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Packages that use IMatrix | |
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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 |
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Subclasses of IMatrix in org.strbio.math | |
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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 | |
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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 | |
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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 | |
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CorrectMatrix(IMatrix x)
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DMatrix(IMatrix x)
copies an IMatrix, making a copy of the data, and casting to doubles. |
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FMatrix(IMatrix x)
copies an IMatrix, making a copy of the data, and casting to floats. |
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IMatrix(IMatrix x)
copies another IMatrix. |
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SimMatrix(IMatrix x)
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StatsMatrix(IMatrix x)
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Uses of IMatrix in org.strbio.mol.lib |
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Fields in org.strbio.mol.lib declared as IMatrix | |
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IMatrix |
PSIBlastMatrices.posMatrix
Position-specific scoring matrix, N x 20. |
Methods in org.strbio.mol.lib that return IMatrix | |
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static IMatrix |
BlastConstants.blosum62()
The Blosum62 matrix, without the BZX* columns. |
Uses of IMatrix in org.strbio.mol.lib.pred2ary |
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Methods in org.strbio.mol.lib.pred2ary with parameters of type IMatrix | |
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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 |
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