang.String	role
int	sendEmailUserId
java.lang.String	shiftlist
(package private) boolean	showpeakpicker
(package private) java.util.ArrayList<ValueTriple>	signalstable
java.lang.String	smilesChiralProv
java.lang.String	smilesNonChiralProv
private int	spectrumid
(package private) java.lang.String	spectrumKeywords
(package private) java.lang.String	spectrumLinks
java.util.Date	thisDate
java.lang.String	thisURL
int	thisUserId
java.lang.String	timeformatted

Constructor Summary

SubmittingData(java.lang.String path)
Constructor for the SubmittingData object

Method Summary

void	addToSignalstable(ValueTriple signal) Adds a signal (an ValueTriple) to the Signalstable attribute of the SubmittingData object
void	clearAssignments() Removes all assignments from signalstable.
private int	getAtomNumber(org.openscience.cdk.interfaces.IAtom atomcompare, org.openscience.cdk.interfaces.IAtomContainer ac) Gets the atom Number of an atom in a molecule by comparing the coordinates.
java.lang.String	getAutonomeName() Gets the autonomeName attribute of the SubmittingData object
java.lang.String	getCasNumber() Gets the casNumber attribute of the SubmittingData object
java.lang.String	getChemName() Gets the chemName attribute of the SubmittingData object
java.lang.String	getChemNameOnlyWithNewline() Gets the chemNameOnlyWithNewline attribute of the SubmittingData object
java.lang.String	getChemNameWithSemicolon() Gets the chemNameWithSemicolon attribute of the SubmittingData object
DBSpectrumType	getChoosenSpectrumType() Gets the choosenSpectrumType attribute of the SubmittingData object
java.lang.String	getComment() Gets the comment attribute of the SubmittingData object
java.util.List<DBConditionType>	getConditions() Gets the conditions attribute of the SubmittingData object, which is a ArrayList of DBConditionType objects
java.lang.String	getConfigurationString()
java.util.List	getConfirmShifts()
java.lang.String	getCoupling(java.lang.String ik) Gets couplings[i][k].
int	getDbmol()
boolean	getDoubleBondConfiguration() Gets the doubleBondConfiguration attribute of the SubmittingData object
int	getEditSpectrum() Gets the editSpectrum attribute of the SubmittingData object
int	getExistingMoleculeId()
java.util.ArrayList	getExistingMoleculeKeywords() Gets the existingMolecuelKeywords attribute of the SubmittingData object
java.util.ArrayList	getExistingSpectrumKeywords() Gets the existingSpectrumKeywords attribute of the SubmittingData object
java.lang.String	getFrequency()
java.util.Map	getIdentifiers() Gets the identifiers attribute of the SubmittingData object
boolean[]	getIsDoubleBondSpecified() Gets the isDoubleBondSpecified attribute of the SubmittingData object
java.lang.String	getKeepAssignmentEntries() Gets the keepAssignmentEntries attribute of the SubmittingData object
int	getLevel() Gets the level attribute of the SubmittingData object
java.util.List	getLiterature() Gets the literature attribute of the SubmittingData object
char	getMeasuredOrCalculated() Gets the measuredOrCalculated attribute of the SubmittingData object
java.lang.String	getMolecule() Gets the molecule attribute of the SubmittingData object
java.lang.String	getMoleculeKeywords() Gets the moleculeKeywords attribute of the SubmittingData object
java.lang.String	getMoleculeLinks() Gets the moleculeLink attribute of the SubmittingData object
java.lang.String	getMoleculeLinksAsLinks() Gets the moleculeLinks, formatted as html.
org.openscience.cdk.interfaces.IMolecule	getMolWithH() Gets the molWithH attribute of the SubmittingData object
org.openscience.cdk.interfaces.IMolecule	getMolWithHCount() Gets the molWithHCount attribute of the SubmittingData object
java.lang.String	getMultiplicity(java.lang.String atoms) Gets the multiplicity of a certain atom.
java.util.ArrayList	getSignalstable() Gets the signalstable attribute of the SubmittingData object
java.lang.String	getSpectrumForApplet() Calls getSpectrumForApplet(false).
java.lang.String	getSpectrumForApplet(boolean withMultiplicities) Return the spectrum in a String, formatted as needed for the spectrumApplet
int	getSpectrumid()
java.lang.String	getSpectrumKeywords() Gets the spectrumKeywords attribute of the SubmittingData object
java.lang.String	getSpectrumLinks() Gets the spectrumLink attribute of the SubmittingData object
java.lang.String	getSpectrumLinksAsLinks() Gets the spectrumLinks, formatted as html.
java.lang.String	getUnassignedSignals()
boolean	isAssignedToNone(org.openscience.cdk.interfaces.IAtom atom) Tells if an atom is assigned to no signal
boolean	isCalculated() Gets the calculated attribute of the SubmittingData object
boolean	isIsDoubleBondSpecifiedNull() Tells if the isDoubleBondSpecified attribute of the SubmittingData object is null (needed because velocity can't do a comparision to null)
