MDocStorage (Marvin API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.view.MDocStorage

```
@PublicAPI
public class MDocStorage
extends java.lang.Object
```
Sparse dynamic document storage and reader.

Since:

Marvin 4.1, 04/13/2006

Version:

5.3, 08/26/2009

Author:

Peter Csizmadia, Szilveszter Juhos

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`class`	`MDocStorage.CancellationException` Exception indicating that records are not available because the user cancelled file reading.
`static interface`	`MDocStorage.Listener` Document production listener.
`class`	`MDocStorage.RecordUnavailableException` Requested record is not available in the source.

Constructor Summary

Constructors
Constructor and Description

MDocStorage()
Constructs a document storage.

MDocStorage(int n)
Constructs a document storage.

Constructors
Constructor and Description
`MDocStorage()` Constructs a document storage.
`MDocStorage(int n)` Constructs a document storage.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addListener(MDocStorage.Listener l)` Adds a listener if it is not yet added.
`boolean`	`aromatize(int k, java.lang.String key, boolean v, int method, java.lang.String[] warn)` Aromatize or dearomatize molecule in the specified cell.
`boolean`	`aromatizeAll(boolean v, int method, java.lang.String[] warn)` Aromatize or dearomatize molecules in all cells.
`boolean`	`clean(int k, java.lang.String key, int dim, java.lang.String opts, MProgressMonitor pm, java.lang.String[] warn)` Clean the specified cell.
`boolean`	`cleanAll(int dim, java.lang.String opts, MProgressMonitor pm, java.lang.String[] warn)` Clean all cells.
`boolean`	`contractOrExpandSgroups(int k, java.lang.String key, boolean contr)` Contract or expand S-groups in the specified cell.
`boolean`	`contractOrExpandSgroupsAll(boolean contract)` Contract or expand S-groups in all molecules.
`int`	`countRecords(MProgressMonitor pmon, int dt, java.lang.Runnable sizeupdater, int max)` Counts the total number of records and sets the size of the document storage.
`int`	`countRecordsInFraction(double q, int ncols, MProgressMonitor pmon)` Deprecated.
`void`	`doSetSetSeqs(Molecule[] mols, int k, java.lang.String key)`
`void`	`fillWithNulls()` Set all stored document entries to null.
`int`	`getCacheCapacity()` Gets the maximum number of cached documents.
`MDocument`	`getCachedDoc(int k, java.lang.String key)` Gets the specified document if it is present in the memory.
`int[]`	`getCachedDocIndices()` Gets the indices of cached records.
`java.lang.Object`	`getCacheLock()` Gets the synchronization lock for caching operations.
`int`	`getCapacity()` Gets the total capacity.
`MDocument`	`getDoc(int k, java.lang.String key)` Gets the specified document.
`MDocument`	`getDoc(int k, java.lang.String key, MProgressMonitor pmon)` Gets the specified document.
`java.lang.String`	`getDocLabel(int k, MDocument doc)` Returns the display label for the given document and document index.
`MDocSource`	`getDocSource()` Gets the document source.
`int`	`getDocSourcePosition()` Gets the current position in the input.
`MFieldAccessor`	`getFieldAccessor()` Gets the field accessor.
`MPropertyContainer`	`getGlobalGUIProperties()` Gets the Global GUI properties.
`int`	`getIDBackgroundRGBA(int k)` Gets the background color's RGBA value in a record.
`int`	`getIDForegroundRGBA(int k)` Gets the foreground color's RGBA value in a record.
`java.lang.String`	`getL(int k, int j)` Gets a text label in a record.
`MDocStorage.Listener[]`	`getListeners()`
`MDocument`	`getMainDoc(int k)` Gets the document at the specified position.
`MDocument`	`getMainDoc(int k, MProgressMonitor pmon)` Gets the document at the specified position.
`int`	`getMaxDimCached()` Gets the maximum molecule dimension.
`DPoint3`	`getMolCenter(int k, java.lang.String key)` Gets a molecule center.
`chemaxon.marvin.paint.internal.MolPainter`	`getMolPainter(int k, java.lang.String key)` Gets a molecule painter.
`int`	`getOffset()` Gets the offset in the document source.
