Changes (Marvin API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.standardizer.Changes

```
@PublicAPI
public class Changes
extends java.lang.Object
```
The change set of the standardization procedure.
Contains a clone of the original molecule, the result molecule and a map of atoms and atom-indexes for each atom of the input molecule. All modifications (added removed and modified) made by the standardization process atoms should be stored here.
The mapping of the indexes can be gathered using the methods newToOld() and oldToNew()
Getting the mapping based on a list of sequential changes on a molecule can be gathered using the methods newToOld(List, Molecule) and newToOld(List, Molecule)
To merge more than one Changes object is possible using append(Changes) method.

Since:

5.11

Author:

Imre Barna

Constructor Summary

Constructors
Constructor and Description
`Changes(Molecule original)` Initializes the changes object.
`Changes(Molecule original, Molecule result)` Initializes the changes object.
`Changes(Molecule molecule, StandardizerAction action)` Initializes the changes object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAllAtoms(java.util.Collection<MolAtom> atoms)` Adds atoms to the "added atom" list.
`void`	`addAllAtoms(java.util.Collection<MolAtom> atoms, boolean cleanRelevant)` Adds atoms to the "added atom" list.
`void`	`addAtom(MolAtom atom)` Adds an atom to the "added atom" list.
`void`	`addAtom(MolAtom atom, boolean cleanRelevant)` Adds an atom to the "added atom" list.
`void`	`append(Changes changes)` Appends a set of changes to the already existing changes.
`StandardizerAction`	`getAction()` Gets the base `StandardizerAction` of the changes
`java.util.List<MolAtom>`	`getAddedAtoms()` Gets the list of atoms added during the standardization procedure
`java.util.List<MolAtom>`	`getCleanRelevantAtoms()` Gets the list of atoms changed during the standardization procedure, and needs to be cleaned
`java.util.List<MolAtom>`	`getModifiedAtoms()` Gets the list of modified atoms during the standardization procedure
`Molecule`	`getOriginal()` Gets the original molecule of the standardization process.
`java.util.List<MolAtom>`	`getRemovedAtoms()` Gets the list of atoms removed during the standardization procedure
`Molecule`	`getResult()` Gets the result molecule of the standardization process
`boolean`	`isModified()` Gets whether any modifications were applied on the molecule.
`void`	`modifyAllAtoms(java.util.Collection<MolAtom> atoms)` Adds atoms to the "modified atom" list.
`void`	`modifyAllAtoms(java.util.Collection<MolAtom> atoms, boolean cleanRelevant)` Adds atoms to the "modified atom" list.
`void`	`modifyAtom(MolAtom atom)` Adds an atom to the "modified atom" list.
`void`	`modifyAtom(MolAtom atom, boolean cleanRelevant)` Adds an atom to the "modified atom" list.
`int[]`	`newToOld()` Returns the new -> old atom index mapping. newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
`static int[]`	`newToOld(java.util.List<Changes> changeList, Molecule target)` Calculates the new -> old atom index mapping based on a list of changes. newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
`int[]`	`oldToNew()` Returns the old -> new atom index mapping. oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
`static int[]`	`oldToNew(java.util.List<Changes> changeList, Molecule target)` Calculates the old -> new atom index mapping based on a list of changes. oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
`void`	`removeAllAtoms(java.util.Collection<MolAtom> atoms)` Adds atoms to the "removed atom" list
`void`	`removeAllAtoms(java.util.Collection<MolAtom> atoms, boolean cleanRelevant)` Adds atoms to the "removed atom" list
`void`	`removeAtom(MolAtom atom)` Adds an atom to the "removed atom" list.
`void`	`removeAtom(MolAtom atom, boolean cleanRelevant)` Adds an atom to the "removed atom" list.
`void`	`setAction(StandardizerAction action)` Sets the base `StandardizerAction` of the changes
`void`	`setModified(boolean modified)` Sets whether any modifications were applied on the molecule.
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Changes
```
public Changes(Molecule original)
```
    Initializes the changes object. Default index mapping is based on the original molecule. A clone of the original molecule is created and stored to represent the molecule in the state before standardization process.
    