boolean	isMeasured() Gets the measured attribute of the SubmittingData object
boolean	isShowpeakpicker()
private boolean	notYetAnyAssignments() Indicates that no assignemnts were done
void	replaceNumbersByAtoms(boolean standalone) Replaces numbers in signalstable by atoms (this is needed after using ParseUtils.parseSpectrumFromSpecFile).
void	save(int user, java.lang.String reviewFlag, java.lang.String URL, java.util.Date now, javax.servlet.ServletConfig servcon, int numberOfSpheres, boolean saveFromBulk) Saves this data to the database
void	save(javax.servlet.ServletConfig servCon) Saves this data to the database
private int	saveMolecule(org.openscience.cdk.interfaces.IMolecule mol, org.openscience.cdk.interfaces.IMolecule molWithH, java.util.Date now, java.lang.String casNumber, int userKey, java.lang.String chemName, java.lang.String moleculeLinks, java.lang.String smilesNonChiral, java.lang.String smilesChiral, boolean isChiral, javax.servlet.ServletConfig servcon, int numberOfSpheres, java.sql.Connection dbconn) Saves a molecule + bonds + atoms to the database
int	saveMoleculeOnly(java.lang.String mdl, org.apache.turbine.util.RunData runData, org.apache.jetspeed.om.security.turbine.TurbineUser user) Saves a molecule to db (no values need to be set before, but molecule properties may be set).
private int	saveSpectrum(java.util.Date now, java.util.List literature, int dbmol, int userKey, DBSpectrumType choosenSpectrumType, java.lang.String spectrumForApplet, java.util.List originalConditions, java.util.List signalstable, org.openscience.cdk.interfaces.IMolecule molWithH, java.lang.String reviewFlag, java.lang.String spectrumLinks, javax.servlet.ServletConfig servcon, DBMolecule existingMolecule, java.sql.Connection dbconn) Saves a spectrum + signals + the rest to the database
java.lang.String	serializeMe() Serializes itself to a String via JSX
void	setAutonomeName(java.lang.String name) Sets the autonomeName attribute of the SubmittingData object
void	setCalculated() Sets the calculated attribute of the SubmittingData object
void	setCasNumber(java.lang.String casNumber) Sets the casNumber attribute of the SubmittingData object
void	setChemName(java.lang.String chemName) Sets the chemName attribute of the SubmittingData object
void	setChoosenSpectrumType(DBSpectrumType spectype) Sets the choosenSpectrumType attribute of the SubmittingData object
void	setComment(java.lang.String comment) Sets the comment attribute of the SubmittingData object
void	setConditions(java.util.ArrayList<DBConditionType> v) Sets the conditions attribute of the SubmittingData object, needs to be a ArrayList of DBConditonType objects
void	setDoubleBondConfiguration(boolean bool) Sets the doubleBondConfiguration attribute of the SubmittingData object
void	setEditSpectrum(int spec) Sets the editSpectrum attribute of the SubmittingData object
void	setExistingMoleculeId(int exist) If you set this and the smilesNonChiralProv, smilesChiralProv, isChiralProv before save, we do not look for an esisting moleucle, but use this
void	setIdentifiers(java.util.Map i) Sets the identifiers attribute of the SubmittingData object
void	setIsDoubleBondSpecified(boolean[] isDoubleBondSpecified) Sets the isDoubleBondSpecified attribute of the SubmittingData object
void	setKeepAssignmentEntries(java.lang.String b) Sets the keepAssignmentEntries attribute of the SubmittingData object
void	setLevel(int level) Sets the level attribute of the SubmittingData object
void	setLiterature(java.util.List literature) Sets the literature attribute of the SubmittingData object
void	setMeasured() Sets the measured attribute of the SubmittingData object
int	setMol(java.lang.String moleculeparameter, boolean checkOnlyOneStructure, boolean changeOrder, boolean no3d) Sets all molecule related attributes, generating hydrogens.
int	setMol(java.lang.String moleculeparameter, org.openscience.cdk.interfaces.IMolecule withh, boolean checkOnlyOneStructure, boolean changeOrder, boolean no3d) Sets all molecule related attributes, taking the hydrogens from input.
void	setMoleculeKeywords(java.lang.String kw) Sets the moleculeKeywords attribute of the SubmittingData object
void	setMoleculeLinks(java.lang.String link) Sets the moleculeLink attribute of the SubmittingData object
private boolean	setMolWithH(org.openscience.cdk.interfaces.IMolecule molWithH) Sets the molWithH and the molWithHCount attribute of the SubmittingData object
void	setShowpeakpicker(boolean showpeakpicker)
void	setSignalstable(java.util.ArrayList v) Sets the signalstable attribute of the SubmittingData object
void	setSpectrumKeywords(java.lang.String kw) Sets the spectrumKeywords attribute of the SubmittingData object
void	setSpectrumLinks(java.lang.String link) Sets the spectrumLink attribute of the SubmittingData object

