org.openscience.nmrshiftdb.om
Class DBSpectrum

java.lang.Object
  org.apache.torque.om.BaseObject
      org.openscience.nmrshiftdb.om.BaseDBSpectrum
          org.openscience.nmrshiftdb.om.DBSpectrum

All Implemented Interfaces:

java.io.Serializable, org.apache.torque.om.Persistent

public class DBSpectrum
extends BaseDBSpectrum
implements org.apache.torque.om.Persistent

You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.

Author:

shk3

See Also:

Serialized Form

Field Summary

(package private) java.text.DecimalFormat	format
(package private) int	intensities
(package private) java.util.List	keywordsVector
(package private) java.util.List	literaturesNew
(package private) java.util.List	measurementConditions
(package private) java.util.Vector	options
(package private) int	otherspectrastringsize
boolean	predict
org.apache.turbine.util.RunData	runData Description of the Field
(package private) java.util.Map<java.lang.Float,java.lang.Float>	searchSignalMap
(package private) static long	serialVersionUID
(package private) double	similarity
(package private) java.lang.StringBuffer	unusedtext

Fields inherited from class org.openscience.nmrshiftdb.om.BaseDBSpectrum

collDBCouplings, collDBRawFileDBSpectrums, collDBSignals, collDBSpectrumDBConditions, collDBSpectrumDBKeywords, collDBSpectrumDBLiteratures, collDBSpectrumHyperlinks, collDBUserDBSpectrumEdits, collDBUserDBSpectrumMarks, collDBUserDBSpectrums

Fields inherited from class org.apache.torque.om.BaseObject

NEW_ID

Constructor Summary

DBSpectrum()

