ur_rna.RNAstructure.backend

Class Dynalign_object

java.lang.Object

ur_rna.RNAstructure.backend.TwoRNA

ur_rna.RNAstructure.backend.Dynalign_object

public class Dynalign_object
extends TwoRNA

Field Summary

Fields

Modifier and Type	Field and Description
private long	swigCPtr

Fields inherited from class ur_rna.RNAstructure.backend.TwoRNA

swigCMemOwn

Constructor Summary

Constructors

Modifier	Constructor and Description
	Dynalign_object()
protected	Dynalign_object(long cPtr, boolean cMemoryOwn)
	Dynalign_object(java.lang.String filename)
	Dynalign_object(java.lang.String filename1, int type1, java.lang.String filename2, int type2)
	Dynalign_object(java.lang.String filename1, int type1, java.lang.String filename2, int type2, boolean IsRNA)
	Dynalign_object(java.lang.String filename1, int type1, java.lang.String filename2, int type2, Thermodynamics thermo1)
	Dynalign_object(java.lang.String filename, short maxtrace, short bpwin, short awin, short percent)
	Dynalign_object(java.lang.String sequence1, java.lang.String sequence2)
	Dynalign_object(java.lang.String sequence1, java.lang.String sequence2, boolean IsRNA)

Method Summary

Modifier and Type	Method and Description
void	delete()
int	Dynalign()
int	Dynalign(short maxtrace)
int	Dynalign(short maxtrace, short bpwin)
int	Dynalign(short maxtrace, short bpwin, short awin)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert, java.lang.String savefile)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert, java.lang.String savefile, boolean optimalonly)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert, java.lang.String savefile, boolean optimalonly, short singlefold_subopt_percent)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert, java.lang.String savefile, boolean optimalonly, short singlefold_subopt_percent, boolean local)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert, java.lang.String savefile, boolean optimalonly, short singlefold_subopt_percent, boolean local, short numProcessors)
int	Dynalign(short maxtrace, short bpwin, short awin, short percent, short imaxseparation, float gap, boolean singleinsert, java.lang.String savefile, boolean optimalonly, short singlefold_subopt_percent, boolean local, short numProcessors, int maxpairs)
protected void	finalize()
int	ForceAlignment(int i, int k)
double	GetBestPairEnergy(int sequence, int i, int j)
protected static long	getCPtr(Dynalign_object obj)
java.lang.String	GetErrorMessage(int error)
int	GetForcedAlignment(int i, int seq)
double	GetLowestEnergy()
int	ReadAlignmentConstraints(java.lang.String filename)
void	SetProgress(ProgressHandler Progress)
void	StopProgress()
int	Templatefromct(java.lang.String ctfilename)
int	Templatefromdsv(java.lang.String dsvfilename, float maxdsvchange)
void	WriteAlignment(java.lang.String filename)

Methods inherited from class ur_rna.RNAstructure.backend.TwoRNA

getCompoundmessage, getCPtr, GetErrorCode, GetErrorDetails, GetErrorMessageString, GetRNA1, GetRNA2, GetTemperature, ResetError, setCompoundmessage, SetErrorDetails, SetTemperature

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

swigCPtr

private transient long swigCPtr

Constructor Detail

Dynalign_object

public Dynalign_object()

Dynalign_object

protected Dynalign_object(long cPtr,
                          boolean cMemoryOwn)

Dynalign_object

public Dynalign_object(java.lang.String filename)

Dynalign_object

public Dynalign_object(java.lang.String filename1,
                       int type1,
                       java.lang.String filename2,
                       int type2)

Dynalign_object

public Dynalign_object(java.lang.String filename1,
                       int type1,
                       java.lang.String filename2,
                       int type2,
                       boolean IsRNA)

Dynalign_object

public Dynalign_object(java.lang.String filename1,
                       int type1,
                       java.lang.String filename2,
                       int type2,
                       Thermodynamics thermo1)

Dynalign_object

public Dynalign_object(java.lang.String filename,
                       short maxtrace,
                       short bpwin,
                       short awin,
                       short percent)

Dynalign_object

public Dynalign_object(java.lang.String sequence1,
                       java.lang.String sequence2)

Dynalign_object

public Dynalign_object(java.lang.String sequence1,
                       java.lang.String sequence2,
                       boolean IsRNA)

Method Detail

delete

public void delete()

Overrides:

delete in class TwoRNA

Dynalign

public int Dynalign()

Dynalign

public int Dynalign(short maxtrace)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert,
                    java.lang.String savefile)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert,
                    java.lang.String savefile,
                    boolean optimalonly)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert,
                    java.lang.String savefile,
                    boolean optimalonly,
                    short singlefold_subopt_percent)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert,
                    java.lang.String savefile,
                    boolean optimalonly,
                    short singlefold_subopt_percent,
                    boolean local)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert,
                    java.lang.String savefile,
                    boolean optimalonly,
                    short singlefold_subopt_percent,
                    boolean local,
                    short numProcessors)

Dynalign

public int Dynalign(short maxtrace,
                    short bpwin,
                    short awin,
                    short percent,
                    short imaxseparation,
                    float gap,
                    boolean singleinsert,
                    java.lang.String savefile,
                    boolean optimalonly,
                    short singlefold_subopt_percent,
                    boolean local,
                    short numProcessors,
                    int maxpairs)

finalize

protected void finalize()

Overrides:

finalize in class TwoRNA

ForceAlignment

public int ForceAlignment(int i,
                          int k)

GetBestPairEnergy

public double GetBestPairEnergy(int sequence,
                                int i,
                                int j)

getCPtr

protected static long getCPtr(Dynalign_object obj)

GetErrorMessage

public java.lang.String GetErrorMessage(int error)

Overrides:

GetErrorMessage in class TwoRNA

GetForcedAlignment

public int GetForcedAlignment(int i,
                              int seq)

GetLowestEnergy

public double GetLowestEnergy()

ReadAlignmentConstraints

public int ReadAlignmentConstraints(java.lang.String filename)

SetProgress

public void SetProgress(ProgressHandler Progress)

StopProgress

public void StopProgress()

Templatefromct

public int Templatefromct(java.lang.String ctfilename)

Templatefromdsv

public int Templatefromdsv(java.lang.String dsvfilename,
                           float maxdsvchange)

WriteAlignment

public void WriteAlignment(java.lang.String filename)