org.openscience.nmrshiftdb.util
Class GeneralUtils

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

public class GeneralUtils
extends java.lang.Object

Contains some utils not fitting in somewhere else

Author:

shk3

Field Summary

static java.util.ArrayList<java.lang.String>	alreadyAttached
(package private) static java.util.ArrayList<java.lang.String>	atomsWithHoseCode
(package private) static java.lang.String	emailSignature
(package private) static GeneralUtils	instance
(package private) static java.util.Properties	jetspeedprops
static int	MAX_HITS_TO_DISPLAY Maximum number of hits to display
(package private) static java.util.HashMap<java.lang.String,org.openscience.cdk.modeling.builder3d.ModelBuilder3D>	mb3d
static java.util.Properties	nmrprops Description of the Field
(package private) static org.apache.log4j.Category	nmrshiftdbLogger
static java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.Integer,java.util.ArrayList<ValueTriple>>>	spectramap
(package private) static org.apache.log4j.Logger	sqlLogger

Constructor Summary

private

GeneralUtils() Constructor for the GeneralUtils object (private since only static methods)

Method Summary

static void	addToStructureHistory(java.lang.String mdl, javax.servlet.http.HttpSession session) Adds an mdl file to the StructureHistory
static org.xmlcml.cml.element.CMLCml	assignCML(org.xmlcml.cml.element.CMLCml cmlcml) Doeas an assignemnt for a spectrum and molecule.
static java.lang.String	checkAgainstCdk(DBMolecule mol) Checks if the values of the C spectra of a certain DBMolecule are inside the CDK prediction range.
static java.lang.String	escape(java.lang.String text) Prepares a string for sql quersis by escaping " and ' and \
static java.lang.String	escapeForHtml(java.lang.String text) Description of the Method
static java.util.ArrayList<java.lang.String>	executeSearch(java.util.ArrayList searchHistory, int[] searches, StringAndInt chiralMessage, java.util.ArrayList<java.lang.Double> similarities, boolean calculatedonly, boolean measuredonly, org.apache.turbine.util.RunData runData, java.lang.String path, boolean not, boolean andor, boolean otherspecified, java.util.List spectrumTypes, boolean logtosql) Executes searches from the searchHistory.
static java.lang.String	generateInchi(java.lang.String mdl) Generates in inchi for a mol file via cambridge web service.
static java.lang.String	generateInchiKey(java.lang.String mdl) Generates in inchi key for a mol file via chemspider web service.
static java.lang.String	getAdminEmail(org.apache.turbine.util.RunData runData) Gets the adminEmail from TurbineRessources.properties
static java.lang.String	getAdminEmail(javax.servlet.ServletConfig config) Gets the adminEmail from TurbineRessources.properties
static java.lang.String	getAsXMLString(java.lang.Object obj) Gets an object as an JSX XML String.
static java.util.ArrayList<java.lang.String>	getAtomsWithHoseCode() Gets a ArrayList containing all element symbols from isotope table except H.
private static org.openscience.cdk.io.IChemObjectReader	getChemObjectReader(java.lang.String file) Gets a chemObjectReader for a file.
static int	getDigitsAfterComma(float value) Tells how many digits after the comma (or .) a float has got.
static java.lang.String	getEmailSignature(org.apache.turbine.util.RunData runData) Gets a standard email signature.
static DBMolecule	getExistingMolecule(org.openscience.cdk.interfaces.IMolecule molWithHCount, org.openscience.cdk.interfaces.IMolecule molWithH, boolean[] isDoubleBondSpecified, javax.servlet.ServletConfig servcon, java.lang.String molecule, StringAndStringAndBoolean ssb) Tells if a molecule is already in the DB
static java.lang.Object	getFromXMLString(java.lang.String xmlString) Gets an object from an JSX xml string.
static GeneralUtils	getInstance()
static java.util.Properties	getJetspeedprops()
static java.util.Map<java.lang.Float,java.lang.Float>	getMatchingSearchShift(java.util.List originalSpectrum, java.util.List searchSpectrum, double similaritypersignal, java.util.Vector unused, boolean doMultiplicityMatch) Creates a map with shifts as keys and the nearest match in the search spectrum as value
static org.openscience.cdk.modeling.builder3d.ModelBuilder3D	getModelBuilder(java.lang.String ff) Gets the modelBuilder attribute of the GeneralUtils class
static java.lang.String	getMultiplicity(int multiplicity, boolean totalname) Returns a letter multiplicity from an int.
static java.lang.String	getNmrshiftdbProperty(java.lang.String property) Gets a property from the NMRSHiftDB.properties file (the nmrprops argument needs to be set before!).
static java.lang.String	getNmrshiftdbProperty(java.lang.String property, org.apache.turbine.util.RunData runData) Gets a property from the NMRSHiftDB.properties file