Method Summary

void	addMark(int mark, org.apache.turbine.om.security.User user, java.lang.String comment) Adds a mark to this DBSpectrum.
void	delete(java.sql.Connection dbconn, boolean doMolecule) Deletes this spectrum plus all associated rows.
java.util.Date	getAsssignedDate() Gets the Date the last assignment of the DBSpectrum object took place
nu.xom.Element	getCmlSpect() Gets this spectrum as cmlSpect.
java.lang.String	getCommentAsString() Gets the comment attribute of the DBSpectrum object
java.lang.String	getConditionType() Gets the condition type of this DBSpectrum object
org.apache.jetspeed.om.security.turbine.TurbineUser	getContributor() Gets the contributor of this DBSpectrum object
DBSpectrum	getCurrentSpectrum() Gives you the current spectrum of the edit chain of this spectrum.
int	getDisplaymark() Returns the mark necessary for a spectrum to be displayed
java.lang.String	getEmailOfAsssignedReviewer() Gets the email of the last reviewer the DBSpectrum object was assigned to
java.lang.String	getFrequency()
java.lang.String	getKeywords() Gets the keywords attribute of the DBSpectrum object.
java.lang.String	getKeywords(boolean separatedByNewline) Gets the keywords attribute of the DBSpectrum object.
java.util.List	getLinks() Gets the links of the DBSpectrum object
java.lang.String	getLinksAsString() Gets the links of the DBSpectrum object as a string
java.util.List	getLiteraturesNew() Gets the DBLiterature objects of the DBSpectrum object
int	getMark() Gets the mark of the DBSpectrum object
java.lang.String	getMarkComment() Gets the Comments for marks of the DBSpectrum object.
private int	getMdlNumberPlus1(DBAtom atom, DBAtom[] atoms) Gets the mdl number of an atom, similar to getMdlNumberPlus1 in DBAtom, but much faster for repeated calls
SubmittingData	getMeAsSubmittingData(boolean useUser, java.lang.String path, boolean no3d) This makes a submittingData object populated with the values from this spectrum and its molecule.
java.util.List	getMeasurementConditions() Gets the Conditions of this DBSpectrum object
java.util.List	getMeasurementConditions(java.sql.Connection dbconn) Gets the Conditions of this DBSpectrum object
java.lang.String	getMeasurementConditionValueWithName(java.lang.String name)
DBCondition	getMeasurementConditionWithName(java.lang.String name) Gets the value of a certain condition of this DBSpectrum object
DBCondition	getMeasurementConditionWithName(java.lang.String name, java.sql.Connection dbconn) Gets the value of a certain condition of this DBSpectrum object
java.lang.String	getNameOfAsssignedReviewer() Gets the name of the last reviwer the DBSpectrum object was assigned to
java.util.Vector	getOptions() Gets the shifts table for this spectrum.
java.lang.String	getOtherSpectraString(int atomNumber)
java.lang.String	getOtherSpectraStringHeader()
int	getOtherSpectraStringSize()
java.util.List	getReviewAssignments() Gets the DBUserDBSpectrum objects related with this spectrum
private float[]	getShifts(int atomNumber) Gets the shifts of a certain atom in this spectrum.
private float[]	getShifts(int atomNumber, DBMolecule mol) Gets the shifts of a certain atom in this spectrum.
private java.util.List	getSignals(int atomNumber) Gets the shifts of a certain atom in this spectrum.
private java.util.List	getSignals(int atomNumber, DBMolecule mol) Gets the shifts of a certain atom in this spectrum.
double	getSimilarity() Returns the similarity in percent between this spectrum and another spectrum, set by initSimilarity
double	getSimilarityFormatted() Returns the similarity with two digits after .
java.lang.String	getSpecfile() Get the Specfile
java.lang.String	getSpecfileOld()
java.lang.String	getSpectrumForApplet() Gets the specFile attribute of the DBSpectrum object as a string
java.lang.String	getSpectrumForAppletNewFormat() Gets the spectrum in the format needed for the new spectrumapplet (R 1.0).
java.lang.String	getSpectrumForAppletNewFormat(DBAtom[] atoms, org.openscience.cdk.interfaces.IMolecule cdkmol) Gets the spectrum in the format needed for the new spectrumapplet (R 1.0).
java.lang.String	getSpectrumForAppletWithMultis()
java.lang.String	getSpectrumTypeName() Gets the spectrumType name of the DBSpectrum object
java.lang.String	getUnassignedText() Gives a string with the unassigned shifts in this spectrum, "" if none.
java.lang.String	getUnusedText() Returns a text telling unsed spectra.
boolean	hasAnyIdentifier() Tells if there is any atom identifier for this spectrum.
boolean	hasAnyIntensities() Tells if any signal in this spectrum has an intensity != 0.
java.util.Map	initSimilarity(java.util.List otherSignalsL, boolean isSubSpectrum) Sets the similarity between this and another spectrum
boolean	isSimilarityNot0() Tells if the similarity of this spectrum is zero or not

