RdcPanda
Class HnNoe

java.lang.Object
  extended by RdcPanda.HnNoe

public class HnNoe
extends java.lang.Object

This class defines data structures related to N-15 labeled NOEs. This class is no longer used and replaced by H1CS. Written by Lincong Wang (2001-2005).


Nested Class Summary
static class HnNoe.h1Comparator
          The Class h1Comparator.
static class HnNoe.hnComparator
          The Class hnComparator.
static class HnNoe.n15Comparator
          The Class n15Comparator.
static class HnNoe.resNoComparator
          The Class resNoComparator.
 
Constructor Summary
HnNoe()
          Instantiates a new hn noe.
HnNoe(double HN, double N15, double H1)
          Instantiates a new hn noe.
HnNoe(int no)
          Instantiates a new hn noe.
HnNoe(int no, java.lang.String resid, double HN, double N15, double H1, double inten)
          Instantiates a new hn noe.
HnNoe(int no, java.lang.String resid, double HN, double N15, double H1, double inten, double uncn)
          Instantiates a new hn noe.
HnNoe(int no, java.lang.String resid, double HN, double N15, double H1, double inten, java.util.Map aMap)
          Instantiates a new hn noe.
HnNoe(int no, java.lang.String resid, double HN, double N15, double H1, int labelType)
          Instantiates a new hn noe.
 
Method Summary
 java.util.Map getAssignMap()
          Gets the assign map.
 double getH1()
          Gets the h1.
 double getHN()
          Gets the hN.
 double getIntensity()
          Gets the intensity.
 int getLabel()
          Gets the label.
 double getN15()
          Gets the n15.
 int getResidueNo()
          Gets the residue no.
 java.lang.String getResidueType()
          Gets the residue type.
 java.util.Vector hnNoeReader(java.lang.String filename)
          A method for reading NOE files The required file format is:.
 java.util.Vector hnNoeReader2(java.lang.String filename)
          Another method for reading NOE files The required file format is:.
 java.util.Vector mergeHnNoe(java.util.Vector pkVec, double epsH, double epsN)
          a method to merge NOE peaks since some NOE peaks are picked with a lightly different CS more than once.
 java.util.Vector NoesyReader(java.lang.String filename)
          Read NOESY peaks in xeasy format The required file format is:.
 java.util.Vector rangeSearch(java.lang.String nucType, double a, double b, java.util.Vector pkVec)
          Extract all the HnNoe objects with proton CS or N15 CS in the range of [a, b] from an array of NOE peaks.
 void setAssignMap(java.util.Map aMap)
          Sets the assign map.
 void setResidueNo(int R)
          Sets the residue no.
 void setResidueType(java.lang.String R)
          Sets the residue type.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

HnNoe

public HnNoe()
Instantiates a new hn noe.


HnNoe

public HnNoe(int no)
Instantiates a new hn noe.

Parameters:
no - the no

HnNoe

public HnNoe(int no,
             java.lang.String resid,
             double HN,
             double N15,
             double H1,
             double inten)
Instantiates a new hn noe.

Parameters:
no - the no
resid - the resid
HN - the hN
N15 - the n15
H1 - the h1
inten - the inten

HnNoe

public HnNoe(int no,
             java.lang.String resid,
             double HN,
             double N15,
             double H1,
             double inten,
             double uncn)
Instantiates a new hn noe.

Parameters:
no - the no
resid - the resid
HN - the hN
N15 - the n15
H1 - the h1
inten - the inten
uncn - the uncn

HnNoe

public HnNoe(int no,
             java.lang.String resid,
             double HN,
             double N15,
             double H1,
             int labelType)
Instantiates a new hn noe.

Parameters:
no - the no
resid - the resid
HN - the hN
N15 - the n15
H1 - the h1
labelType - the label type

HnNoe

public HnNoe(int no,
             java.lang.String resid,
             double HN,
             double N15,
             double H1,
             double inten,
             java.util.Map aMap)
Instantiates a new hn noe.

Parameters:
no - the no
resid - the resid
HN - the hN
N15 - the n15
H1 - the h1
inten - the inten
aMap - the a map

HnNoe

public HnNoe(double HN,
             double N15,
             double H1)
Instantiates a new hn noe.

Parameters:
HN - the hN
N15 - the n15
H1 - the h1
Method Detail

getResidueNo

public int getResidueNo()
Gets the residue no.

Returns:
the residue no

getLabel

public int getLabel()
Gets the label.

Returns:
the label

getResidueType

public java.lang.String getResidueType()
Gets the residue type.

Returns:
the residue type

getHN

public double getHN()
Gets the hN.

Returns:
the hN

getN15

public double getN15()
Gets the n15.

Returns:
the n15

getH1

public double getH1()
Gets the h1.

Returns:
the h1

getIntensity

public double getIntensity()
Gets the intensity.

Returns:
the intensity

getAssignMap

public java.util.Map getAssignMap()
Gets the assign map.

Returns:
the assign map

setResidueNo

public void setResidueNo(int R)
Sets the residue no.

Parameters:
R - the new residue no

setResidueType

public void setResidueType(java.lang.String R)
Sets the residue type.

Parameters:
R - the new residue type

setAssignMap

public void setAssignMap(java.util.Map aMap)
Sets the assign map.

Parameters:
aMap - the new assign map

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

hnNoeReader

public java.util.Vector hnNoeReader(java.lang.String filename)
A method for reading NOE files The required file format is:.

Parameters:
filename - the name of the file
Returns:
a vector of HnNOE object

NoesyReader

public java.util.Vector NoesyReader(java.lang.String filename)
Read NOESY peaks in xeasy format The required file format is:.

Parameters:
filename - the name of the file
Returns:
a vector of HnNOE object

hnNoeReader2

public java.util.Vector hnNoeReader2(java.lang.String filename)
Another method for reading NOE files The required file format is:.

Parameters:
filename - the name of the file
Returns:
a vector of HnNOE object

rangeSearch

public java.util.Vector rangeSearch(java.lang.String nucType,
                                    double a,
                                    double b,
                                    java.util.Vector pkVec)
Extract all the HnNoe objects with proton CS or N15 CS in the range of [a, b] from an array of NOE peaks.

Parameters:
nucType - the type of nucleus: H1 or N15
a - the lower limit of the range
b - the up limit of the range
pkVec - an array of NOE peaks.
Returns:
the vector

mergeHnNoe

public java.util.Vector mergeHnNoe(java.util.Vector pkVec,
                                   double epsH,
                                   double epsN)
a method to merge NOE peaks since some NOE peaks are picked with a lightly different CS more than once.

Parameters:
pkVec - the pk vec
epsH - the eps h
epsN - the eps n
Returns:
the vector