Class Model


  • public abstract class Model
    extends java.lang.Object
    Project: User: rufenec Date: 1/24/13 Time: 5:02 PM
    • Constructor Detail

      • Model

        public Model​(GeomFactory factory,
                     int mode)
    • Method Detail

      • cleanReaction

        public void cleanReaction​(boolean cleanAll)
      • scale

        public void scale​(float dx,
                          float dy)
      • getSelectedReaction

        public Reaction getSelectedReaction()
      • setFragments

        public void setFragments​(StereoMolecule[] fragment)
      • getReaction

        public Reaction getReaction()
      • setReaction

        public void setReaction​(Reaction rxn)
      • setMarkushStructure

        public void setMarkushStructure​(MarkushStructure markush)
      • setDisplayMode

        public void setDisplayMode​(int dMode)
      • getMode

        public int getMode()
      • isAtomColorSupported

        public boolean isAtomColorSupported()
      • setAtomColorSupported

        public void setAtomColorSupported​(boolean acs)
      • cleanupCoordinates

        protected void cleanupCoordinates​(boolean multifragment,
                                          boolean invent)
      • analyzeFragmentMembership

        public void analyzeFragmentMembership()
      • isOnProductSide

        public boolean isOnProductSide​(double x,
                                       double y)
      • mapReaction

        public void mapReaction​(int atom,
                                java.awt.geom.Point2D left,
                                java.awt.geom.Point2D right)
      • getNextMapNo

        public int getNextMapNo()
        *********************************************************************************************************
      • popUndo

        public void popUndo()
      • pushUndo

        public void pushUndo()
      • getESRType

        public int getESRType()
      • setESRType

        public void setESRType​(int type)
      • removeChangeListener

        public void removeChangeListener​(IChangeListener l)
      • setDisplaySize

        public void setDisplaySize​(java.awt.Dimension displaySize)
      • getDisplaySize

        public java.awt.Dimension getDisplaySize()
      • setValue

        public final void setValue​(StereoMolecule value,
                                   boolean b)
      • setValue

        public void setValue​(Reaction rxn)
      • changed

        public void changed()
      • valueInvalidated

        public void valueInvalidated()
      • getMoleculeAt

        public StereoMolecule getMoleculeAt​(java.awt.geom.Point2D pt,
                                            boolean includeBond)
      • selectFragmentByAtom

        public void selectFragmentByAtom​(int rootAtom)
      • getFragmentAt

        public StereoMolecule getFragmentAt​(java.awt.geom.Point2D pt,
                                            boolean includeBond)
      • rowFromESRType

        public static int rowFromESRType​(int type)
      • esrTypeFromRow

        public static int esrTypeFromRow​(int row)
      • getSelectedAtom

        public int getSelectedAtom()
      • setSelectedAtom

        public void setSelectedAtom​(int theAtom)
      • getSelectedBond

        public int getSelectedBond()
      • setSelectedBond

        public void setSelectedBond​(int theBond)
      • setMode

        public final void setMode​(int mode)
      • getDrawingObjects

        public java.util.List<IDrawingObject> getDrawingObjects()
      • addDrawingObject

        public void addDrawingObject​(IDrawingObject o)
      • isReaction

        public boolean isReaction()
      • isFragment

        public boolean isFragment()
      • setFragment

        public void setFragment​(boolean fragment)
      • setNewMolecule

        public void setNewMolecule()
      • needsLayout

        public void needsLayout​(boolean set)
      • needsLayout

        public boolean needsLayout()
      • getDisplayMode

        public int getDisplayMode()
      • getIDCode

        public java.lang.String getIDCode()
      • getKeyStrokeBuffer

        public java.lang.StringBuilder getKeyStrokeBuffer()
      • getAtomKeyStrokeValidity

        public int getAtomKeyStrokeValidity​(java.lang.String s)
      • getMarkushCount

        public int getMarkushCount()
      • tryAutoMapReaction

        public void tryAutoMapReaction()
      • getMolFile

        public java.lang.String getMolFile​(boolean v3)
      • setMolFile

        public void setMolFile​(java.lang.String molFile)
      • getSmiles

        public java.lang.String getSmiles()
      • setSmiles

        public void setSmiles​(java.lang.String smiles)
      • getReactantCount

        public int getReactantCount()
      • flip

        public void flip​(boolean horiz)
      • addMolecule

        public void addMolecule​(StereoMolecule mol,
                                double x,
                                double y)
      • getSelectedDrawingObject

        public IDrawingObject getSelectedDrawingObject()
      • setSelectedDrawingObject

        public void setSelectedDrawingObject​(IDrawingObject sel)
      • cleanMolecule

        public void cleanMolecule​(boolean invent,
                                  boolean selectedOnly)
      • analyzeReaction

        public abstract void analyzeReaction()
      • copyMolecule

        public abstract boolean copyMolecule​(boolean selected)
      • copyReaction

        public abstract boolean copyReaction​(boolean selected)
      • pasteMolecule

        public abstract StereoMolecule pasteMolecule​(double cx,
                                                     double cy)
      • pasteReaction

        public abstract Reaction pasteReaction​(double cx,
                                               double cy)
      • setImageProvider

        public void setImageProvider​(ImageProvider p)