Methods inherited from class org.openscience.nmrshiftdb.om.BaseDBSpectrum

addDBCoupling, addDBRawFileDBSpectrum, addDBSignal, addDBSpectrumDBCondition, addDBSpectrumDBKeyword, addDBSpectrumDBLiterature, addDBSpectrumHyperlink, addDBUserDBSpectrum, addDBUserDBSpectrumEdit, addDBUserDBSpectrumMark, copy, copyInto, getByName, getByPeerName, getByPosition, getComment, getCommentSoundex, getDate, getDBCouplings, getDBCouplings, getDBCouplings, getDBCouplings, getDBCouplingsJoinDBAtomRelatedByAtomId1, getDBCouplingsJoinDBAtomRelatedByAtomId2, getDBCouplingsJoinDBSpectrum, getDBMolecule, getDBRawFileDBSpectrums, getDBRawFileDBSpectrums, getDBRawFileDBSpectrums, getDBRawFileDBSpectrums, getDBRawFileDBSpectrumsJoinDBRawFile, getDBRawFileDBSpectrumsJoinDBSpectrum, getDBSignals, getDBSignals, getDBSignals, getDBSignals, getDBSignalsJoinDBSpectrum, getDBSpectrumDBConditions, getDBSpectrumDBConditions, getDBSpectrumDBConditions, getDBSpectrumDBConditions, getDBSpectrumDBConditionsJoinDBCondition, getDBSpectrumDBConditionsJoinDBSpectrum, getDBSpectrumDBKeywords, getDBSpectrumDBKeywords, getDBSpectrumDBKeywords, getDBSpectrumDBKeywords, getDBSpectrumDBKeywordsJoinDBKeyword, getDBSpectrumDBKeywordsJoinDBSpectrum, getDBSpectrumDBLiteratures, getDBSpectrumDBLiteratures, getDBSpectrumDBLiteratures, getDBSpectrumDBLiteratures, getDBSpectrumDBLiteraturesJoinDBLiterature, getDBSpectrumDBLiteraturesJoinDBSpectrum, getDBSpectrumHyperlinks, getDBSpectrumHyperlinks, getDBSpectrumHyperlinks, getDBSpectrumHyperlinks, getDBSpectrumHyperlinksJoinDBSpectrum, getDBSpectrumType, getDBUserDBSpectrumEdits, getDBUserDBSpectrumEdits, getDBUserDBSpectrumEdits, getDBUserDBSpectrumEdits, getDBUserDBSpectrumEditsJoinDBSpectrum, getDBUserDBSpectrumEditsJoinNmrshiftdbUser, getDBUserDBSpectrumMarks, getDBUserDBSpectrumMarks, getDBUserDBSpectrumMarks, getDBUserDBSpectrumMarks, getDBUserDBSpectrumMarksJoinDBSpectrum, getDBUserDBSpectrumMarksJoinNmrshiftdbUser, getDBUserDBSpectrums, getDBUserDBSpectrums, getDBUserDBSpectrums, getDBUserDBSpectrums, getDBUserDBSpectrumsJoinDBSpectrum, getDBUserDBSpectrumsJoinNmrshiftdbUser, getFieldNames, getFingerprint, getLiterature, getLiteratureSoundex, getMoleculeId, getNmrshiftdbUser, getPeer, getPrimaryKey, getReviewFlag, getReviewKey, getSimpleSpecfile, getSpectrumId, getSpectrumTypeId, getUserId, initDBCouplings, initDBRawFileDBSpectrums, initDBSignals, initDBSpectrumDBConditions, initDBSpectrumDBKeywords, initDBSpectrumDBLiteratures, initDBSpectrumHyperlinks, initDBUserDBSpectrumEdits, initDBUserDBSpectrumMarks, initDBUserDBSpectrums, save, save, save, setComment, setCommentSoundex, setDate, setDBMolecule, setDBMoleculeKey, setDBSpectrumType, setDBSpectrumTypeKey, setFingerprint, setLiterature, setLiteratureSoundex, setMoleculeId, setNmrshiftdbUser, setNmrshiftdbUserKey, setPrimaryKey, setPrimaryKey, setReviewFlag, setReviewKey, setSimpleSpecfile, setSpecfile, setSpectrumId, setSpectrumTypeId, setUserId, toString

Methods inherited from class org.apache.torque.om.BaseObject

equals, equals, getLog, hashCode, isModified, isNew, log, resetModified, setModified, setNew, setPrimaryKey

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.apache.torque.om.Persistent

getPrimaryKey, isModified, isNew, save, save, save, setModified, setNew, setPrimaryKey, setPrimaryKey

Field Detail

serialVersionUID

static final long serialVersionUID

See Also:

Constant Field Values

runData

public org.apache.turbine.util.RunData runData

Description of the Field

predict

public boolean predict

measurementConditions

java.util.List measurementConditions

similarity

double similarity

searchSignalMap

java.util.Map<java.lang.Float,java.lang.Float> searchSignalMap

intensities

int intensities

options

java.util.Vector options

unusedtext

java.lang.StringBuffer unusedtext

format

java.text.DecimalFormat format

literaturesNew

java.util.List literaturesNew

keywordsVector

java.util.List keywordsVector

otherspectrastringsize

int otherspectrastringsize

Constructor Detail

DBSpectrum

public DBSpectrum()

Method Detail

getSpecfileOld

public java.lang.String getSpecfileOld()

getSpecfile

public java.lang.String getSpecfile()

Description copied from class: BaseDBSpectrum

Get the Specfile

Overrides:

getSpecfile in class BaseDBSpectrum

Returns:

String

getConditionType

public java.lang.String getConditionType()
                                  throws java.lang.Exception

