Package org.helm.notation2

Class MonomerStore

java.lang.Object
org.helm.notation2.MonomerStore
public class MonomerStore
extends Object
This class represents a store for monomers. It is mainly used to seperate the monomers coming from a single (XHELM) file from the monomers within the local database.
Author:
maisel

  • Constructor Details

  • Method Details

    • getMonomerDB

      public Map<String,​Map<String,​Monomer>> getMonomerDB()
      returns MonomerDB
      Returns:
      MonomerDB as Map<String, Map<String, Monomer>>

    • getSmilesMonomerDB

      public Map<String,​Monomer> getSmilesMonomerDB()
      returns SmilesMonomerDB
      Returns:
      SmilesMonomerDB as Map<String, Monomer>

    • addMonomer

      public void addMonomer​(Monomer monomer) throws IOException, MonomerException
      Adds a monomer to the store
      Parameters:
      monomer - given monomer
      Throws:
      IOException - if the monomer store can not be saved
      MonomerException - if the monomer is not valid

    • addMonomer

      public void addMonomer​(Monomer monomer, boolean dbChanged) throws IOException, MonomerException
      Adds a monomer to the store and optionally sets the dbChanged flag
      Parameters:
      monomer - given monomer
      dbChanged - if db was changed
      Throws:
      IOException - if the monomer store can not be saved
      MonomerException - if the monomer is not valid

    • hasMonomer

      public boolean hasMonomer​(String polymerType, String alternateId)
      Checks if a specific monomer exists in the store
      Parameters:
      polymerType - polymer type of monomer
      alternateId - alternateId of monomer
      Returns:
      true if monomer exists, false if not

    • getMonomer

      public Monomer getMonomer​(String polymerType, String alternateId)
      Returns the monomer specified by polymerType and alternatId
      Parameters:
      polymerType - polymer type of monomer
      alternateId - alternateId of monomer
      Returns:
      the matching monomer

    • getMonomer

      public Monomer getMonomer​(String smiles)
      Returns the monomer by smiles string
      Parameters:
      smiles - given smiles
      Returns:
      the matching monomer

    • getMonomers

      public Map<String,​Monomer> getMonomers​(String polymerType)
      Returns all monomers by polymerType
      Parameters:
      polymerType - given polymer type
      Returns:
      All monomers with polymerType

    • addNewMonomer

      public void addNewMonomer​(Monomer monomer) throws IOException, MonomerException
      Adds a monomer to the store and makes it a temporary new monomer
      Parameters:
      monomer - given monomer
      Throws:
      IOException - if the monomer can not be saved
      MonomerException - if the monomer is not valid

    • isMonomerStoreEmpty

      public boolean isMonomerStoreEmpty()
      Checks for the empty store
      Returns:
      true if the store is empty, false if not

    • clearMonomers

      public void clearMonomers()
      Clears the MonomerStore

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getPolymerTypeSet

      public Set<String> getPolymerTypeSet()
      Returns the polymer type set
      Returns:
      the polymer type set as Set<String>

    • getAllMonomersList

      public List<Monomer> getAllMonomersList()
      This method returns all monomers of the store as list sorted by polymer type
      Returns:
      all monomers of store as List<{@link Monomer}>