    Parameters:
    
    original - the original molecule
  - Changes
```
public Changes(Molecule original,
               Molecule result)
```
    Initializes the changes object. Default index mapping is based on the original molecule. The clone of the original molecule is stored to represent the molecule in the state before standardization process.
    
    Parameters:
    
    original - the original molecule
    
    result - the result molecule to be standardized. should be different of the original molecule
  - Changes
```
public Changes(Molecule molecule,
               StandardizerAction action)
```
    Initializes the changes object. Default index mapping is based on the original molecule. A clone of the original molecule is created and stored to represent the molecule in the state before standardization process.
    
    Parameters:
    
    molecule - the original molecule
    
    action - the action generating the changes
- Method Detail
  - getOriginal
```
public Molecule getOriginal()
```
    Gets the original molecule of the standardization process. (It is a clone of the original molecule in the state before the standardization)
    
    Returns:
    
    the clone of the original molecule in the state before the standardization process
  - getResult
```
public Molecule getResult()
```
    Gets the result molecule of the standardization process
    
    Returns:
    
    the result molecule of the standardization process
  - getAddedAtoms
```
public java.util.List<MolAtom> getAddedAtoms()
```
    Gets the list of atoms added during the standardization procedure
    
    Returns:
    
    the list of atoms added during the standardization procedure. This list should be not modified, as it affects the changes object!
  - getRemovedAtoms
```
public java.util.List<MolAtom> getRemovedAtoms()
```
    Gets the list of atoms removed during the standardization procedure
    
    Returns:
    
    the list of atoms removed during the standardization procedure. This list should be not modified, as it affects the changes object!
  - getModifiedAtoms
```
public java.util.List<MolAtom> getModifiedAtoms()
```
    Gets the list of modified atoms during the standardization procedure
    
    Returns:
    
    the list of modified atoms during the standardization procedure. This list should be not modified, as it affects the changes object!
  - getCleanRelevantAtoms
```
public java.util.List<MolAtom> getCleanRelevantAtoms()
```
    Gets the list of atoms changed during the standardization procedure, and needs to be cleaned
    
    Returns:
    
    the list of atoms changed during the standardization procedure. This list should be not modified, as it affects the changes object!
  - addAtom
```
public void addAtom(MolAtom atom)
```
    Adds an atom to the "added atom" list.
    
    Parameters:
    
    atom - an atom to be added to the "added atom" list.
  - addAtom
```
public void addAtom(MolAtom atom,
                    boolean cleanRelevant)
```
    Adds an atom to the "added atom" list.
    
    Parameters:
    
    atom - an atom to be added to the "added atom" list.
    
    cleanRelevant - whether the atom is relevant for cleaning the output molecule
  - removeAtom
```
public void removeAtom(MolAtom atom)
```
    Adds an atom to the "removed atom" list.
    
    Parameters:
    
    atom - an atom to be added to the "removed atom" list.
  - removeAtom
```
public void removeAtom(MolAtom atom,
                       boolean cleanRelevant)
```
    Adds an atom to the "removed atom" list.
    
    Parameters:
    
    atom - an atom to be added to the "removed atom" list.
    
    cleanRelevant - whether the atom is relevant for cleaning the output molecule
  - modifyAtom
```
public void modifyAtom(MolAtom atom)
```
    Adds an atom to the "modified atom" list.
    
    Parameters:
    
    atom - an atom to be added to the "modified atom" list.
  - modifyAtom
```
public void modifyAtom(MolAtom atom,
                       boolean cleanRelevant)
```
    Adds an atom to the "modified atom" list.
    
    Parameters:
    
    atom - an atom to be added to the "modified atom" list.
    
    cleanRelevant - whether the atom is relevant for cleaning the output molecule
  - addAllAtoms
```
public void addAllAtoms(java.util.Collection<MolAtom> atoms)
```
    Adds atoms to the "added atom" list.
    
