Uses of Class
org.strbio.math.DVector

Packages that use DVector

org.strbio.math	These classes perform functions related to mathematics and statistics.
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.util.graph	These classes perform utility functions related to 2D and 3D graphics.

Uses of DVector in org.strbio.math

Subclasses of DVector in org.strbio.math

class

DHalfMatrix like an upper triangular DMatrix.

Methods in org.strbio.math that return DVector

static DVector	DVector.add(DVector a, DVector b) Adds two DVector's and returns a new DVector containing the sum.
static DVector	DVector.append(DVector x, DVector y) Returns a new DVector containing the first argument appended to the second.
DVector	DVector.cross(DVector x) Returns the cross product of multiplying this with another vector.
static DVector	DVector.cross(DVector x, DVector y) Returns the cross product of multiplying two vectors.
static DVector	DVector.divide(DVector a, double b) Divides a DVector by a double, and returns a new DVector containing the result.
DVector	DVectorSet.getDimension(int d) get a DVector of returning the d'th coordinate for each point.
DVector	DVector.makeZScores() returns a vector containing the Z scores for all data in the array.
static DVector	DVector.multiply(DMatrix b, DVector a) Multplies a DVector by a DMatrix, and returns a new DVector with the result.
static DVector	DVector.multiply(double b, DVector a) Multiplies a DVector by an int and returns a new DVector containing the result.
static DVector	DVector.multiply(DVector a, DMatrix b) Multplies a DVector by a DMatrix, and returns a new DVector with the result.
static DVector	DVector.multiply(DVector a, double b) Multiplies a DVector by an int and returns a new DVector containing the result.
DVector	DVectorSet.p(int i) short for point(i)
DVector	DVectorSet.point(int i) Return the i'th point in the set.
static DVector	DVector.reverse(DVector x) returns a vector which is the reverse of this one.
static DVector	DVector.subtract(DVector a, DVector b) Subtracts one DVector's from another returns a new DVector containing the difference.

Methods in org.strbio.math with parameters of type DVector

void	DVectorSet.add(DVector q) add in a single point to this set, without duplicating it.
void	DVector.add(DVector x) Adds another DVector to this one.
static DVector	DVector.add(DVector a, DVector b) Adds two DVector's and returns a new DVector containing the sum.
void	DVectorSet.addFast(DVector q) add in a single point, without checking dimensionality.
void	DVector.append(DVector x) appends the contents of another DVector to this one.
static DVector	DVector.append(DVector x, DVector y) Returns a new DVector containing the first argument appended to the second.
double	DVector.covar(DVector y) Returns the covariance of values in this array with those in another array.
DVector	DVector.cross(DVector x) Returns the cross product of multiplying this with another vector.
static DVector	DVector.cross(DVector x, DVector y) Returns the cross product of multiplying two vectors.
double	DVector.distance(DVector x) Returns the distance between this point and one pointed two by another DVector.
static double	DVector.distance(DVector a, DVector b) Returns the distance between two points pointed to by DVectors a and b.
static DVector	DVector.divide(DVector a, double b) Divides a DVector by a double, and returns a new DVector containing the result.
double	DVector.dot(DVector x) Returns the dot product of multiplying this with another vector.
static double	DVector.dot(DVector x, DVector y) Returns the dot product of multiplying two vectors.
IVector	DVectorSet.findNClosest(int n, DVector v) What are the indices of the N closest values to a DVector?
double[]	DVector.linearFit(DVector y) This will return the best linear fit to a bunch of points, assuming that this DVector contains x's, and DVectory y contains y's.
static DVector	DVector.multiply(DMatrix b, DVector a) Multplies a DVector by a DMatrix, and returns a new DVector with the result.
static DVector	DVector.multiply(double b, DVector a) Multiplies a DVector by an int and returns a new DVector containing the result.
static DVector	DVector.multiply(DVector a, DMatrix b) Multplies a DVector by a DMatrix, and returns a new DVector with the result.
static DVector	DVector.multiply(DVector a, double b) Multiplies a DVector by an int and returns a new DVector containing the result.
double	DVector.pearson(DVector y) Returns the Pearson correlation coefficient R of values in this array with values in another array.
void	DVectorSet.remove(DVector q) Remove a DVector from the set.
static DVector	DVector.reverse(DVector x) returns a vector which is the reverse of this one.
void	DVectorSet.setPointAt(int i, DVector p) set the i'th point in the set.
void	DVectorSet.setPointAtFast(int i, DVector p) set the i'th point in the set.
void	DVector.subtract(DVector x) Subtracts another DVector from this one.
static DVector	DVector.subtract(DVector a, DVector b) Subtracts one DVector's from another returns a new DVector containing the difference.