Methods inherited from class java.lang.Object

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

Field Detail

thisUserId

public int thisUserId

sendEmailUserId

public int sendEmailUserId

thisURL

public java.lang.String thisURL

thisDate

public java.util.Date thisDate

role

public java.lang.String role

reviews

public java.util.ArrayList reviews

reviewFlag

public java.lang.String reviewFlag

literatureOld

public java.lang.String literatureOld

smilesNonChiralProv

public java.lang.String smilesNonChiralProv

smilesChiralProv

public java.lang.String smilesChiralProv

isChiralProv

public boolean isChiralProv

newAtomNumbersMap

public java.util.Map newAtomNumbersMap

existingMoleculeId

private int existingMoleculeId

spectrumid

private int spectrumid

dbmol

private int dbmol

enterconstants

public boolean enterconstants

literaturecomplete

public java.lang.String literaturecomplete

shiftlist

public java.lang.String shiftlist

accept

public org.apache.torque.om.NumberKey accept

coordinatesetid3

public int coordinatesetid3

molcoord

public org.openscience.cdk.interfaces.IMolecule molcoord

noreview

public boolean noreview

level

int level

keepAssignmentEntries

java.lang.String keepAssignmentEntries

editSpectrum

int editSpectrum

dbatoms

public int[] dbatoms

path

java.lang.String path

ringSet

private org.openscience.cdk.interfaces.IRingSet ringSet

rawfile

public DBRawFile rawfile

showpeakpicker

boolean showpeakpicker

norenumber

public boolean norenumber

molecule

java.lang.String molecule

signalstable

java.util.ArrayList<ValueTriple> signalstable

chemName

java.lang.String chemName

conditions

java.util.List<DBConditionType> conditions

choosenSpectrumType

DBSpectrumType choosenSpectrumType

moleculeLinks

java.lang.String moleculeLinks

spectrumLinks

java.lang.String spectrumLinks

casNumber

java.lang.String casNumber

molWithHCount

org.openscience.cdk.interfaces.IMolecule molWithHCount

molWithH

org.openscience.cdk.interfaces.IMolecule molWithH

moleculeKeywords

java.lang.String moleculeKeywords

spectrumKeywords

java.lang.String spectrumKeywords

existingMoleculeKeywords

java.util.ArrayList existingMoleculeKeywords

existingSpectrumKeywords

java.util.ArrayList existingSpectrumKeywords

autonomeName

java.lang.String autonomeName

comment

java.lang.String comment

isDoubleBondSpecified

boolean[] isDoubleBondSpecified

doubleBondConfiguration

boolean doubleBondConfiguration

literature

java.util.List literature

identifiers

java.util.Map identifiers

measuredOrCalculated

char measuredOrCalculated

literatureForIdentifiers

public int literatureForIdentifiers

multis

public java.util.Map multis

couplings

public java.lang.String[][] couplings

fullfillsOrder

public int fullfillsOrder

timeformatted

public java.lang.String timeformatted

moleculeWith3d

private org.openscience.cdk.interfaces.IMolecule moleculeWith3d

Constructor Detail

SubmittingData

public SubmittingData(java.lang.String path)
               throws java.lang.Exception

Constructor for the SubmittingData object

Throws:

java.lang.Exception - Something wrong with the database