`int[]`	`getSelectedAtoms(int k, java.lang.String key)` Gets the selected atom indices.
`int`	`getSize()` Gets the total number of entries.
`java.lang.String`	`getT(int k, int j)` Gets a text field in a record.
`boolean`	`hydrogenize(int k, java.lang.String key, boolean hydr, java.lang.String[] warn)` Hydrogenize molecule in the specified cell.
`boolean`	`hydrogenizeAll(boolean hydr, java.lang.String[] warn)` Hydrogenize molecules in all cells.
`boolean`	`isEnabledT(int k, int j)` Tests whether a text field is enabled.
`boolean`	`isFixed(int k)` Tests whether a record is fixed.
`boolean`	`isFractionQuicklyAvailable(double x)` Tests whether the specified fraction of the total (estimated) number of records is quickly available.
`boolean`	`isRewindable()` Tests whether the document storage is rewindable.
`boolean`	`isSizeFinal()` Tests whether the storage size is final.
`void`	`removeListener(MDocStorage.Listener l)` Removes a listener.
`void`	`setAtomSetSeq(int k, java.lang.String key, int atom, int seq)` Sets the atom set sequence number of an atom.
`void`	`setAtomSetSeq(int k, java.lang.String key, java.lang.String str, int setSeq)` Sets atom set sequence numbers.
`void`	`setAtomSetSeqs(int k, java.lang.String key, int[] seqs)` Sets atom set sequence numbers.
`void`	`setBondSetSeq(int k, java.lang.String key, int firstAtomIndex, int secondAtomIndex, int seq)` Sets bond set sequence numbers.
`void`	`setBondSetSeq(int k, java.lang.String key, java.lang.String str, int setSeq)` Sets bond set sequence numbers.
`void`	`setBondSetSeqAll(int k, java.lang.String key, int seq)` Sets all bond set sequence numbers.
`void`	`setBondSetSeqs(int k, java.lang.String key, java.util.List<int[]> seqs)` Sets bond set sequence numbers.
`void`	`setCacheCapacity(int max)` Sets the maximum number of cached documents.
`void`	`setDocSource(MDocSource dp, int offset, int max)` Sets the document source.
`void`	`setEnabledT(int k, int j, boolean l)` Set the enabled state of a text field in a record.
`void`	`setFieldAccessor(MFieldAccessor fa)` Sets the field accessor.
`void`	`setFixed(int k)` Sets a document as fixed.
`boolean`	`setIDBackgroundRGBA(int k, int rgba)` Sets the background color's RGBA value in a record.
`boolean`	`setIDForegroundRGBA(int k, int rgba)` Sets the foreground color's RGBA value in a record.
`void`	`setL(int k, int j, java.lang.String l)` Sets a text label in a record.
`void`	`setListeners(MDocStorage.Listener[] arr)`
`void`	`setMolCenter(int k, java.lang.String key, DPoint3 p)` Sets a molecule center.
`void`	`setMolPainter(int k, java.lang.String key, chemaxon.marvin.paint.internal.MolPainter p)` Sets a molecule painter.
`void`	`setSelectedAtoms(int k, java.lang.String key, int[] sel)` Sets the selected atom indices.
`void`	`setSelectedAtoms(int k, java.lang.String key, java.lang.String str)` Sets the selected atom indices.
`void`	`setSize(int n)` Sets the total number of entries.
`void`	`setT(int k, int j, java.lang.String l)` Sets a text field in a record.
`void`	`storeDoc(MDocument doc, int k, java.lang.String key)` Store new document and free the oldest accessed if the number of documents is too much to fit in memory.
`void`	`storeMainDoc(MDocument doc, int k)` Store new document and free the oldest accessed if the number of documents is too much to fit in memory.

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

- Constructor Detail
  - MDocStorage
```
public MDocStorage()
```
    Constructs a document storage.
  - MDocStorage
```
public MDocStorage(int n)
```
    Constructs a document storage.
    
    Parameters:
    
    n - number of documents to store
- Method Detail
  - getDocSource
```
public MDocSource getDocSource()
```
    Gets the document source.
    
    Returns:
    
    the document source
    
    Since:
    
    Marvin 4.1.6, 03/08/2007
  - setDocSource
```
public void setDocSource(MDocSource dp,
                         int offset,
                         int max)
```
    Sets the document source.
    