    Parameters:
    
    atoms - atoms to be added to the "added atom" list.
  - addAllAtoms
```
public void addAllAtoms(java.util.Collection<MolAtom> atoms,
                        boolean cleanRelevant)
```
    Adds atoms to the "added atom" list.
    
    Parameters:
    
    atoms - atoms to be added to the "added atom" list.
    
    cleanRelevant - whether the atoms are relevant for cleaning the output molecule
  - removeAllAtoms
```
public void removeAllAtoms(java.util.Collection<MolAtom> atoms)
```
    Adds atoms to the "removed atom" list
    
    Parameters:
    
    atoms - atoms to be added to the "removed atom" list
  - removeAllAtoms
```
public void removeAllAtoms(java.util.Collection<MolAtom> atoms,
                           boolean cleanRelevant)
```
    Adds atoms to the "removed atom" list
    
    Parameters:
    
    atoms - atoms to be added to the "removed atom" list
    
    cleanRelevant - whether the atoms are relevant for cleaning the output molecule
  - modifyAllAtoms
```
public void modifyAllAtoms(java.util.Collection<MolAtom> atoms)
```
    Adds atoms to the "modified atom" list.
    
    Parameters:
    
    atoms - atoms to be added to the "modified atom" list.
  - modifyAllAtoms
```
public void modifyAllAtoms(java.util.Collection<MolAtom> atoms,
                           boolean cleanRelevant)
```
    Adds atoms to the "modified atom" list.
    
    Parameters:
    
    atoms - atoms to be added to the "modified atom" list.
    
    cleanRelevant - whether the atoms are relevant for cleaning the output molecule
  - setModified
```
public void setModified(boolean modified)
```
    Sets whether any modifications were applied on the molecule.
    
    Parameters:
    
    modified - whether any modifications were applied on the molecule.
  - isModified
```
public boolean isModified()
```
    Gets whether any modifications were applied on the molecule.
    
    Returns:
    
    whether any modifications were applied on the molecule.
  - oldToNew
```
public int[] oldToNew()
```
    Returns the old -> new atom index mapping.
    oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
    
    Returns:
    
    the old -> new atom index mapping
  - newToOld
```
public int[] newToOld()
```
    Returns the new -> old atom index mapping.
    newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
    
    Returns:
    
    the new -> old atom index mapping
  - oldToNew
```
public static int[] oldToNew(java.util.List<Changes> changeList,
                             Molecule target)
```
    Calculates the old -> new atom index mapping based on a list of changes.
    oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
    
    Parameters:
    
    changeList - the target list of changes
    
    target - the target molecule (needed in case of no changes)
    
    Returns:
    
    the old -> new atom index mapping based on a list of changes
  - newToOld
```
public static int[] newToOld(java.util.List<Changes> changeList,
                             Molecule target)
```
    Calculates the new -> old atom index mapping based on a list of changes.
    newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
    
    Parameters:
    
    changeList - the target list of changes
    
    target - the target molecule (needed in case of no changes)
    
    Returns:
    
    the new -> old atom index mapping based on a list of changes
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - append
```
public void append(Changes changes)
```
    Appends a set of changes to the already existing changes. Added / Removed / Modified molecules contained by the parameter are added to this object.
    
    Parameters:
    
    changes - the set of changes to be appended
  - getAction
```
public StandardizerAction getAction()
```
    Gets the base StandardizerAction of the changes
    
    Returns:
    
    the base StandardizerAction of the changes
  - setAction
```
public void setAction(StandardizerAction action)
```
    Sets the base StandardizerAction of the changes
    
    Parameters:
    
    action - the base StandardizerAction of the changes

Class Changes

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Changes

Changes

Changes

Method Detail

getOriginal

getResult

getAddedAtoms

getRemovedAtoms

getModifiedAtoms

getCleanRelevantAtoms

addAtom

addAtom

removeAtom

removeAtom

modifyAtom

modifyAtom

addAllAtoms

addAllAtoms

removeAllAtoms

removeAllAtoms

modifyAllAtoms

modifyAllAtoms

setModified

isModified

oldToNew

newToOld

oldToNew

newToOld

toString

append

getAction

setAction