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Class PeptVect 

java.lang.Object
   |
   +----PeptVect
public class PeptVect
extends Object

Variable Index

o FaverageIntensity
o FFactor
multiply factor, used to equalize two vector intensities, each intensity is returned with intensity*FFactor
o FIntDecal
FIntDecal: value added to all intensities returned
o FLog
o FMassDecal
FMassDecal: value that should be added to all masses returned
o FmaxDX
o FmaxIntensity
o FmaxMass
the highest mass of peptides
o FminDX
the smallest value of margins, the leftmost mass to plot is actually defined by FminDX and not FminMass
o FminIntensity
the smallest intensity of peptides note that when an intensity is unknown, 0 should be used for more coherence
o FminMass
the smallest mass of peptides
o FSelected
o FsumIntensity
sum of intensities of all available elements in the peptide vector, used to calculate the mean value of intensities
o peptides
the vector of peptides itself, keep private (see warning above)
o prevVector

Constructor Index

o PeptVect()

Method Index

o addPept(PeptElt)
add a Peptide element and adjust max, min and average values
o addPept(PeptVect, int)
add a peptide at Index to a target Vector (sort of copy, because we do not expose the vector, this should be used)
o clearPept()
reset max and min, remove all peptides and reset mean values and sums
o Count()
number of elements in the Peptide vector (obvious, huh?)
o delPept(PeptElt)
remove a peptide element, if used - TODO: adjust mean/average min and max values
o getAverageIntensity()
o getDx1(int)
get displaced left margin of a given peptide
o getDx2(int)
get the displaced right margin of a given peptide
o getFactor()
o getIntDecal(float)
o getIntensity(int)
get the displaced and log-ed intensity of a given peptide, besides, we use FFactor to equalize vectors of peptides
o getLog()
o getMass(int)
get displaced mass of a peptide defined by index
o getMassDecal(float)
o getMaxDX()
FmaxDX defines the rightnmost mass as we consider margin values, if not, use getMinMass and getMaxMass
o getMaxIntensity()
o getMaxMass()
o getMc(int)
get the amount of missed cleavages, only if available
o getMcDesc(int)
get the annotation of the missed cleavage site for a given peptide
o getMinDX()
get the leftmost mass margin value, we displace the FminDX value by the FMassDecal (which is 0 by default) and substract 10% of the value because we plot graphs, and it's not convenient to see small regions or get masses on the Y axis
o getMinIntensity()
min and max intensity, besides, if FLog is set, we can log() all intensity values to get better view of more equal intensities (note that log concerves the bijective property where x>y -> log(x)>log(y)
o getMinMass()
real smallest mass displaced and 10% less for plotting
o getPept(int)
return an element from the vector, keep private (see warning above)
o getPosition(int)
get the position of a peptide defined by index in the resulting protein
o getRealDx1(int)
get real left margin of a given peptide
o getRealDx2(int)
get real right margin of a given peptide
o getRealIntensity(int)
real intensity of a peptide, with no displacement
o getRealMass(int)
real mass of a peptide, with no displacement (no range checking, we know what our prog does, right?:)
o getSelected()
o getSequence(int)
get the peptide genetic sequence
o ReadPeakVector(String)
read a peak vector, format of each element is: Mass Intensity LeftX RightX MC MC-Annotation Position Sequence you can have as many of those as wanted in a row NOTE: when intensity is 0, the intensity of the closest mass value will be taken from prevVector, this is used because we have always two series where only the first has intensities
o setFactor(float)
o setIntDecal(float)
o setLog(boolean)
o setMassDecal(float)
o setSelected(int)

Variables

o prevVector 
 static PeptVect prevVector
o FMassDecal 
 private float FMassDecal
FMassDecal: value that should be added to all masses returned

o FIntDecal 
 private float FIntDecal
FIntDecal: value added to all intensities returned

o peptides 
 private Vector peptides
the vector of peptides itself, keep private (see warning above)

o FsumIntensity 
 private float FsumIntensity
sum of intensities of all available elements in the peptide vector, used to calculate the mean value of intensities

o FminMass 
 private float FminMass
the smallest mass of peptides

o FmaxMass 
 private float FmaxMass
the highest mass of peptides

o FminIntensity 
 private float FminIntensity
the smallest intensity of peptides note that when an intensity is unknown, 0 should be used for more coherence

o FmaxIntensity 
 private float FmaxIntensity
o FminDX 
 private float FminDX
the smallest value of margins, the leftmost mass to plot is actually defined by FminDX and not FminMass

o FmaxDX 
 private float FmaxDX
o FaverageIntensity 
 private float FaverageIntensity
o FLog 
 private boolean FLog
o FFactor 
 private float FFactor
multiply factor, used to equalize two vector intensities, each intensity is returned with intensity*FFactor

o FSelected 
 private int FSelected

Constructors

o PeptVect 
 public PeptVect()

