Class MDocStorage


  • @PublicAPI
    public class MDocStorage
    extends Object
    Sparse dynamic document storage and reader.
    Since:
    Marvin 4.1, 04/13/2006
    • 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
      • 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
      • getDocLabel

        public 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,
                                Runnable sizeupdater,
                                int max)
                         throws 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:
        IOException - if read error occurred
        Since:
        Marvin 5.2, 01/22/2009
      • countRecordsInFraction

        @Deprecated
        public int countRecordsInFraction​(double q,
                                          int ncols,
                                          MProgressMonitor pmon)
                                   throws 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:
        IOException - if read error occurred
      • 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 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,
                                      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,
                             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:
        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:
        IndexOutOfBoundsException - if the specified index is negative or larger than the number of capacity
      • getMolPainter

        public chemaxon.marvin.paint.internal.MolPainter getMolPainter​(int k,
                                                                       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,
                                  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,
                                    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,
                                 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,
                                      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,
                                     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,
                                     String key,
                                     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,
                                   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,
                                  String key,
                                  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,
                                  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,
                                   String key,
                                   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,
                                  String key,
                                  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,
                                  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,
                                     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,
                                 String key)
      • getL

        public 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,
                         String l)
        Sets a text label in a record.
        Parameters:
        k - the record index
        j - label index
        l - the label or null
      • getT

        public 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,
                         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,
                                               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,
                                      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,
                                   String key,
                                   boolean hydr,
                                   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,
                                    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,
                                 String key,
                                 boolean v,
                                 int method,
                                 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,
                                String opts,
                                MProgressMonitor pm,
                                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,
                             String key,
                             int dim,
                             String opts,
                             MProgressMonitor pm,
                             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