fr.orsay.lri.varna.models.rna
Class ModeleBP

java.lang.Object
  extended by fr.orsay.lri.varna.models.rna.ModeleBP
All Implemented Interfaces:
Serializable, Comparable<ModeleBP>

public class ModeleBP
extends Object
implements Serializable, Comparable<ModeleBP>

See Also:
Serialized Form

Nested Class Summary
static class ModeleBP.Edge
           
static class ModeleBP.Stericity
           
 
Field Summary
private  ModeleBP.Edge _edge3
           
private  ModeleBP.Edge _edge5
           
private  ModeleBase _partner3
           
private  ModeleBase _partner5
           
private  ModeleBP.Stericity _stericity
           
private  ModeleBPStyle _style
           
static String PARAM_COLOR
           
static String PARAM_EDGE3
           
static String PARAM_EDGE5
           
static String PARAM_STERICITY
           
static String PARAM_THICKNESS
           
private static long serialVersionUID
           
static String VALUE_CIS
           
static String VALUE_HOOGSTEEN
           
static String VALUE_SUGAR
           
static String VALUE_TRANS
           
static String VALUE_WATSON_CRICK
           
 
Constructor Summary
ModeleBP(ModeleBase part5, ModeleBase part3)
           
ModeleBP(ModeleBase part5, ModeleBase part3, ModeleBP.Edge edge5, ModeleBP.Edge edge3, ModeleBP.Stericity ster)
           
ModeleBP(String text)
           
 
Method Summary
 void assignParameters(String parametersValue)
           
 int compareTo(ModeleBP mb)
           
 ModeleBP.Edge getEdgePartner3()
           
 ModeleBP.Edge getEdgePartner5()
           
 int getIndex3()
           
 int getIndex5()
           
 ModeleBase getPartner(ModeleBase mb)
           
 ModeleBase getPartner3()
           
 ModeleBase getPartner5()
           
 ModeleBP.Stericity getStericity()
           
 ModeleBPStyle getStyle()
           
 boolean isCanonical()
           
 boolean isCanonicalAU()
           
 boolean isCanonicalGC()
           
 boolean isCIS()
           
 boolean isTRANS()
           
 boolean isWobbleUG()
           
 void setEdge3(ModeleBP.Edge e)
           
 void setEdge5(ModeleBP.Edge e)
           
 void setPartner3(ModeleBase mb)
           
 void setPartner5(ModeleBase mb)
           
 void setStericity(ModeleBP.Stericity s)
           
 void setStyle(ModeleBPStyle e)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

serialVersionUID

private static final long serialVersionUID
See Also:
Constant Field Values

_partner5

private ModeleBase _partner5

_edge5

private ModeleBP.Edge _edge5

_partner3

private ModeleBase _partner3

_edge3

private ModeleBP.Edge _edge3

_stericity

private ModeleBP.Stericity _stericity

_style

private ModeleBPStyle _style

PARAM_COLOR

public static final String PARAM_COLOR
See Also:
Constant Field Values

PARAM_THICKNESS

public static final String PARAM_THICKNESS
See Also:
Constant Field Values

PARAM_EDGE5

public static final String PARAM_EDGE5
See Also:
Constant Field Values

PARAM_EDGE3

public static final String PARAM_EDGE3
See Also:
Constant Field Values

PARAM_STERICITY

public static final String PARAM_STERICITY
See Also:
Constant Field Values

VALUE_WATSON_CRICK

public static final String VALUE_WATSON_CRICK
See Also:
Constant Field Values

VALUE_HOOGSTEEN

public static final String VALUE_HOOGSTEEN
See Also:
Constant Field Values

VALUE_SUGAR

public static final String VALUE_SUGAR
See Also:
Constant Field Values

VALUE_CIS

public static final String VALUE_CIS
See Also:
Constant Field Values

VALUE_TRANS

public static final String VALUE_TRANS
See Also:
Constant Field Values
Constructor Detail

ModeleBP

public ModeleBP(ModeleBase part5,
                ModeleBase part3)

ModeleBP

public ModeleBP(ModeleBase part5,
                ModeleBase part3,
                ModeleBP.Edge edge5,
                ModeleBP.Edge edge3,
                ModeleBP.Stericity ster)

ModeleBP

public ModeleBP(String text)
         throws fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError,
                fr.orsay.lri.varna.exceptions.ExceptionParameterError
Throws:
fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError
fr.orsay.lri.varna.exceptions.ExceptionParameterError
Method Detail

setStericity

public void setStericity(ModeleBP.Stericity s)

setEdge5

public void setEdge5(ModeleBP.Edge e)

setEdge3

public void setEdge3(ModeleBP.Edge e)

setStyle

public void setStyle(ModeleBPStyle e)

getStyle

public ModeleBPStyle getStyle()

isCanonicalGC

public boolean isCanonicalGC()

isCanonicalAU

public boolean isCanonicalAU()

isWobbleUG

public boolean isWobbleUG()

isCanonical

public boolean isCanonical()

getStericity

public ModeleBP.Stericity getStericity()

isCIS

public boolean isCIS()

isTRANS

public boolean isTRANS()

getEdgePartner5

public ModeleBP.Edge getEdgePartner5()

getEdgePartner3

public ModeleBP.Edge getEdgePartner3()

getPartner

public ModeleBase getPartner(ModeleBase mb)

getPartner5

public ModeleBase getPartner5()

getPartner3

public ModeleBase getPartner3()

getIndex5

public int getIndex5()

getIndex3

public int getIndex3()

setPartner5

public void setPartner5(ModeleBase mb)

setPartner3

public void setPartner3(ModeleBase mb)

assignParameters

public void assignParameters(String parametersValue)
                      throws fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError,
                             fr.orsay.lri.varna.exceptions.ExceptionParameterError
Throws:
fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError
fr.orsay.lri.varna.exceptions.ExceptionParameterError

toString

public String toString()
Overrides:
toString in class Object

compareTo

public int compareTo(ModeleBP mb)
Specified by:
compareTo in interface Comparable<ModeleBP>