    Parameters:
    
    dp - the document (molecule) source
    
    offset - number of documents to skip in the source
    
    max - maximum allowed number of documents or 0 (no restriction)
  - getFieldAccessor
```
public MFieldAccessor getFieldAccessor()
```
    Gets the field accessor.
    
    Returns:
    
    the field accessor
    
    Since:
    
    Marvin 5.0, 11/09/2007
  - setFieldAccessor
```
public void setFieldAccessor(MFieldAccessor fa)
```
    Sets the field accessor.
    
    Parameters:
    
    fa - the field accessor
    
    Since:
    
    Marvin 5.0, 11/09/2007
  - getOffset
```
public int getOffset()
```
    Gets the offset in the document source.
    
    Returns:
    
    the first record index
    
    Since:
    
    Marvin 5.0, 11/18/2007
  - getDocSourcePosition
```
public int getDocSourcePosition()
```
    Gets the current position in the input.
    
    Returns:
    
    the position or -1 if there is no document source
  - addListener
```
public void addListener(MDocStorage.Listener l)
```
    Adds a listener if it is not yet added.
    
    Parameters:
    
    l - the listener
  - removeListener
```
public void removeListener(MDocStorage.Listener l)
```
    Removes a listener.
    
    Parameters:
    
    l - the listener
  - getListeners
```
public MDocStorage.Listener[] getListeners()
```
  - setListeners
```
public void setListeners(MDocStorage.Listener[] arr)
```
  - getSize
```
public int getSize()
```
    Gets the total number of entries.
    
    Returns:
    
    the total number of entries
  - setSize
```
public void setSize(int n)
```
    Sets the total number of entries. (Resize the arrays.)
    
    Parameters:
    
    n - new capacity (maximum number of documents)
  - isSizeFinal
```
public boolean isSizeFinal()
```
    Tests whether the storage size is final.
    
    Returns:
    
    true is the storage will not grow, false if it may grow
  - getCapacity
```
public int getCapacity()
```
    Gets the total capacity.
    
    Returns:
    
    the maximum number of entries (without reallocation)
  - getCacheCapacity
```
public int getCacheCapacity()
```
    Gets the maximum number of cached documents.
    
    Returns:
    
    the cache capacity or 0 if everything is stored
  - setCacheCapacity
```
public void setCacheCapacity(int max)
```
    Sets the maximum number of cached documents.
    
    Parameters:
    
    max - maximum number of documents in memory or 0 to store everything
  - getCachedDocIndices
```
public int[] getCachedDocIndices()
```
    Gets the indices of cached records.
    
    Returns:
    
    array of indices
  - isRewindable
```
public boolean isRewindable()
```
    Tests whether the document storage is rewindable. It is rewindable if either the document source is rewindable (e.g. a seekable input stream) or all documents are stored permanently in memory after reading (if cache size equals the total capacity).
    
    Returns:
    
    true if backward seeking is possible, false otherwise
  - getDoc
```
public MDocument getDoc(int k,
                        java.lang.String key)
                 throws MDocStorage.RecordUnavailableException,
                        java.io.IOException
```
    Gets the specified document.
    
    Parameters:
    
    k - the record index
    
    key - the molecule (or document) field name, null for the main document (molecule)
    
    Throws:
    
    MDocStorage.RecordUnavailableException - if the requested record is not available (probably end of file reached too early)
    
    java.io.IOException - if read error occured
    
    Since:
    
    Marvin 5.2, 02/10/2009
  - getDoc
```
public MDocument getDoc(int k,
                        java.lang.String key,
                        MProgressMonitor pmon)
                 throws MDocStorage.RecordUnavailableException,
                        MDocStorage.CancellationException,
                        java.io.IOException
```
    Gets the specified document.
    
    Parameters:
    
    k - the record index
    
    key - the molecule (or document) field name, null for the main document (molecule)
    
    pmon - progress monitor or null
    
    Throws:
    
    MDocStorage.RecordUnavailableException - if the requested record is not available (probably end of file reached too early)
    
    MDocStorage.CancellationException - if the user cancelled the operation
    
    java.io.IOException - if read error occured
  - getMainDoc
```
public MDocument getMainDoc(int k)
                     throws MDocStorage.RecordUnavailableException,
                            java.io.IOException
```
    Gets the document at the specified position.
    