Gets the condition type of this DBSpectrum object

Returns:

The conditionType, "m"=measured spectrum, "c"=calculatedSpectrum

Throws:

java.lang.Exception - Description of Exception

getLinks

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

Gets the links of the DBSpectrum object

Returns:

The links

Throws:

java.lang.Exception - Database problems

getSimilarity

public double getSimilarity()

Returns the similarity in percent between this spectrum and another spectrum, set by initSimilarity

Returns:

A double from 0 to 100

isSimilarityNot0

public boolean isSimilarityNot0()

Tells if the similarity of this spectrum is zero or not

Returns:

The similarityNot0 value

getSimilarityFormatted

public double getSimilarityFormatted()

Returns the similarity with two digits after .

Returns:

A double from 0 to 100

getOptions

public java.util.Vector getOptions()
                            throws java.lang.Exception

Gets the shifts table for this spectrum. This is a vector of ValuesForVelocityBean objects. In case the runData object is set a prediction is done.

Returns:

The shifts table.

Throws:

java.lang.Exception - Database problems.

getMdlNumberPlus1

private int getMdlNumberPlus1(DBAtom atom,
                              DBAtom[] atoms)
                       throws NmrshiftdbException

Gets the mdl number of an atom, similar to getMdlNumberPlus1 in DBAtom, but much faster for repeated calls

Parameters:

atom - The atom to ask for

atoms - All atoms of this molecule, as you get them with DBMolecule.getAtomsAsArrayInMDLOrder

Returns:

The mdl number

Throws:

NmrshiftdbException - No such atom in atoms. This means the atoms passed where from another molecule than the atom.

getMeasurementConditions

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

Gets the Conditions of this DBSpectrum object

Returns:

A vector of DBConditions

Throws:

java.lang.Exception - Description of Exception

getMeasurementConditions

public java.util.List getMeasurementConditions(java.sql.Connection dbconn)
                                        throws java.lang.Exception

Gets the Conditions of this DBSpectrum object

Returns:

A vector of DBConditions

Throws:

java.lang.Exception - Description of Exception

getMeasurementConditionWithName

public DBCondition getMeasurementConditionWithName(java.lang.String name)
                                            throws java.lang.Exception

Gets the value of a certain condition of this DBSpectrum object

Parameters:

name - The name of the conditon to tell.

Returns:

The value.

Throws:

java.lang.Exception - Description of Exception.

getFrequency

public java.lang.String getFrequency()
                              throws java.lang.Exception

Throws:

java.lang.Exception

getMeasurementConditionWithName

public DBCondition getMeasurementConditionWithName(java.lang.String name,
                                                   java.sql.Connection dbconn)
                                            throws java.lang.Exception

Gets the value of a certain condition of this DBSpectrum object

Parameters:

name - The name of the conditon to tell.

Returns:

The value.

Throws:

java.lang.Exception - Description of Exception.

getMeasurementConditionValueWithName

public java.lang.String getMeasurementConditionValueWithName(java.lang.String name)
                                                      throws java.lang.Exception

Throws:

java.lang.Exception

getSpectrumForApplet

public java.lang.String getSpectrumForApplet()

Gets the specFile attribute of the DBSpectrum object as a string

Returns:

The specFile value

getContributor

public org.apache.jetspeed.om.security.turbine.TurbineUser getContributor()
                                                                   throws java.lang.Exception

Gets the contributor of this DBSpectrum object

Returns:

The contributor value

Throws:

java.lang.Exception - Something went wrong with reading the database

getSpectrumForAppletWithMultis

public java.lang.String getSpectrumForAppletWithMultis()
                                                throws java.lang.Exception

Throws:

java.lang.Exception

getSpectrumTypeName

public java.lang.String getSpectrumTypeName()
                                     throws java.lang.Exception

Gets the spectrumType name of the DBSpectrum object

Returns:

The spectrumType name value

Throws:

java.lang.Exception - Problems with reading database

getReviewAssignments

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

Gets the DBUserDBSpectrum objects related with this spectrum

Returns:

The reviewAssignments, vector of DBUserDBSpectrum obejects

Throws:

java.lang.Exception - Database problems

getNameOfAsssignedReviewer

public java.lang.String getNameOfAsssignedReviewer()
                                            throws java.lang.Exception

Gets the name of the last reviwer the DBSpectrum object was assigned to

Returns:

The name

Throws:

java.lang.Exception - Database problems

getEmailOfAsssignedReviewer

public java.lang.String getEmailOfAsssignedReviewer()
                                             throws java.lang.Exception

Gets the email of the last reviewer the DBSpectrum object was assigned to

Returns:

The email

Throws:

java.lang.Exception - Database problems

getAsssignedDate

public java.util.Date getAsssignedDate()
                                throws java.lang.Exception

Gets the Date the last assignment of the DBSpectrum object took place

Returns:

The asssignment Date value

Throws:

java.lang.Exception - Database problems

getCommentAsString

public java.lang.String getCommentAsString()

Gets the comment attribute of the DBSpectrum object

Returns:

The comment value

getLinksAsString

public java.lang.String getLinksAsString()
                                  throws java.lang.Exception

Gets the links of the DBSpectrum object as a string

Returns:

The links value

Throws:

java.lang.Exception - Description of Exception

getLiteraturesNew

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

Gets the DBLiterature objects of the DBSpectrum object

Returns:

The literature value

Throws:

java.lang.Exception - Description of Exception

getKeywords

public java.lang.String getKeywords()
                             throws java.lang.Exception

Gets the keywords attribute of the DBSpectrum object.

Returns:

The keywords value.

Throws:

java.lang.Exception - Database problems.

getKeywords

public java.lang.String getKeywords(boolean separatedByNewline)
                             throws java.lang.Exception

Gets the keywords attribute of the DBSpectrum object.

Parameters:

separatedByNewline - If true keywords are separated by \n else by ,.

Returns:

The keywords value.

Throws:

java.lang.Exception - Database problems.

getMeAsSubmittingData

public SubmittingData getMeAsSubmittingData(boolean useUser,
                                            java.lang.String path,
                                            boolean no3d)
                                     throws java.lang.Exception

This makes a submittingData object populated with the values from this spectrum and its molecule.

Parameters:

useUser - Description of Parameter

path - Description of Parameter

Returns:

The SubmittingData object.

Throws:

java.lang.Exception - Database problems.

getMark

public int getMark()
            throws java.lang.Exception

Gets the mark of the DBSpectrum object

Returns:

The mark value

Throws:

java.lang.Exception - Description of Exception

getMarkComment

public java.lang.String getMarkComment()
                                throws java.lang.Exception

Gets the Comments for marks of the DBSpectrum object.

Returns:

The comment value.

Throws:

java.lang.Exception - Database problems.

getDisplaymark

public int getDisplaymark()
                   throws java.io.FileNotFoundException,
                          java.io.IOException

Returns the mark necessary for a spectrum to be displayed

Returns:

The displaymark value

Throws:

java.io.FileNotFoundException - Description of Exception

java.io.IOException - Description of Exception

getCmlSpect

public nu.xom.Element getCmlSpect()
                           throws org.xmlcml.cml.base.CMLException,
                                  org.apache.torque.TorqueException

Gets this spectrum as cmlSpect.

Returns:

The cmlSpect value.

Throws:

java.lang.Exception - Database problems

org.xmlcml.cml.base.CMLException - xml problems.

org.apache.torque.TorqueException - Something wrong with database reading.

getUnusedText

public java.lang.String getUnusedText()

Returns a text telling unsed spectra. Initialized by initSimilarity().

Returns:

The unusedText value.

hasAnyIntensities

public boolean hasAnyIntensities()
                          throws java.lang.Exception

Tells if any signal in this spectrum has an intensity != 0.

Returns:

True=yes, false=no.

Throws:

java.lang.Exception - Database problems.

initSimilarity

public java.util.Map initSimilarity(java.util.List otherSignalsL,
                                    boolean isSubSpectrum)

Sets the similarity between this and another spectrum

Parameters:

isSubSpectrum - Is this a subspectrum search ?

otherSignalsL - Description of Parameter

Returns:

Description of the Returned Value

hasAnyIdentifier

public boolean hasAnyIdentifier()
                         throws java.lang.Exception

Tells if there is any atom identifier for this spectrum.