Constructors in org.strbio.math with parameters of type DVector

DVector(DVector x)
copies another DVector.

Uses of DVector in org.strbio.mol

Fields in org.strbio.mol declared as DVector

DVector	Atom.coord Atomic coordinates.
DVector	ProfResPSI.posScore Position dependent alignment score, as in PSI-BLAST.

Methods in org.strbio.mol that return DVector

DVector	ThreadSet.calcMatchRank() Calculate vector of ranks, showing one rank for each match.
DVector	ThreadSet.calcMatchZ() Calculate vector of z scores, showing one z score for each match.
DVector	Monomer.centerOfMass() Return a new DVector(3) containing the center of mass for the monomer.
DVector	Polymer.centerOfMass() Return a new DVector(3) containing the center of mass for the polymer.
DVector	ThreadSet.getEstPMatch(int i) Get a DVector of estimated probabilities for one of the proteins in the seqs set, or null if this has not been calculated.
DVector	ThreadSet.probabilityOfFindingMatch() Calculates confidence vector... this is a DVector of the length of the number of folds.

Methods in org.strbio.mol with parameters of type DVector

void	Monomer.centerOfMass(DVector cm) Finds the center of mass for the monomer and puts in in the DVector(3) that you pass it.
void	Polymer.centerOfMass(DVector cm) Finds the center of mass for the monomer and puts in in the DVector(3) that you pass it.
void	Atom.translate(DVector trans) translate an atom by adding a DVector(3) to its coordinates.
void	Monomer.translate(DVector trans) translate all atoms by adding a DVector(3) to their coordinates.
void	Molecule.translate(DVector trans) translate all atoms by adding a DVector(3) to their coordinates.
void	Polymer.translate(DVector trans) translate all monomers by adding a DVector(3) to their coordinates.

Uses of DVector in org.strbio.mol.lib

Fields in org.strbio.mol.lib declared as DVector

DVector	AlignmentParametersEA.asns1 asns1 values for each match (there is no such thing for non-matches
DVector	AlignmentParametersEA.avgScoreMatch scores for each match (gapped alignment score)
DVector	AlignmentParametersEA.avgScoreNonMatch scores for each non-match
DVector	ThreadResults.pMatch A vector of the probabilities that each protein in the library is a match.
DVector	FRParameters.scoreMatch composite score for each match (weighted sum of scores from all methods)
DVector	FRParameters.scoreNonMatch scores for each non-match
DVector	AlignmentParametersEA.totalZMatch z score of total score for each match.
DVector	AlignmentParametersEA.totalZNonMatch z score of total score for each non-match.

Methods in org.strbio.mol.lib that return DVector

static DVector	DayhoffMatrices.DayhoffFreq() Dayhoff frequencies for each amino acid.
DVector	Sippl90.getTabulated(char a, char b, int k) Returns a vector of deltaE(a,b,k).
static DVector	BlastConstants.standardProb() What BLAST thinks are the standard probabilities of each residue occurring.

Uses of DVector in org.strbio.util.graph

Fields in org.strbio.util.graph declared as DVector

protected DVector

BarPlot.bars This is a vector containint the y coordinates of the bars.

Methods in org.strbio.util.graph with parameters of type DVector

void	ClickablePointPlot.ClickListener.clicked(DVector d) This function gets called with the DVector that was clicked on, or null if nothing was clicked.
protected void	PointPlot.paintVectorAt(int x, int y, DVector v, java.awt.Graphics g) Draw one of the points somewhere.
protected void	PointColorPlot.paintVectorAt(int x, int y, DVector v, java.awt.Graphics g) This is a function to put a dot wherever a point should be plotted.
void	BarPlot.setBars(DVector x) Sets the bars being drawn.

Constructors in org.strbio.util.graph with parameters of type DVector

BarPlot(DVector x)
initialize with a set of bars.