    Parameters:
    
    k - the record index
    
    Returns:
    
    the document or null
    
    Throws:
    
    MDocStorage.RecordUnavailableException - if the requested record is not available (probably end of file reached too early)
    
    java.io.IOException - if read error occured
    
    Since:
    
    Marvin 5.2, 02/10/2009
  - getMainDoc
```
public MDocument getMainDoc(int k,
                            MProgressMonitor pmon)
                     throws MDocStorage.RecordUnavailableException,
                            MDocStorage.CancellationException,
                            java.io.IOException
```
    Gets the document at the specified position.
    
    Parameters:
    
    k - the record index
    
    pmon - progress monitor or null
    
    Returns:
    
    the document or null
    
    Throws:
    
    MDocStorage.RecordUnavailableException - if the requested record is not available (probably end of file reached too early)
    
    MDocStorage.CancellationException - if the user cancelled the operation
    
    java.io.IOException - if read error occured
  - getDocLabel
```
public java.lang.String getDocLabel(int k,
                                    MDocument doc)
```
    Returns the display label for the given document and document index. The default implementation returns k+1 as String, where k is the document index.
    
    Parameters:
    
    k - the document index
    
    doc - the document
    
    Returns:
    
    the document label
    
    Since:
    
    Marvin 5.0
  - countRecords
```
public int countRecords(MProgressMonitor pmon,
                        int dt,
                        java.lang.Runnable sizeupdater,
                        int max)
                 throws java.io.IOException
```
    Counts the total number of records and sets the size of the document storage.
    
    Parameters:
    
    pmon - progress monitor or null
    
    dt - time interval in milliseconds for calling size update
    
    sizeupdater - optional runnable to be called if the total number of records changed or null
    
    max - the maximum record index where counting should stop
    
    Returns:
    
    the number of records or -1 if the user canceled the progress monitor
    
    Throws:
    
    java.io.IOException - if read error occured
    
    Since:
    
    Marvin 5.2, 01/22/2009
  - countRecordsInFraction
```
@Deprecated
public int countRecordsInFraction(double q,
                                              int ncols,
                                              MProgressMonitor pmon)
                                       throws java.io.IOException
```
    Deprecated.
    
    Counts the number of records between the start and the specified fraction of the total, estimated number of records.
    
    Parameters:
    
    q - the fraction, floating point number between 0 and 1
    
    ncols - the number of columns (1 if there are no more columns)
    
    pmon - progress monitor or null
    
    Returns:
    
    the estimated number of records in the specified fraction or -1 if the user canceled the progress monitor
    
    Throws:
    
    java.io.IOException - if read error occured
  - isFractionQuicklyAvailable
```
public boolean isFractionQuicklyAvailable(double x)
```
    Tests whether the specified fraction of the total (estimated) number of records is quickly available. A record is quickly available if its file position is known (because it was previously retrieved or skipped) or it is in the memory (if no document source is present).
    
    Parameters:
    
    x - the fraction, floating point number between 0 and 1
    
    Returns:
    
    true if the specified fraction is quickly available, false otherwise
  - getCacheLock
```
public java.lang.Object getCacheLock()
```
    Gets the synchronization lock for caching operations.
    
    Returns:
    
    the lock object
    
    Since:
    
    Marvin 5.0, 12/04/2007
  - getMaxDimCached
```
public int getMaxDimCached()
```
    Gets the maximum molecule dimension.
    
    Returns:
    
    the maximum dimension
  - getCachedDoc
```
public MDocument getCachedDoc(int k,
                              java.lang.String key)
```
    Gets the specified document if it is present in the memory.
    
    Parameters:
    
    k - the record index
    
    key - the molecule (or document) field name, null for the main document (molecule)
    
    Returns:
    
    the document or null
    
    Since:
    
    Marvin 5.0, 11/18/2007
  - storeDoc
```
public void storeDoc(MDocument doc,
                     int k,
                     java.lang.String key)
```
    Store new document and free the oldest accessed if the number of documents is too much to fit in memory.
    