Returns:

True=yes, false=no.

Throws:

java.lang.Exception - Database problems.

addMark

public void addMark(int mark,
                    org.apache.turbine.om.security.User user,
                    java.lang.String comment)
             throws java.lang.Exception

Adds a mark to this DBSpectrum.

Parameters:

mark - The mark.

user - The user marking.

comment - The feature to be added to the Mark attribute

Throws:

java.lang.Exception - Database problems.

delete

public void delete(java.sql.Connection dbconn,
                   boolean doMolecule)
            throws java.lang.Exception

Deletes this spectrum plus all associated rows.

Parameters:

dbconn - The connection to use.

Throws:

java.lang.Exception - Database problems.

getShifts

private float[] getShifts(int atomNumber,
                          DBMolecule mol)
                   throws java.lang.Exception

Gets the shifts of a certain atom in this spectrum.

Parameters:

atomNumber - The mdl number of the atom to look for.

Returns:

The shifts value.

Throws:

java.lang.Exception - Database problems.

getShifts

private float[] getShifts(int atomNumber)
                   throws java.lang.Exception

Gets the shifts of a certain atom in this spectrum.

Parameters:

atomNumber - The mdl number of the atom to look for.

Returns:

The shifts value.

Throws:

java.lang.Exception - Database problems.

getSignals

private java.util.List getSignals(int atomNumber,
                                  DBMolecule mol)
                           throws java.lang.Exception

Gets the shifts of a certain atom in this spectrum.

Parameters:

atomNumber - The mdl number of the atom to look for.

Returns:

The shifts value.

Throws:

java.lang.Exception - Database problems.

getSignals

private java.util.List getSignals(int atomNumber)
                           throws java.lang.Exception

Gets the shifts of a certain atom in this spectrum.

Parameters:

atomNumber - The mdl number of the atom to look for.

Returns:

The shifts value.

Throws:

java.lang.Exception - Database problems.

getSpectrumForAppletNewFormat

public java.lang.String getSpectrumForAppletNewFormat()
                                               throws java.lang.Exception

Gets the spectrum in the format needed for the new spectrumapplet (R 1.0). Assignments are to heavy atoms in H spectra.

Returns:

The shifts value.

Throws:

java.lang.Exception - Database problems.

getSpectrumForAppletNewFormat

public java.lang.String getSpectrumForAppletNewFormat(DBAtom[] atoms,
                                                      org.openscience.cdk.interfaces.IMolecule cdkmol)
                                               throws java.lang.Exception

Gets the spectrum in the format needed for the new spectrumapplet (R 1.0). Assignments are to heavy atoms in H spectra.

Returns:

The shifts value.

Throws:

java.lang.Exception - Database problems.

getOtherSpectraStringHeader

public java.lang.String getOtherSpectraStringHeader()
                                             throws java.lang.Exception

Throws:

java.lang.Exception

getOtherSpectraString

public java.lang.String getOtherSpectraString(int atomNumber)
                                       throws java.lang.Exception

Throws:

java.lang.Exception

getOtherSpectraStringSize

public int getOtherSpectraStringSize()
                              throws java.lang.Exception

Throws:

java.lang.Exception

getUnassignedText

public java.lang.String getUnassignedText()
                                   throws org.apache.torque.TorqueException

Gives a string with the unassigned shifts in this spectrum, "" if none.

Returns:

The string

Throws:

org.apache.torque.TorqueException - Probably a database problem

getCurrentSpectrum

public DBSpectrum getCurrentSpectrum()
                              throws org.apache.torque.NoRowsException,
                                     org.apache.torque.TooManyRowsException,
                                     org.apache.torque.TorqueException

Gives you the current spectrum of the edit chain of this spectrum. If this spectrum has not been edited, this spectrum will be returned.

Returns:

The current instance of this spectrum.

Throws:

org.apache.torque.NoRowsException

org.apache.torque.TooManyRowsException

org.apache.torque.TorqueException