toxTree.data
Class MoleculesFile

java.lang.Object
  extended by org.openscience.cdk.ChemObject
      extended by toxTree.data.MoleculesFile
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IChemObjectListener

public class MoleculesFile
extends org.openscience.cdk.ChemObject
implements org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.IChemObjectListener

See Also:
Serialized Form

Field Summary
protected  boolean bufferProperties
           
protected  int foundIndex
           
protected  org.openscience.cdk.fingerprint.Fingerprinter fp
           
protected  TTLogger logger
           
protected static java.lang.String NA
           
protected  java.beans.PropertyChangeSupport propertyChangeSupport
           
static java.lang.String propertyFingerprint
           
protected  org.openscience.cdk.io.random.RandomAccessReader reader
           
protected  int selectedIndex
           
protected  org.openscience.cdk.smiles.SmilesGenerator smigen
           
protected  SortedPropertyList sortedProperties
           
protected  java.util.Hashtable[] updatedProperties
           
 
Constructor Summary
MoleculesFile(java.io.File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
           
MoleculesFile(java.io.File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)
           
MoleculesFile(java.lang.String resource, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)
           
 
Method Summary
 void add(org.openscience.cdk.interfaces.IAtomContainerSet arg0)
           
 void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer a)
           
 void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0, double arg1)
           
 void addPropertyChangeListener(java.beans.PropertyChangeListener listener)
           
 void addPropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener)
           
 java.lang.Iterable<org.openscience.cdk.interfaces.IAtomContainer> atomContainers()
           
 void close()
           
 org.openscience.cdk.io.random.RandomAccessReader createReader(java.io.File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)
           
 boolean equals(java.lang.Object obj)
           
protected  void finalize()
           
 int find(org.openscience.cdk.interfaces.IAtomContainer mol)
          TODO introduce isomorphism check to handle nonunique fingerprints
 void firePropertyChange(java.beans.PropertyChangeEvent event)
           
 void firePropertyChange(java.lang.String propertyName, java.lang.Object oldValue, java.lang.Object newValue)
           
 java.lang.Object first()
           
 org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(int index)
           
 int getAtomContainerCount()
           
 java.util.BitSet getFingerprint(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 java.lang.Double getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
           
 java.lang.Double getMultiplier(int arg0)
           
 java.lang.Double[] getMultipliers()
           
 java.util.Map getProperties(int index)
           
 java.lang.Object getProperty(int index, java.lang.Object key)
           
 org.openscience.cdk.io.random.RandomAccessReader getReader()
           
 int getSelectedIndex()
           
 java.util.Collection<java.lang.Comparable> getValuesPerField(java.lang.Object field, int limit)
           
 boolean hasNext()
           
 boolean hasPrevious()
           
 int indexOf(java.lang.Object property, java.lang.Object value)
           
 boolean isBuffered(int index, java.lang.Object key)
           
 boolean isBufferProperties()
           
 java.lang.Object last()
           
 java.lang.Object next()
           
 int nextIndex()
           
protected  void prepareProperty(java.lang.Object property)
           
 java.lang.Object previous()
           
 int previousIndex()
           
 void removeAllAtomContainers()
           
 void removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0)
           
 void removeAtomContainer(int arg0)
           
 void removePropertyChangeListener(java.beans.PropertyChangeListener listener)
           
 void removePropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener)
           
 void replaceAtomContainer(int arg0, org.openscience.cdk.interfaces.IAtomContainer arg1)
           
 void setAtomContainers(org.openscience.cdk.interfaces.IAtomContainer[] molecules)
           
 void setBufferProperties(boolean bufferProperties)
           
 boolean setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0, java.lang.Double arg1)
           
 void setMultiplier(int arg0, java.lang.Double arg1)
           
 boolean setMultipliers(java.lang.Double[] arg0)
           
 void setProperty(int index, java.lang.Object key, java.lang.Object value)
           
 java.lang.Object setSelectedIndex(int index)
           
 void sortAtomContainers(java.util.Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)
           
 void sortBy(java.lang.Object property, boolean ascending)
           
 void stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
           
 java.lang.String toString()
           
 
Methods inherited from class org.openscience.cdk.ChemObject
addListener, clone, compare, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
 
Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
 
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
 

Field Detail

propertyFingerprint

public static java.lang.String propertyFingerprint

smigen

protected org.openscience.cdk.smiles.SmilesGenerator smigen

fp

protected org.openscience.cdk.fingerprint.Fingerprinter fp

NA

protected static java.lang.String NA

reader

protected org.openscience.cdk.io.random.RandomAccessReader reader

updatedProperties

protected final java.util.Hashtable[] updatedProperties

selectedIndex

protected int selectedIndex

bufferProperties

protected boolean bufferProperties

propertyChangeSupport

protected java.beans.PropertyChangeSupport propertyChangeSupport

foundIndex

protected int foundIndex

logger

protected TTLogger logger

sortedProperties

protected SortedPropertyList sortedProperties
Constructor Detail

MoleculesFile

public MoleculesFile(java.lang.String resource,
                     org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                     org.openscience.cdk.io.listener.IReaderListener listener)
              throws java.lang.Exception
Throws:
java.lang.Exception

MoleculesFile

public MoleculesFile(java.io.File file,
                     org.openscience.cdk.interfaces.IChemObjectBuilder builder)
              throws java.lang.Exception
Throws:
java.lang.Exception