Method Detail

setChemName

public void setChemName(java.lang.String chemName)

Sets the chemName attribute of the SubmittingData object

Parameters:

chemName - The new chemName value

setCasNumber

public void setCasNumber(java.lang.String casNumber)

Sets the casNumber attribute of the SubmittingData object

Parameters:

casNumber - The new casNumber value

setLevel

public void setLevel(int level)

Sets the level attribute of the SubmittingData object

Parameters:

level - The new level value

setAutonomeName

public void setAutonomeName(java.lang.String name)

Sets the autonomeName attribute of the SubmittingData object

Parameters:

name - The new autonomeName value

setDoubleBondConfiguration

public void setDoubleBondConfiguration(boolean bool)

Sets the doubleBondConfiguration attribute of the SubmittingData object

Parameters:

bool - The new doubleBondConfiguration value

setIsDoubleBondSpecified

public void setIsDoubleBondSpecified(boolean[] isDoubleBondSpecified)

Sets the isDoubleBondSpecified attribute of the SubmittingData object

Parameters:

isDoubleBondSpecified - The new isDoubleBondSpecified value

setComment

public void setComment(java.lang.String comment)

Sets the comment attribute of the SubmittingData object

Parameters:

comment - The new comment value

setLiterature

public void setLiterature(java.util.List literature)

Sets the literature attribute of the SubmittingData object

Parameters:

literature - The new literature value

setConditions

public void setConditions(java.util.ArrayList<DBConditionType> v)

Sets the conditions attribute of the SubmittingData object, needs to be a ArrayList of DBConditonType objects

Parameters:

v - The new conditions value

setMoleculeLinks

public void setMoleculeLinks(java.lang.String link)

Sets the moleculeLink attribute of the SubmittingData object

Parameters:

link - The new moleculeLink value

setSpectrumLinks

public void setSpectrumLinks(java.lang.String link)

Sets the spectrumLink attribute of the SubmittingData object

Parameters:

link - The new spectrumLink value

setSignalstable

public void setSignalstable(java.util.ArrayList v)

Sets the signalstable attribute of the SubmittingData object

Parameters:

v - The new signalstable value

setKeepAssignmentEntries

public void setKeepAssignmentEntries(java.lang.String b)

Sets the keepAssignmentEntries attribute of the SubmittingData object

Parameters:

b - The new keepAssignmentEntries value

setMeasured

public void setMeasured()
                 throws java.lang.Exception

Sets the measured attribute of the SubmittingData object

Throws:

java.lang.Exception - Description of Exception

setCalculated

public void setCalculated()
                   throws java.lang.Exception

Sets the calculated attribute of the SubmittingData object

Throws:

java.lang.Exception - Description of Exception

getConfigurationString

public java.lang.String getConfigurationString()

getUnassignedSignals

public java.lang.String getUnassignedSignals()

getConfirmShifts

public java.util.List getConfirmShifts()
                                throws java.lang.Exception

