Uses of Class
org.strbio.math.IMatrix

Packages that use IMatrix
org.strbio.math These classes perform functions related to mathematics and statistics. 
org.strbio.mol.lib These classes represent conceptual objects used in structural biology algorithms. 
org.strbio.mol.lib.pred2ary These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes. 
 

Uses of IMatrix in org.strbio.math
 

Subclasses of IMatrix in org.strbio.math
 class CorrectMatrix
          If your prediction is yes/no, or if you are only interested in stats on correctness and incorrectness, you can create a matrix which is 2xN, where N is the number of possible categories in reality, and data[0][i] indicates the number of wrong predictions of things belonging to catogory i (you predicted them as something other than i), while data[1][i] indicates the number of correct predictions of things belonging to category i.
 class SimMatrix
          This is a NxN matrix, where data[i][j] indicates the number of times something was actually i, but predicted to be j.
 class StatsMatrix
          This class describes a special kind of integer matrix which is used for keeping stats on how well a predictive procedure is performing.
 

Methods in org.strbio.math that return IMatrix
static IMatrix IMatrix.add(IMatrix a, IMatrix b)
          Adds two IMatrix's and returns a new IMatrix containing the sum.
static IMatrix IMatrix.multiply(IMatrix a, int b)
          Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
static IMatrix IMatrix.multiply(int b, IMatrix a)
          Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
static IMatrix IMatrix.subtract(IMatrix a, IMatrix b)
          Subtracts one IMatrix's from another returns a new IMatrix containing the difference.
 

Methods in org.strbio.math with parameters of type IMatrix
 void IMatrix.add(IMatrix x)
          Adds another IMatrix to this one.
static IMatrix IMatrix.add(IMatrix a, IMatrix b)
          Adds two IMatrix's and returns a new IMatrix containing the sum.
static IMatrix IMatrix.multiply(IMatrix a, int b)
          Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
static IMatrix IMatrix.multiply(int b, IMatrix a)
          Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
 void IMatrix.subtract(IMatrix x)
          Subtracts another IMatrix from this one.
static IMatrix IMatrix.subtract(IMatrix a, IMatrix b)
          Subtracts one IMatrix's from another returns a new IMatrix containing the difference.
 

Constructors in org.strbio.math with parameters of type IMatrix
CorrectMatrix(IMatrix x)
           
DMatrix(IMatrix x)
          copies an IMatrix, making a copy of the data, and casting to doubles.
FMatrix(IMatrix x)
          copies an IMatrix, making a copy of the data, and casting to floats.
IMatrix(IMatrix x)
          copies another IMatrix.
SimMatrix(IMatrix x)
           
StatsMatrix(IMatrix x)
           
 

Uses of IMatrix in org.strbio.mol.lib
 

Fields in org.strbio.mol.lib declared as IMatrix
 IMatrix PSIBlastMatrices.posMatrix
          Position-specific scoring matrix, N x 20.
 

Methods in org.strbio.mol.lib that return IMatrix
static IMatrix BlastConstants.blosum62()
          The Blosum62 matrix, without the BZX* columns.
 

Uses of IMatrix in org.strbio.mol.lib.pred2ary
 

Methods in org.strbio.mol.lib.pred2ary with parameters of type IMatrix
 void PredClassProfile.estAccy(IMatrix ea_h, IMatrix ea_e, IMatrix ea_c)
          estimate accuracy on this protein
 void TPSet.estAccy(IMatrix ea_h, IMatrix ea_e, IMatrix ea_c)
          estimate accuracy, replacing h, e, predStructure, and the SM matrices
 void TPSet.estAccyCount(IMatrix ea_h, IMatrix ea_e, IMatrix ea_c)
          make count matrices for est_accy