MoleculesFile

public MoleculesFile(java.io.File file,
                     org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                     org.openscience.cdk.io.listener.IReaderListener listener)
              throws java.lang.Exception
Throws:
java.lang.Exception
Method Detail

createReader

public org.openscience.cdk.io.random.RandomAccessReader createReader(java.io.File file,
                                                                     org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                     org.openscience.cdk.io.listener.IReaderListener listener)
                                                              throws java.lang.Exception
Throws:
java.lang.Exception

close

public void close()

finalize

protected void finalize()
                 throws java.lang.Throwable
Overrides:
finalize in class java.lang.Object
Throws:
java.lang.Throwable

first

public java.lang.Object first()

last

public java.lang.Object last()

setSelectedIndex

public java.lang.Object setSelectedIndex(int index)

getSelectedIndex

public int getSelectedIndex()

setAtomContainers

public void setAtomContainers(org.openscience.cdk.interfaces.IAtomContainer[] molecules)

getAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(int index)
Specified by:
getAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAllAtomContainers

public void removeAllAtomContainers()
Specified by:
removeAllAtomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

getAtomContainerCount

public int getAtomContainerCount()
Specified by:
getAtomContainerCount in interface org.openscience.cdk.interfaces.IAtomContainerSet

hasNext

public boolean hasNext()

next

public java.lang.Object next()

hasPrevious

public boolean hasPrevious()

previous

public java.lang.Object previous()

nextIndex

public int nextIndex()

previousIndex

public int previousIndex()

getProperties

public java.util.Map getProperties(int index)

isBuffered

public boolean isBuffered(int index,
                          java.lang.Object key)

getProperty

public java.lang.Object getProperty(int index,
                                    java.lang.Object key)

setProperty

public final void setProperty(int index,
                              java.lang.Object key,
                              java.lang.Object value)

stateChanged

public void stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
Specified by:
stateChanged in interface org.openscience.cdk.interfaces.IChemObjectListener

toString

public java.lang.String toString()
Specified by:
toString in interface org.openscience.cdk.interfaces.IChemObject
Overrides:
toString in class java.lang.Object

isBufferProperties

public boolean isBufferProperties()

setBufferProperties

public void setBufferProperties(boolean bufferProperties)

equals

public boolean equals(java.lang.Object obj)
Overrides:
equals in class java.lang.Object

getReader

public org.openscience.cdk.io.random.RandomAccessReader getReader()

addPropertyChangeListener

public void addPropertyChangeListener(java.beans.PropertyChangeListener listener)

removePropertyChangeListener

public void removePropertyChangeListener(java.beans.PropertyChangeListener listener)

addPropertyChangeListener

public void addPropertyChangeListener(java.lang.String propertyName,
                                      java.beans.PropertyChangeListener listener)

removePropertyChangeListener

public void removePropertyChangeListener(java.lang.String propertyName,
                                         java.beans.PropertyChangeListener listener)

firePropertyChange

public void firePropertyChange(java.lang.String propertyName,
                               java.lang.Object oldValue,
                               java.lang.Object newValue)

firePropertyChange

public void firePropertyChange(java.beans.PropertyChangeEvent event)

prepareProperty

protected void prepareProperty(java.lang.Object property)
                        throws java.lang.Exception
Throws:
java.lang.Exception

indexOf

public int indexOf(java.lang.Object property,
                   java.lang.Object value)
            throws java.lang.Exception
Throws:
java.lang.Exception

sortBy

public void sortBy(java.lang.Object property,
                   boolean ascending)
            throws java.lang.Exception
Throws:
java.lang.Exception

getValuesPerField

public java.util.Collection<java.lang.Comparable> getValuesPerField(java.lang.Object field,
                                                                    int limit)

add

public void add(org.openscience.cdk.interfaces.IAtomContainerSet arg0)
Specified by:
add in interface org.openscience.cdk.interfaces.IAtomContainerSet

addAtomContainer

public void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer a)
Specified by:
addAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

addAtomContainer

public void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0,
                             double arg1)
Specified by:
addAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

atomContainers

public java.lang.Iterable<org.openscience.cdk.interfaces.IAtomContainer> atomContainers()
Specified by:
atomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public java.lang.Double getMultiplier(int arg0)
Specified by:
getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public java.lang.Double getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
Specified by:
getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultipliers

public java.lang.Double[] getMultipliers()
Specified by:
getMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0)
Specified by:
removeAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(int arg0)
Specified by:
removeAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

replaceAtomContainer

public void replaceAtomContainer(int arg0,
                                 org.openscience.cdk.interfaces.IAtomContainer arg1)
Specified by:
replaceAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultiplier

public boolean setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0,
                             java.lang.Double arg1)
Specified by:
setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultiplier

public void setMultiplier(int arg0,
                          java.lang.Double arg1)
Specified by:
setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultipliers

public boolean setMultipliers(java.lang.Double[] arg0)
Specified by:
setMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

find

public int find(org.openscience.cdk.interfaces.IAtomContainer mol)
         throws java.lang.Exception
TODO introduce isomorphism check to handle nonunique fingerprints

Throws:
java.lang.Exception

getFingerprint

public java.util.BitSet getFingerprint(org.openscience.cdk.interfaces.IAtomContainer mol)
                                throws java.lang.Exception
Throws:
java.lang.Exception

sortAtomContainers

public void sortAtomContainers(java.util.Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)
Specified by:
sortAtomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet


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