    Parameters:
    
    doc - the new document
    
    k - record index (minus doc source offset)
    
    key - the molecule (or document) field name, null for the main document (molecule)
  - storeMainDoc
```
public void storeMainDoc(MDocument doc,
                         int k)
```
    Store new document and free the oldest accessed if the number of documents is too much to fit in memory.
    
    Parameters:
    
    doc - the new document
    
    k - record index (minus doc source offset)
  - isFixed
```
public boolean isFixed(int k)
```
    Tests whether a record is fixed.
    
    Parameters:
    
    k - the record index
    
    Returns:
    
    true if the document object will remain in memory until the end of life of this storage object, false if it can be freed and reloaded dynamically to save memory
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the specified index is negative.
  - setFixed
```
public void setFixed(int k)
```
    Sets a document as fixed. Fixed documents are never freed, they remain in memory until the end of life of this storage object.
    
    Parameters:
    
    k - the document entry index
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the specified index is negative or larger than the number of capacity
  - getMolPainter
```
public chemaxon.marvin.paint.internal.MolPainter getMolPainter(int k,
                                                               java.lang.String key)
```
    Gets a molecule painter.
    
    Parameters:
    
    k - the document entry index
    
    key - the molecule field name, null for the main document (molecule)
    
    Returns:
    
    the molecule painter or null
  - setMolPainter
```
public void setMolPainter(int k,
                          java.lang.String key,
                          chemaxon.marvin.paint.internal.MolPainter p)
```
    Sets a molecule painter.
    
    Parameters:
    
    k - the document entry index
    
    key - the molecule field name, null for the main document (molecule)
    
    p - the painter
  - getMolCenter
```
public DPoint3 getMolCenter(int k,
                            java.lang.String key)
```
    Gets a molecule center.
    
    Parameters:
    
    k - the document entry index
    
    key - the molecule field name, null for the main document (molecule)
    
    Returns:
    
    the center
  - setMolCenter
```
public void setMolCenter(int k,
                         java.lang.String key,
                         DPoint3 p)
```
    Sets a molecule center.
    
    Parameters:
    
    k - the document entry index
    
    key - the molecule field name, null for the main document (molecule)
    
    p - the center point
  - getSelectedAtoms
```
public int[] getSelectedAtoms(int k,
                              java.lang.String key)
```
    Gets the selected atom indices.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    Returns:
    
    selected atom indices
  - setSelectedAtoms
```
public void setSelectedAtoms(int k,
                             java.lang.String key,
                             int[] sel)
```
    Sets the selected atom indices.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    sel - array containing the selected atom indices
  - setSelectedAtoms
```
public void setSelectedAtoms(int k,
                             java.lang.String key,
                             java.lang.String str)
```
    Sets the selected atom indices.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    str - string containing a comma separated list of atom indices
  - setAtomSetSeqs
```
public void setAtomSetSeqs(int k,
                           java.lang.String key,
                           int[] seqs)
```
    Sets atom set sequence numbers.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    seqs - array of atom set sequence numbers
  - setAtomSetSeq
```
public void setAtomSetSeq(int k,
                          java.lang.String key,
                          java.lang.String str,
                          int setSeq)
```
    Sets atom set sequence numbers.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    str - string containing a comma separated list of atom indices
    
    setSeq - atom set sequence number
  - setAtomSetSeq
```
public void setAtomSetSeq(int k,
                          java.lang.String key,
                          int atom,
                          int seq)
```
    Sets the atom set sequence number of an atom.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    atom - atom index
    
    seq - atom set sequence number
  - setBondSetSeqs
```
public void setBondSetSeqs(int k,
                           java.lang.String key,
                           java.util.List<int[]> seqs)
```
    Sets bond set sequence numbers.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    seqs - vector of bond set sequence numbers
  - setBondSetSeq
```
public void setBondSetSeq(int k,
                          java.lang.String key,
                          java.lang.String str,
                          int setSeq)
```
    Sets bond set sequence numbers.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    str - string containing a comma separated list of bonds in j1-j2 format, where j1 and j2 are atom indices
    
    setSeq - bond set sequence number
  - setBondSetSeq
```
public void setBondSetSeq(int k,
                          java.lang.String key,
                          int firstAtomIndex,
                          int secondAtomIndex,
                          int seq)
```
    Sets bond set sequence numbers.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    firstAtomIndex - first atom index
    
    secondAtomIndex - second atom index
    
    seq - bond set sequence number
  - setBondSetSeqAll
```
public void setBondSetSeqAll(int k,
                             java.lang.String key,
                             int seq)
```
    Sets all bond set sequence numbers.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    seq - bond set sequence number
  - doSetSetSeqs
```
public void doSetSetSeqs(Molecule[] mols,
                         int k,
                         java.lang.String key)
```
  - getL
```
public java.lang.String getL(int k,
                             int j)
```
    Gets a text label in a record.
    