static java.lang.String	getNmrshiftdbProperty(java.lang.String property, javax.servlet.ServletConfig servcon) Gets a property from the NMRSHiftDB.properties file
private static java.util.List	getPathList(java.io.File f) break a path down into individual elements and add to a list.
static java.lang.String	getRelativePath(java.io.File home, java.io.File f) get relative path of File 'f' with respect to 'home' directory example : home = /a/b/c f = /a/d/e/x.txt s = getRelativePath(home,f) = ../../d/e/x.txt
static java.lang.String	getShort(java.lang.String input)
static java.lang.String	getShortInChI(java.lang.String input)
static java.lang.String	getSmtpServer(org.apache.turbine.util.RunData runData) Gets the smtpServer from TurbineRessources.properties
static java.lang.String	getSmtpServer(javax.servlet.ServletConfig config) Gets the smtpServer from TurbineRessources.properties
static java.util.ArrayList	getVectorWithSessionBindingAttributeFromSession(javax.servlet.http.HttpSession session, java.lang.String attribute) Gets an ArrayListWithSessionBinding attribute from the session
static void	initProps(javax.servlet.ServletConfig servcon)
static java.lang.String	logError(java.lang.Throwable ex, java.lang.String message, org.apache.turbine.util.RunData data, boolean critical) Logs an error
static void	logToSql(java.lang.String message, org.apache.turbine.util.RunData runData) Logs something to the sql log file
static void	makeJpg(java.lang.String mol, java.lang.String filename, javax.servlet.ServletConfig servletConfig, int width, int height, boolean drawnumbers) Makes a jpeg out of a mol file.
static java.lang.String	makeSimpleSpecfile(java.lang.String specfile, boolean dropIntensity) Removes atom numbers from a specfile string.
private static java.lang.String	matchPathLists(java.util.List r, java.util.List f) figure out a string representing the relative path of 'f' with respect to 'r'
static void	parseJcamp(SubmittingData subData, java.lang.String jcamp, org.apache.turbine.util.RunData runData, java.lang.String mode) Parses a jcmap file to a submittingData object.
static java.util.ArrayList<ValueTriple>	parseSpectrum(DBSpectrum spectrum)
private static java.lang.String	processChemFile(org.openscience.cdk.interfaces.IChemFile chemFile)
private static void	processChemFile(org.openscience.cdk.interfaces.IChemFile chemFile, java.lang.StringBuffer messages, org.apache.turbine.util.RunData data, java.lang.String attributename) Tries to read a chemfile via cdk to a cdk molecule, which is set to the session with attributename as key.
private static java.lang.String	processChemModel(org.openscience.cdk.interfaces.IChemModel chemModel)
private static void	processChemModel(org.openscience.cdk.interfaces.IChemModel chemModel, java.lang.StringBuffer messages, org.apache.turbine.util.RunData data, java.lang.String attributename) Tries to read a chemmodel via cdk to a cdk molecule, which is set to the session with attributename as key.
static void	processFileItem(org.apache.turbine.util.upload.FileItem fi, java.lang.StringBuffer messages, org.apache.turbine.util.RunData data, java.lang.String attributename) Tries to read a FileItem via cdk to a cdk molecule, which is set to the session with attributename as key.
static java.lang.String	readToMol(java.lang.String input)
static java.lang.StringBuffer	removeLastComma(java.lang.StringBuffer s) Removes the last character from a string buffer if it is a , or ;.
static java.lang.String	replace(java.lang.String str, java.lang.String pattern, java.lang.String replace) Replaces a string in a string with another string
static java.lang.String	resolveNameFromPubchem(java.lang.String name) Converts any sort of name into an InChI using Pubchem.
static org.openscience.cdk.interfaces.IMolecule	saturate(org.openscience.cdk.interfaces.IMolecule cdkmol) saturates a molecule with (implicit) protons and bonds.
static org.apache.jetspeed.om.security.turbine.TurbineUser	selectReviewer(org.apache.jetspeed.om.security.turbine.TurbineUser user) Selects a reviewer
static boolean	sendEmailToEventReceivers(java.lang.String header, java.lang.String body, org.apache.turbine.util.RunData runData, int error) Sends an email to all admineventreceiver role owners
static void	serializeSubdata(SubmittingData subData, javax.servlet.ServletConfig servcon)
static void	setJetspeedprops(java.util.Properties jetspeedprops)
private static float	similarity(java.util.ArrayList al1, java.util.ArrayList al2, boolean isSubSpectrum)
static void	zipDir(java.io.File zipDir, java.util.zip.ZipOutputStream zos, java.io.File rawdatadir) Recursivly zips a directory in an zipoutputstream