Methods

o setMassDecal 
 public boolean setMassDecal(float Value)
o getMassDecal 
 public float getMassDecal(float Value)
o setIntDecal 
 public boolean setIntDecal(float Value)
o getIntDecal 
 public float getIntDecal(float Value)
o addPept 
 public void addPept(PeptElt p)
add a Peptide element and adjust max, min and average values

o delPept 
 public void delPept(PeptElt p)
remove a peptide element, if used - TODO: adjust mean/average min and max values

o getPept 
 private PeptElt getPept(int i)
return an element from the vector, keep private (see warning above)

o Count 
 public int Count()
number of elements in the Peptide vector (obvious, huh?)

o clearPept 
 public void clearPept()
reset max and min, remove all peptides and reset mean values and sums

o getAverageIntensity 
 public float getAverageIntensity()
o getMinDX 
 public float getMinDX()
get the leftmost mass margin value, we displace the FminDX value by the FMassDecal (which is 0 by default) and substract 10% of the value because we plot graphs, and it's not convenient to see small regions or get masses on the Y axis

o getMaxDX 
 public float getMaxDX()
FmaxDX defines the rightnmost mass as we consider margin values, if not, use getMinMass and getMaxMass

o getMinMass 
 public float getMinMass()
real smallest mass displaced and 10% less for plotting

o getMinIntensity 
 public float getMinIntensity()
min and max intensity, besides, if FLog is set, we can log() all intensity values to get better view of more equal intensities (note that log concerves the bijective property where x>y -> log(x)>log(y)

o getMaxMass 
 public float getMaxMass()
o getMaxIntensity 
 public float getMaxIntensity()
o getRealMass 
 public float getRealMass(int Index)
real mass of a peptide, with no displacement (no range checking, we know what our prog does, right?:)

o getRealIntensity 
 public float getRealIntensity(int Index)
real intensity of a peptide, with no displacement

o getMass 
 public float getMass(int Index)
get displaced mass of a peptide defined by index

o getMc 
 public int getMc(int Index)
get the amount of missed cleavages, only if available

o getMcDesc 
 public String getMcDesc(int Index)
get the annotation of the missed cleavage site for a given peptide

o getPosition 
 public String getPosition(int Index)
get the position of a peptide defined by index in the resulting protein

o getSequence 
 public String getSequence(int Index)
get the peptide genetic sequence

o getIntensity 
 public float getIntensity(int Index)
get the displaced and log-ed intensity of a given peptide, besides, we use FFactor to equalize vectors of peptides

o getDx1 
 public float getDx1(int Index)
get displaced left margin of a given peptide

o getRealDx1 
 public float getRealDx1(int Index)
get real left margin of a given peptide

o getRealDx2 
 public float getRealDx2(int Index)
get real right margin of a given peptide

o getDx2 
 public float getDx2(int Index)
get the displaced right margin of a given peptide

o ReadPeakVector 
 public void ReadPeakVector(String s)
read a peak vector, format of each element is: Mass Intensity LeftX RightX MC MC-Annotation Position Sequence you can have as many of those as wanted in a row NOTE: when intensity is 0, the intensity of the closest mass value will be taken from prevVector, this is used because we have always two series where only the first has intensities

o addPept 
 public void addPept(PeptVect Vector,
                     int Index)
add a peptide at Index to a target Vector (sort of copy, because we do not expose the vector, this should be used)

o setLog 
 public boolean setLog(boolean Value)
o getLog 
 public boolean getLog()
o setFactor 
 public boolean setFactor(float Value)
o getFactor 
 public float getFactor()
o setSelected 
 public boolean setSelected(int Value)
o getSelected 
 public int getSelected()
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