    Parameters:
    
    k - the record index
    
    j - label index
    
    Returns:
    
    the label or null
  - setL
```
public void setL(int k,
                 int j,
                 java.lang.String l)
```
    Sets a text label in a record.
    
    Parameters:
    
    k - the record index
    
    j - label index
    
    l - the label or null
  - getT
```
public java.lang.String getT(int k,
                             int j)
```
    Gets a text field in a record.
    
    Parameters:
    
    k - the record index
    
    j - text field index
    
    Returns:
    
    the text or null
  - setT
```
public void setT(int k,
                 int j,
                 java.lang.String l)
```
    Sets a text field in a record.
    
    Parameters:
    
    k - the record index
    
    j - label index
    
    l - the text or null
  - isEnabledT
```
public boolean isEnabledT(int k,
                          int j)
```
    Tests whether a text field is enabled.
    
    Parameters:
    
    k - the record index
    
    j - text field index
    
    Returns:
    
    true if enabled, false otherwise
  - setEnabledT
```
public void setEnabledT(int k,
                        int j,
                        boolean l)
```
    Set the enabled state of a text field in a record.
    
    Parameters:
    
    k - the record index
    
    j - label index
    
    l - enable (true) or disable (false)
  - getIDBackgroundRGBA
```
public int getIDBackgroundRGBA(int k)
```
    Gets the background color's RGBA value in a record.
    
    Parameters:
    
    k - the record index
    
    Returns:
    
    the RGB value or 0 if unset
    
    Since:
    
    Marvin 5.2, 02/22/2009
  - setIDBackgroundRGBA
```
public boolean setIDBackgroundRGBA(int k,
                                   int rgba)
```
    Sets the background color's RGBA value in a record.
    
    Parameters:
    
    k - the record index
    
    rgba - the RGBA value or 0 to reset the default color
    
    Returns:
    
    true if the color changed, false otherwise
    
    Since:
    
    Marvin 5.2, 02/22/2009
  - getIDForegroundRGBA
```
public int getIDForegroundRGBA(int k)
```
    Gets the foreground color's RGBA value in a record.
    
    Parameters:
    
    k - the record index
    
    Returns:
    
    the RGB value or 0 if unset
    
    Since:
    
    Marvin 5.2, 02/22/2009
  - setIDForegroundRGBA
```
public boolean setIDForegroundRGBA(int k,
                                   int rgba)
```
    Sets the foreground color's RGBA value in a record.
    
    Parameters:
    
    k - the record index
    
    rgba - the RGBA value or 0 to reset the default color
    
    Returns:
    
    true if the color changed, false otherwise
    
    Since:
    
    Marvin 5.2.1, 04/14/2009
  - fillWithNulls
```
public void fillWithNulls()
```
    Set all stored document entries to null.
  - contractOrExpandSgroupsAll
```
public boolean contractOrExpandSgroupsAll(boolean contract)
```
    Contract or expand S-groups in all molecules.
    
    Parameters:
    
    contract - contract (true or expand (false)
    
    Returns:
    
    true if the document is changed, false otherwise
  - contractOrExpandSgroups
```
public boolean contractOrExpandSgroups(int k,
                                       java.lang.String key,
                                       boolean contr)
```
    Contract or expand S-groups in the specified cell.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    contr - contract (true or expand (false)
    
    Returns:
    
    true if the document is changed, false otherwise
  - hydrogenizeAll
```
public boolean hydrogenizeAll(boolean hydr,
                              java.lang.String[] warn)
```
    Hydrogenize molecules in all cells.
    