Methods inherited from class java.lang.Object

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

Field Detail

nmrprops

public static java.util.Properties nmrprops

Description of the Field

MAX_HITS_TO_DISPLAY

public static final int MAX_HITS_TO_DISPLAY

Maximum number of hits to display

See Also:

Constant Field Values

sqlLogger

static org.apache.log4j.Logger sqlLogger

nmrshiftdbLogger

static org.apache.log4j.Category nmrshiftdbLogger

jetspeedprops

static java.util.Properties jetspeedprops

emailSignature

static java.lang.String emailSignature

atomsWithHoseCode

static java.util.ArrayList<java.lang.String> atomsWithHoseCode

mb3d

static java.util.HashMap<java.lang.String,org.openscience.cdk.modeling.builder3d.ModelBuilder3D> mb3d

instance

static GeneralUtils instance

alreadyAttached

public static java.util.ArrayList<java.lang.String> alreadyAttached

spectramap

public static java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.Integer,java.util.ArrayList<ValueTriple>>> spectramap

Constructor Detail

GeneralUtils

private GeneralUtils()

Constructor for the GeneralUtils object (private since only static methods)

Method Detail

getInstance

public static GeneralUtils getInstance()

getAdminEmail

public static java.lang.String getAdminEmail(org.apache.turbine.util.RunData runData)
                                      throws java.io.IOException

Gets the adminEmail from TurbineRessources.properties

Parameters:

runData - The RunData object

Returns:

The adminEmail value

Throws:

java.io.IOException - Error reading file

getShort

public static java.lang.String getShort(java.lang.String input)

getShortInChI

public static java.lang.String getShortInChI(java.lang.String input)

getAtomsWithHoseCode

public static java.util.ArrayList<java.lang.String> getAtomsWithHoseCode()
                                                                  throws java.lang.Exception

Gets a ArrayList containing all element symbols from isotope table except H.

Returns:

The atomsWithHoseCode value

Throws:

java.lang.Exception - Description of Exception

getAdminEmail

public static java.lang.String getAdminEmail(javax.servlet.ServletConfig config)
                                      throws java.io.IOException

Gets the adminEmail from TurbineRessources.properties

Parameters:

config - Teh servletConfig object

Returns:

The adminEmail value

Throws:

java.io.IOException - Error reading file

getSmtpServer

public static java.lang.String getSmtpServer(org.apache.turbine.util.RunData runData)
                                      throws java.io.IOException

Gets the smtpServer from TurbineRessources.properties

Parameters:

runData - The RunData object

Returns:

The smtpServer value

Throws:

java.io.IOException - Error reading file

getSmtpServer

public static java.lang.String getSmtpServer(javax.servlet.ServletConfig config)
                                      throws java.io.IOException

Gets the smtpServer from TurbineRessources.properties

Parameters:

config - Description of Parameter

Returns:

The smtpServer value

Throws:

java.io.IOException - Error reading file

getVectorWithSessionBindingAttributeFromSession

public static java.util.ArrayList getVectorWithSessionBindingAttributeFromSession(javax.servlet.http.HttpSession session,
                                                                                  java.lang.String attribute)

Gets an ArrayListWithSessionBinding attribute from the session

Parameters:

session - The current session

attribute - Description of Parameter

Returns:

The StructuresHistory value

getNmrshiftdbProperty

public static java.lang.String getNmrshiftdbProperty(java.lang.String property,
                                                     javax.servlet.ServletConfig servcon)
                                              throws java.io.FileNotFoundException,
                                                     java.io.IOException

Gets a property from the NMRSHiftDB.properties file

Parameters:

property - The property to get

servcon - The current ServletConfig object

Returns:

The nmrshiftdbProperty value

Throws:

java.io.FileNotFoundException - Properties file not found

java.io.IOException - Could not read properties file

initProps

public static void initProps(javax.servlet.ServletConfig servcon)
                      throws java.io.FileNotFoundException,
                             java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

getNmrshiftdbProperty

public static java.lang.String getNmrshiftdbProperty(java.lang.String property)
                                              throws java.io.FileNotFoundException,
                                                     java.io.IOException

Gets a property from the NMRSHiftDB.properties file (the nmrprops argument needs to be set before!).

Parameters:

property - The property to get

Returns:

The nmrshiftdbProperty value

Throws:

java.io.FileNotFoundException - Properties file not found

java.io.IOException - Could not read properties file

getNmrshiftdbProperty

public static java.lang.String getNmrshiftdbProperty(java.lang.String property,
                                                     org.apache.turbine.util.RunData runData)
                                              throws java.io.FileNotFoundException,
                                                     java.io.IOException

Gets a property from the NMRSHiftDB.properties file

Parameters:

property - The property to get

runData - The current RunData object

Returns:

The nmrshiftdbProperty value

Throws:

java.io.FileNotFoundException - Properties file not found

java.io.IOException - Could not read properties file

getExistingMolecule

public static DBMolecule getExistingMolecule(org.openscience.cdk.interfaces.IMolecule molWithHCount,
                                             org.openscience.cdk.interfaces.IMolecule molWithH,
                                             boolean[] isDoubleBondSpecified,
                                             javax.servlet.ServletConfig servcon,
                                             java.lang.String molecule,
                                             StringAndStringAndBoolean ssb)
                                      throws java.io.IOException,
                                             java.lang.Exception

Tells if a molecule is already in the DB

Parameters:

molWithHCount - The mol without the Hs

molWithH - With Hs

isDoubleBondSpecified - The ArrayList indicating if double bond orientations are specified as needed for SmilesGenerator, null if none is specified

servcon - The current ServletConfig

molecule - The mdl file

ssb - Description of Parameter

Returns:

The existing molecule if there is one, null if none

Throws:

java.io.IOException - Problems reading properties files

java.lang.Exception - Database problems

getEmailSignature

public static java.lang.String getEmailSignature(org.apache.turbine.util.RunData runData)
                                          throws java.io.IOException

Gets a standard email signature.

Parameters:

runData - Ther runData object.

Returns:

The emailSignature value.

Throws:

java.io.IOException - Problems reading properties.

getAsXMLString

public static java.lang.String getAsXMLString(java.lang.Object obj)
                                       throws java.io.IOException

Gets an object as an JSX XML String.

Parameters:

obj - The object to serialize.

Returns:

The xml string.

Throws:

java.io.IOException - IO problems.

getFromXMLString

public static java.lang.Object getFromXMLString(java.lang.String xmlString)
                                         throws java.io.IOException,
                                                java.lang.ClassNotFoundException

Gets an object from an JSX xml string.

Parameters:

xmlString - The xml string.

Returns:

The object.

Throws:

java.io.IOException - IO problem.

java.lang.ClassNotFoundException - The class to create must be found.

getMultiplicity

public static java.lang.String getMultiplicity(int multiplicity,
                                               boolean totalname)

Returns a letter multiplicity from an int.

Parameters:

multiplicity - The mult to translate.

totalname - true=long name, false=one letter name.

Returns:

The multiplicity value.

getDigitsAfterComma

public static int getDigitsAfterComma(float value)

Tells how many digits after the comma (or .) a float has got.

Parameters:

value - The float to axamine.

Returns:

Number of digits.

getModelBuilder

public static org.openscience.cdk.modeling.builder3d.ModelBuilder3D getModelBuilder(java.lang.String ff)
                                                                             throws org.openscience.cdk.exception.CDKException

Gets the modelBuilder attribute of the GeneralUtils class

Parameters:

ff - Description of Parameter

Returns:

The modelBuilder value

Throws:

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

removeLastComma

public static java.lang.StringBuffer removeLastComma(java.lang.StringBuffer s)

Removes the last character from a string buffer if it is a , or ;.