Throws:

java.lang.Exception

setIdentifiers

public void setIdentifiers(java.util.Map i)

Sets the identifiers attribute of the SubmittingData object

Parameters:

i - The new identifiers value

setChoosenSpectrumType

public void setChoosenSpectrumType(DBSpectrumType spectype)
                            throws java.lang.Exception

Sets the choosenSpectrumType attribute of the SubmittingData object

Parameters:

spectype - The new choosenSpectrumType value

Throws:

java.lang.Exception - Description of Exception

setMol

public int setMol(java.lang.String moleculeparameter,
                  org.openscience.cdk.interfaces.IMolecule withh,
                  boolean checkOnlyOneStructure,
                  boolean changeOrder,
                  boolean no3d)
           throws org.openscience.cdk.exception.CDKException,
                  java.io.IOException,
                  java.lang.Exception

Sets all molecule related attributes, taking the hydrogens from input.

Parameters:

moleculeparameter - The molecule as mdl file.

withh - The molecule with all Hs

checkOnlyOneStructure - Perform check if it is only one structure.

changeOrder - true=Change oder of atoms to cs go first, Hs last, false=leave as is.

no3d - generate 2d coordinates from 3d if true

Returns:

0=all OK, 1=empty file, 2=NO2 group replaced, 3=multiple structures.

Throws:

org.openscience.cdk.exception.CDKException - Description of Exception.

java.io.IOException - Description of Exception.

java.lang.Exception - Description of Exception.

setMol

public int setMol(java.lang.String moleculeparameter,
                  boolean checkOnlyOneStructure,
                  boolean changeOrder,
                  boolean no3d)
           throws org.openscience.cdk.exception.CDKException,
                  java.io.IOException,
                  java.lang.Exception

Sets all molecule related attributes, generating hydrogens.

Parameters:

moleculeparameter - The molecule as mdl file.

checkOnlyOneStructure - Perform check if it is only one structure.

changeOrder - true=Change oder of atoms to cs go first, Hs last, false=leave as is.

no3d - generate 2d coordinates from 3d if true

Returns:

0=all OK, 1=empty file, 2=NO2 group replaced, 3=multiple structures.

Throws:

org.openscience.cdk.exception.CDKException - Description of Exception.

java.io.IOException - Description of Exception.

java.lang.Exception - Description of Exception.

setEditSpectrum

public void setEditSpectrum(int spec)

Sets the editSpectrum attribute of the SubmittingData object

Parameters:

spec - The new editSpectrum value

setMoleculeKeywords

public void setMoleculeKeywords(java.lang.String kw)

Sets the moleculeKeywords attribute of the SubmittingData object

Parameters:

kw - The new moleculeKeywords value

setSpectrumKeywords

public void setSpectrumKeywords(java.lang.String kw)

Sets the spectrumKeywords attribute of the SubmittingData object

Parameters:

kw - The new spectrumKeywords value

getIdentifiers

public java.util.Map getIdentifiers()

Gets the identifiers attribute of the SubmittingData object

Returns:

The identifiers value

getMeasuredOrCalculated

public char getMeasuredOrCalculated()

Gets the measuredOrCalculated attribute of the SubmittingData object

Returns:

The measuredOrCalculated value

getDoubleBondConfiguration

public boolean getDoubleBondConfiguration()

Gets the doubleBondConfiguration attribute of the SubmittingData object

Returns:

The doubleBondConfiguration value

getIsDoubleBondSpecified

public boolean[] getIsDoubleBondSpecified()

Gets the isDoubleBondSpecified attribute of the SubmittingData object

Returns:

The isDoubleBondSpecified value

isIsDoubleBondSpecifiedNull

public boolean isIsDoubleBondSpecifiedNull()

Tells if the isDoubleBondSpecified attribute of the SubmittingData object is null (needed because velocity can't do a comparision to null)

Returns:

The isDoubleBondSpecifiedNull value

getEditSpectrum

public int getEditSpectrum()

Gets the editSpectrum attribute of the SubmittingData object

Returns:

The editSpectrum value

getMoleculeKeywords

public java.lang.String getMoleculeKeywords()

Gets the moleculeKeywords attribute of the SubmittingData object

Returns:

The molecuelKeywords value

getExistingMoleculeKeywords

public java.util.ArrayList getExistingMoleculeKeywords()

Gets the existingMolecuelKeywords attribute of the SubmittingData object

Returns:

The existingMolecuelKeywords value

getSpectrumKeywords

public java.lang.String getSpectrumKeywords()

Gets the spectrumKeywords attribute of the SubmittingData object

Returns:

The spectrumKeywords value

getAutonomeName

public java.lang.String getAutonomeName()

Gets the autonomeName attribute of the SubmittingData object

Returns:

The autonomeName value

getComment

public java.lang.String getComment()

Gets the comment attribute of the SubmittingData object

Returns:

The comment value

getExistingSpectrumKeywords

public java.util.ArrayList getExistingSpectrumKeywords()

Gets the existingSpectrumKeywords attribute of the SubmittingData object

Returns:

The existingSpectrumKeywords value

getChemName

public java.lang.String getChemName()

Gets the chemName attribute of the SubmittingData object

Returns:

The chemName value

getChemNameWithSemicolon

public java.lang.String getChemNameWithSemicolon()

Gets the chemNameWithSemicolon attribute of the SubmittingData object

Returns:

The chemNameWithSemicolon value

getChemNameOnlyWithNewline

public java.lang.String getChemNameOnlyWithNewline()

Gets the chemNameOnlyWithNewline attribute of the SubmittingData object

Returns:

The chemNameOnlyWithNewline value

getCasNumber

public java.lang.String getCasNumber()

Gets the casNumber attribute of the SubmittingData object

Returns:

The casNumber value

getLevel

public int getLevel()

Gets the level attribute of the SubmittingData object

Returns:

The level value

getLiterature

public java.util.List getLiterature()

Gets the literature attribute of the SubmittingData object

Returns:

The literature value

getConditions

public java.util.List<DBConditionType> getConditions()

Gets the conditions attribute of the SubmittingData object, which is a ArrayList of DBConditionType objects

Returns:

The conditions value

getMolecule

public java.lang.String getMolecule()

Gets the molecule attribute of the SubmittingData object

Returns:

The molecule value

getMoleculeLinks

public java.lang.String getMoleculeLinks()

Gets the moleculeLink attribute of the SubmittingData object

Returns:

The moleculeLink value

getSpectrumLinksAsLinks

public java.lang.String getSpectrumLinksAsLinks()

Gets the spectrumLinks, formatted as html.

Returns:

The spectrumLink value

getMoleculeLinksAsLinks

public java.lang.String getMoleculeLinksAsLinks()

Gets the moleculeLinks, formatted as html.

Returns:

The moleculeLink value

getSpectrumLinks

public java.lang.String getSpectrumLinks()

Gets the spectrumLink attribute of the SubmittingData object

Returns:

The spectrumLink value

getSignalstable

public java.util.ArrayList getSignalstable()

Gets the signalstable attribute of the SubmittingData object

Returns:

The signalstable value

getKeepAssignmentEntries

public java.lang.String getKeepAssignmentEntries()

Gets the keepAssignmentEntries attribute of the SubmittingData object

Returns:

The keepAssignmentEntries value

getChoosenSpectrumType

public DBSpectrumType getChoosenSpectrumType()

Gets the choosenSpectrumType attribute of the SubmittingData object

Returns:

The choosenSpectrumType value

getMolWithHCount

public org.openscience.cdk.interfaces.IMolecule getMolWithHCount()

Gets the molWithHCount attribute of the SubmittingData object

Returns:

The molWithHCount value

getMolWithH

public org.openscience.cdk.interfaces.IMolecule getMolWithH()

Gets the molWithH attribute of the SubmittingData object

Returns:

The molWithH value

isMeasured

public boolean isMeasured()

Gets the measured attribute of the SubmittingData object

Returns:

The measured value

isCalculated

public boolean isCalculated()

Gets the calculated attribute of the SubmittingData object

Returns:

The calculated value

isAssignedToNone

public boolean isAssignedToNone(org.openscience.cdk.interfaces.IAtom atom)

Tells if an atom is assigned to no signal

Parameters:

atom - The numbe of the atom in the mol

Returns:

false=is assigned, true=not assigned

getSpectrumForApplet

public java.lang.String getSpectrumForApplet()

Calls getSpectrumForApplet(false).

Returns:

The spectrumForApplet value

getSpectrumForApplet

public java.lang.String getSpectrumForApplet(boolean withMultiplicities)

Return the spectrum in a String, formatted as needed for the spectrumApplet

Parameters:

withMultiplicities - Shall S D T Q get appended?

Returns:

Description of the Returned Value

getCoupling

public java.lang.String getCoupling(java.lang.String ik)

Gets couplings[i][k].

Parameters:

ik - row count,column count.

Returns:

The coupling value.

getMultiplicity

public java.lang.String getMultiplicity(java.lang.String atoms)

Gets the multiplicity of a certain atom.

Parameters:

atoms - The atom number as in molWithH as string.

Returns:

The multiplicity value.

clearAssignments

public void clearAssignments()

Removes all assignments from signalstable.

addToSignalstable

public void addToSignalstable(ValueTriple signal)

Adds a signal (an ValueTriple) to the Signalstable attribute of the SubmittingData object

Parameters:

signal - The signal to be added to the Signalstable attribute

save

public void save(javax.servlet.ServletConfig servCon)
          throws java.lang.Exception

Saves this data to the database

Parameters:

servcon - The current ServletConfig

Throws:

java.lang.Exception - Problems with database

save

public void save(int user,
                 java.lang.String reviewFlag,
                 java.lang.String URL,
                 java.util.Date now,
                 javax.servlet.ServletConfig servcon,
                 int numberOfSpheres,
                 boolean saveFromBulk)
          throws java.lang.Exception

Saves this data to the database

Parameters:

user - The logged in user

reviewFlag - The review flag the new spectrum is supposed to have.

URL - The URL of the machine the program runs on

now - The current date

servcon - The current ServletConfig

numberOfSpheres - The number of spheres to use (as in nmrshiftdb.properties)

saveFromBulk - Is this a save from a bulkload ?

Throws:

java.lang.Exception - Problems with database

serializeMe

public java.lang.String serializeMe()
                             throws java.io.IOException

Serializes itself to a String via JSX

Returns:

This serialized

Throws:

java.io.IOException - Something wrong in JSX

replaceNumbersByAtoms

public void replaceNumbersByAtoms(boolean standalone)
                           throws java.lang.Exception

Replaces numbers in signalstable by atoms (this is needed after using ParseUtils.parseSpectrumFromSpecFile).

Parameters:

standalone - Description of Parameter

Throws:

java.lang.Exception - Description of Exception

saveMoleculeOnly

public int saveMoleculeOnly(java.lang.String mdl,
                            org.apache.turbine.util.RunData runData,
                            org.apache.jetspeed.om.security.turbine.TurbineUser user)
                     throws java.lang.Exception

Saves a molecule to db (no values need to be set before, but molecule properties may be set).

Parameters:

mdl - The molecule to save.

runData - The current runData object.

user - The user this molecule is expected to belong to.

Returns:

The saved molecule or this molecule from db, if already existing.

Throws:

java.lang.Exception - Databae problems.

setMolWithH

private boolean setMolWithH(org.openscience.cdk.interfaces.IMolecule molWithH)
                     throws java.lang.Exception

Sets the molWithH and the molWithHCount attribute of the SubmittingData object

Parameters:

molWithH - The new molWithH value

Returns:

Description of the Returned Value

Throws:

java.lang.Exception - Description of Exception

getAtomNumber

private int getAtomNumber(org.openscience.cdk.interfaces.IAtom atomcompare,
                          org.openscience.cdk.interfaces.IAtomContainer ac)

Gets the atom Number of an atom in a molecule by comparing the coordinates.