    Parameters:
    
    hydr - hydrogenize (true or dehydrogenize (false)
    
    warn - 1-element array to store the warning message, or null
    
    Returns:
    
    true if the document is changed, false otherwise
  - hydrogenize
```
public boolean hydrogenize(int k,
                           java.lang.String key,
                           boolean hydr,
                           java.lang.String[] warn)
```
    Hydrogenize molecule in the specified cell.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    hydr - hydrogenize (true or dehydrogenize (false)
    
    warn - 1-element array to store the warning message, or null
    
    Returns:
    
    true if the document is changed, false otherwise
  - aromatizeAll
```
public boolean aromatizeAll(boolean v,
                            int method,
                            java.lang.String[] warn)
```
    Aromatize or dearomatize molecules in all cells.
    
    Parameters:
    
    v - aromatize (true or dearomatize (false)
    
    method - aromatization method or 0
    
    warn - 1-element array to store the warning message, or null
    
    Returns:
    
    true if the document is changed, false otherwise
    
    Since:
    
    Marvin 4.1.1, 09/08/2006
  - aromatize
```
public boolean aromatize(int k,
                         java.lang.String key,
                         boolean v,
                         int method,
                         java.lang.String[] warn)
```
    Aromatize or dearomatize molecule in the specified cell.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    v - aromatize (true or dearomatize (false)
    
    method - aromatization method or 0
    
    warn - 1-element array to store the warning message, or null
    
    Returns:
    
    true if the document is changed, false otherwise
    
    Since:
    
    Marvin 4.1.1, 09/08/2006
  - cleanAll
```
public boolean cleanAll(int dim,
                        java.lang.String opts,
                        MProgressMonitor pm,
                        java.lang.String[] warn)
```
    Clean all cells.
    
    Parameters:
    
    dim - dimension, 2 or 3
    
    opts - cleaning options or null
    
    pm - progress monitor to use or null
    
    warn - 1-element array to store the warning message, or null
    
    Returns:
    
    true if the document is changed, false otherwise
    
    Since:
    
    Marvin 5.0, 09/09/2007
  - clean
```
public boolean clean(int k,
                     java.lang.String key,
                     int dim,
                     java.lang.String opts,
                     MProgressMonitor pm,
                     java.lang.String[] warn)
```
    Clean the specified cell.
    
    Parameters:
    
    k - the record index
    
    key - the molecule field name, null for the main document (molecule)
    
    dim - dimension, 2 or 3
    
    opts - cleaning options or null
    
    pm - progress monitor to use or null
    
    warn - 1-element array to store the warning message, or null
    
    Returns:
    
    true if the document is changed, false otherwise
    
    Since:
    
    Marvin 5.0, 09/09/2007
  - getGlobalGUIProperties
```
public MPropertyContainer getGlobalGUIProperties()
```
    Gets the Global GUI properties.
    
    Returns:
    
    the properties
    
    Since:
    
    Marvin 5.0, 10/16/2006

Class MDocStorage

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MDocStorage

MDocStorage

Method Detail

getDocSource

setDocSource

getFieldAccessor

setFieldAccessor

getOffset

getDocSourcePosition

addListener

removeListener

getListeners

setListeners

getSize

setSize

isSizeFinal

getCapacity

getCacheCapacity

setCacheCapacity

getCachedDocIndices

isRewindable

getDoc

getDoc

getMainDoc

getMainDoc

getDocLabel

countRecords

countRecordsInFraction

isFractionQuicklyAvailable

getCacheLock

getMaxDimCached

getCachedDoc

storeDoc

storeMainDoc

isFixed

setFixed

getMolPainter

setMolPainter

getMolCenter

setMolCenter

getSelectedAtoms

setSelectedAtoms

setSelectedAtoms

setAtomSetSeqs

setAtomSetSeq

setAtomSetSeq

setBondSetSeqs

setBondSetSeq

setBondSetSeq

setBondSetSeqAll

doSetSetSeqs

getL

setL

getT

setT

isEnabledT

setEnabledT

getIDBackgroundRGBA

setIDBackgroundRGBA

getIDForegroundRGBA

setIDForegroundRGBA

fillWithNulls

contractOrExpandSgroupsAll

contractOrExpandSgroups

hydrogenizeAll

hydrogenize

aromatizeAll

aromatize

cleanAll

clean

getGlobalGUIProperties