Parameters:

s - The string buffer to deal with.

Returns:

Description of the Returned Value

logError

public static java.lang.String logError(java.lang.Throwable ex,
                                        java.lang.String message,
                                        org.apache.turbine.util.RunData data,
                                        boolean critical)

Logs an error

Parameters:

ex - The thrown excpetion

message - Some individual message

data - The current RunData

Returns:

A text to display

sendEmailToEventReceivers

public static boolean sendEmailToEventReceivers(java.lang.String header,
                                                java.lang.String body,
                                                org.apache.turbine.util.RunData runData,
                                                int error)

Sends an email to all admineventreceiver role owners

Parameters:

header - The header of the email

body - The body of the email

runData - The runData object

error - Is this an error or an info message (0=info, 1=non-critical error, 2=error)

Returns:

false=sending failed, true=worked

selectReviewer

public static org.apache.jetspeed.om.security.turbine.TurbineUser selectReviewer(org.apache.jetspeed.om.security.turbine.TurbineUser user)
                                                                          throws java.lang.Exception

Selects a reviewer

Parameters:

user - The user currently logged in

Returns:

The choosen reviewer

Throws:

java.lang.Exception - Description of Exception

addToStructureHistory

public static void addToStructureHistory(java.lang.String mdl,
                                         javax.servlet.http.HttpSession session)
                                  throws org.openscience.cdk.exception.CDKException

Adds an mdl file to the StructureHistory

Parameters:

mdl - The mdl to be added

session - The current session

Throws:

org.openscience.cdk.exception.CDKException

logToSql

public static void logToSql(java.lang.String message,
                            org.apache.turbine.util.RunData runData)
                     throws java.lang.Exception

Logs something to the sql log file

Parameters:

message - The message to log

runData - The runData object

Throws:

java.lang.Exception - Description of Exception

replace

public static java.lang.String replace(java.lang.String str,
                                       java.lang.String pattern,
                                       java.lang.String replace)

Replaces a string in a string with another string

Parameters:

str - The string in which replacing has to take place

pattern - The pattern to replace

replace - The string the pattern has to be replaced with

Returns:

The changed string

checkAgainstCdk

public static java.lang.String checkAgainstCdk(DBMolecule mol)
                                        throws java.io.IOException,
                                               java.lang.Exception

Checks if the values of the C spectra of a certain DBMolecule are inside the CDK prediction range.

Parameters:

mol - The CDMolecule to check.

Returns:

A text either "" or a description of problems.

Throws:

java.io.IOException - Problems with serialisation.

java.lang.Exception - Database problems.

makeSimpleSpecfile

public static java.lang.String makeSimpleSpecfile(java.lang.String specfile,
                                                  boolean dropIntensity)

Removes atom numbers from a specfile string.

Parameters:

specfile - The original specfile.

dropIntensity - true=also drop intensities if they are zero.

Returns:

The new specfile.

escape

public static java.lang.String escape(java.lang.String text)

Prepares a string for sql quersis by escaping " and ' and \

Parameters:

text - The text to be escaped

Returns:

The escaped text

escapeForHtml

public static java.lang.String escapeForHtml(java.lang.String text)

Description of the Method

Parameters:

text - Description of Parameter

Returns:

Description of the Returned Value

similarity

private static float similarity(java.util.ArrayList al1,
                                java.util.ArrayList al2,
                                boolean isSubSpectrum)

parseSpectrum

public static java.util.ArrayList<ValueTriple> parseSpectrum(DBSpectrum spectrum)
                                                      throws org.apache.torque.TorqueException

Throws:

org.apache.torque.TorqueException

getMatchingSearchShift

public static java.util.Map<java.lang.Float,java.lang.Float> getMatchingSearchShift(java.util.List originalSpectrum,
                                                                                    java.util.List searchSpectrum,
                                                                                    double similaritypersignal,
                                                                                    java.util.Vector unused,
                                                                                    boolean doMultiplicityMatch)

Creates a map with shifts as keys and the nearest match in the search spectrum as value

Parameters:

originalSpectrum - The original spectrum

searchSpectrum - The search spectrum

similaritypersignal - Description of Parameter

unused - Description of Parameter

Returns:

The matchingSearchShift value

executeSearch

public static java.util.ArrayList<java.lang.String> executeSearch(java.util.ArrayList searchHistory,
                                                                  int[] searches,
                                                                  StringAndInt chiralMessage,
                                                                  java.util.ArrayList<java.lang.Double> similarities,
                                                                  boolean calculatedonly,
                                                                  boolean measuredonly,
                                                                  org.apache.turbine.util.RunData runData,
                                                                  java.lang.String path,
                                                                  boolean not,
                                                                  boolean andor,
                                                                  boolean otherspecified,
                                                                  java.util.List spectrumTypes,
                                                                  boolean logtosql)
                                                           throws NmrshiftdbException,
                                                                  java.lang.Exception

Executes searches from the searchHistory.

Parameters:

searches - The searches to execute. Each figure in searches means the search in this position in sarchHistory will be executed, all searches are AND linked.

searchHistory - The search history.

chiralMessage - Return messages about chiral/non-chiral structure search.

similarities - Holds similarites (as Doubles) in case similarity search was done (must be empty ArrayList).

calculatedonly - Search only calculated spectra.

measuredonly - Search only measured spectra.

runData - Current runData, null if used in client.

path - Description of Parameter

not - Description of Parameter

andor - Description of Parameter

otherspecified - Description of Parameter

Returns:

ArrayList of molecule ids (as Strings).

Throws:

java.lang.Exception - Database problems

NmrshiftdbException - Description of Exception

parseJcamp

public static void parseJcamp(SubmittingData subData,
                              java.lang.String jcamp,
                              org.apache.turbine.util.RunData runData,
                              java.lang.String mode)
                       throws java.io.IOException,
                              org.jcamp.parser.JCAMPException,
                              NmrshiftdbException,
                              java.lang.Exception

Parses a jcmap file to a submittingData object.

Parameters:

subData - The signalstable of this will be filled.

jcamp - The path to the file to read.

Throws:

java.io.IOException - Description of Exception

org.jcamp.parser.JCAMPException - Description of Exception

NmrshiftdbException - Description of Exception

java.lang.Exception - Description of Exception

processFileItem

public static void processFileItem(org.apache.turbine.util.upload.FileItem fi,
                                   java.lang.StringBuffer messages,
                                   org.apache.turbine.util.RunData data,
                                   java.lang.String attributename)

Tries to read a FileItem via cdk to a cdk molecule, which is set to the session with attributename as key.

Parameters:

fi - The FileItem to read.

messages - Error messages get appended here.

data - The current runData

attributename - The key for the session.

generateInchi

public static java.lang.String generateInchi(java.lang.String mdl)
                                      throws java.lang.Exception

Generates in inchi for a mol file via cambridge web service.

Parameters:

mdl - The mdl to generate for.

Returns:

The inchi

Throws:

java.lang.Exception - Description of Exception

resolveNameFromPubchem

public static java.lang.String resolveNameFromPubchem(java.lang.String name)
                                               throws java.io.IOException

Converts any sort of name into an InChI using Pubchem.

Parameters:

name - The name

Returns:

The InChI. Null if not found in pubchem.

Throws:

java.io.IOException - Probelems reading from pubchem.

generateInchiKey

public static java.lang.String generateInchiKey(java.lang.String mdl)
                                         throws java.lang.Exception

Generates in inchi key for a mol file via chemspider web service.

Parameters:

mdl - The mdl to generate for.

Returns:

The inchi

Throws:

java.lang.Exception - Description of Exception

makeJpg

public static void makeJpg(java.lang.String mol,
                           java.lang.String filename,
                           javax.servlet.ServletConfig servletConfig,
                           int width,
                           int height,
                           boolean drawnumbers)
                    throws java.lang.Exception

Makes a jpeg out of a mol file.

Parameters:

mol - The mol file.

filename - The file to write the jpeg to

servletConfig - The current servlet configuration.

width - Width of jpeg.

height - Height of jpeg

drawnumbers - Should numbers be contained=

Throws:

java.lang.Exception - Description of Exception

saturate

public static org.openscience.cdk.interfaces.IMolecule saturate(org.openscience.cdk.interfaces.IMolecule cdkmol)
                                                         throws java.lang.Exception

saturates a molecule with (implicit) protons and bonds.