Parameters:

atom - The atom.

ac - The molecule.

Returns:

The atomNumber value

notYetAnyAssignments

private boolean notYetAnyAssignments()

Indicates that no assignemnts were done

Returns:

true=no assignemnts, yes=some assignments

saveMolecule

private int saveMolecule(org.openscience.cdk.interfaces.IMolecule mol,
                         org.openscience.cdk.interfaces.IMolecule molWithH,
                         java.util.Date now,
                         java.lang.String casNumber,
                         int userKey,
                         java.lang.String chemName,
                         java.lang.String moleculeLinks,
                         java.lang.String smilesNonChiral,
                         java.lang.String smilesChiral,
                         boolean isChiral,
                         javax.servlet.ServletConfig servcon,
                         int numberOfSpheres,
                         java.sql.Connection dbconn)
                  throws java.lang.Exception

Saves a molecule + bonds + atoms to the database

Parameters:

mol - The molecule as a cdk molecule without the implicit hs, but with HydrogenCount set

molWithH - The molecule as a cdk molecule with the implicit hs

now - The date

casNumber - The cas number

userKey - The submitter

chemName - The chemical names, as typed by the user

moleculeLinks - The links for the molecule

isChiral - Is there any chirality in the molecule

servcon - The current ServletConfig

smilesNonChiral - Description of Parameter

smilesChiral - Description of Parameter

numberOfSpheres - The number of spheres to use (as in nmrshiftdb.properties)

dbconn - Description of Parameter

Returns:

The saved molecule

Throws:

java.lang.Exception - Something wrong with the database

saveSpectrum

private int saveSpectrum(java.util.Date now,
                         java.util.List literature,
                         int dbmol,
                         int userKey,
                         DBSpectrumType choosenSpectrumType,
                         java.lang.String spectrumForApplet,
                         java.util.List originalConditions,
                         java.util.List signalstable,
                         org.openscience.cdk.interfaces.IMolecule molWithH,
                         java.lang.String reviewFlag,
                         java.lang.String spectrumLinks,
                         javax.servlet.ServletConfig servcon,
                         DBMolecule existingMolecule,
                         java.sql.Connection dbconn)
                  throws java.lang.Exception

Saves a spectrum + signals + the rest to the database

Parameters:

now - The date

literature - Literature

dbmol - The Molecule the spectrum is assigned to

userKey - The submitter

choosenSpectrumType - The spectrum type of this spectrum

spectrumForApplet - The spectrum as given by the getSpectrumForApplet method of subData

originalConditions - The conditions as in the conditions ArrayList of submittingData

signalstable - The signals as a ArrayList of valueTriples

molWithH - The molecule as cdk molecule including implicit hs

reviewFlag - The value the reviewFlag should be set to

spectrumLinks - The links for the spectrum

servcon - The current ServletConfig

existingMolecule - Description of Parameter

dbconn - Description of Parameter

Returns:

The saved spectrum

Throws:

java.lang.Exception - Something wrong with the database

getDbmol

public int getDbmol()

Returns:

The id used for saving the molecule in MOLECULE table

getSpectrumid

public int getSpectrumid()

Returns:

The id used for saving the spectrum in SPECTRUM table

getExistingMoleculeId

public int getExistingMoleculeId()

Returns:

If no new entry was put in MOLECULE, this will contain the id of the existing entry used (if new entry 0)

setExistingMoleculeId

public void setExistingMoleculeId(int exist)

If you set this and the smilesNonChiralProv, smilesChiralProv, isChiralProv before save, we do not look for an esisting moleucle, but use this

Parameters:

exist - the id of the existing molecule

isShowpeakpicker

public boolean isShowpeakpicker()

setShowpeakpicker

public void setShowpeakpicker(boolean showpeakpicker)

getFrequency

public java.lang.String getFrequency()