Parameters:

cdkmol - The molecule to saturate.

Returns:

The molecule with implicit protons. original molecule will have explicit protons.

Throws:

java.lang.Exception - Description of Exception

zipDir

public static void zipDir(java.io.File zipDir,
                          java.util.zip.ZipOutputStream zos,
                          java.io.File rawdatadir)
                   throws java.io.IOException

Recursivly zips a directory in an zipoutputstream

Parameters:

zipDir - The directory.

zos - The stream

Throws:

java.io.IOException - Description of Exception

getPathList

private static java.util.List getPathList(java.io.File f)

break a path down into individual elements and add to a list. example : if a path is /a/b/c/d.txt, the breakdown will be [d.txt,c,b,a]

Parameters:

f - input file

Returns:

a List collection with the individual elements of the path in reverse order

matchPathLists

private static java.lang.String matchPathLists(java.util.List r,
                                               java.util.List f)

figure out a string representing the relative path of 'f' with respect to 'r'

Parameters:

r - home path

f - path of file

getRelativePath

public static java.lang.String getRelativePath(java.io.File home,
                                               java.io.File f)

get relative path of File 'f' with respect to 'home' directory example : home = /a/b/c f = /a/d/e/x.txt s = getRelativePath(home,f) = ../../d/e/x.txt

Parameters:

home - base path, should be a directory, not a file, or it doesn't make sense

f - file to generate path for

Returns:

path from home to f as a string

getChemObjectReader

private static org.openscience.cdk.io.IChemObjectReader getChemObjectReader(java.lang.String file)
                                                                     throws java.io.IOException

Gets a chemObjectReader for a file.

Parameters:

file - The file.

Returns:

The chemObjectReader.

Throws:

java.io.IOException - Description of Exception

processChemFile

private static void processChemFile(org.openscience.cdk.interfaces.IChemFile chemFile,
                                    java.lang.StringBuffer messages,
                                    org.apache.turbine.util.RunData data,
                                    java.lang.String attributename)

Tries to read a chemfile via cdk to a cdk molecule, which is set to the session with attributename as key.

Parameters:

chemFile - The chemfile.

messages - Error messages get appended here.

data - The current runData

attributename - The key for the session.

processChemModel

private static void processChemModel(org.openscience.cdk.interfaces.IChemModel chemModel,
                                     java.lang.StringBuffer messages,
                                     org.apache.turbine.util.RunData data,
                                     java.lang.String attributename)

Tries to read a chemmodel via cdk to a cdk molecule, which is set to the session with attributename as key.

Parameters:

chemModel - The chemModel to read.

messages - Error messages get appended here.

data - The current runData

attributename - The key for the session.

readToMol

public static java.lang.String readToMol(java.lang.String input)
                                  throws java.lang.Exception

Throws:

java.lang.Exception

processChemFile

private static java.lang.String processChemFile(org.openscience.cdk.interfaces.IChemFile chemFile)
                                         throws java.lang.Exception

Throws:

java.lang.Exception

processChemModel

private static java.lang.String processChemModel(org.openscience.cdk.interfaces.IChemModel chemModel)
                                          throws java.lang.Exception

Throws:

java.lang.Exception

getJetspeedprops

public static java.util.Properties getJetspeedprops()

setJetspeedprops

public static void setJetspeedprops(java.util.Properties jetspeedprops)

serializeSubdata

public static void serializeSubdata(SubmittingData subData,
                                    javax.servlet.ServletConfig servcon)
                             throws java.io.IOException

Throws:

java.io.IOException

assignCML

public static org.xmlcml.cml.element.CMLCml assignCML(org.xmlcml.cml.element.CMLCml cmlcml)
                                               throws java.lang.Exception

Doeas an assignemnt for a spectrum and molecule. The input must conform to NMRShiftDB convention (http://nmrshiftdb.sourceforge.net/nmrshiftdb-convention.html). If a 1H spectrum is predicted, the molecule must contain all explicit Hs, in other cases it may contain some or all, but this must be after all atoms with other elements in the atomlist. The input file must not contain atomRefs in the signals.

Parameters:

cmlcml - The input

Returns:

The input with atomRefs in signals

Throws:

java.lang.Exception