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API User's Guide  Class Hierarchy
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Index of all Fields and Methods

A

addPept(PeptElt). Method in class PeptVect
add a Peptide element and adjust max, min and average values
addPept(PeptVect, int). Method in class PeptVect
add a peptide at Index to a target Vector (sort of copy, because we do not expose the vector, this should be used)
addZoom(PeptVect, float, float). Method in class IMassZoom
add a new zoom vector, adjust multiply factor and recalc the minmax values
addZoom(PeptVect, String, String). Method in class IMassZoom
add zoom from minMass to maxMass
adjustMinMax(). Method in class IMassZoom
adjustMinMax(PeptVect). Method in class IMassGraph
aHeight. Static variable in class BioGraph
aWidth. Static variable in class BioGraph
Axis. Variable in class BaseGraph

B

BaseGraph(int, int, int, int). Constructor for class BaseGraph
graph constructor
BaseMassGraph(int, int, int, int). Constructor for class BaseMassGraph
BioGraph(). Constructor for class BioGraph
default constructor, well, this does actually nothing, but is is considered as _correct_ to make a void constructor and a copy constructor (too lazy to do that:)
Bold. Variable in class DragText
Border. Variable in class BaseGraph
BorderColor. Variable in class BaseGraph
BTFactor. Variable in class BioGraph
BTGrid. Variable in class BioGraph
BTLegend. Variable in class BioGraph
BTLog. Variable in class BioGraph
BTScale. Variable in class BioGraph
BTTolerance. Variable in class BioGraph

C

c4. Variable in class BaseGraph
calcAxis(). Method in class BaseGraph
graph charting algorithm
calcRealX(int). Method in class BaseGraph
calculate a real X/Y value from a plotted point same for Y
calcRealY(int). Method in class BaseGraph
calcRelX(float). Method in class BaseGraph
calculate a relative point from a real value same for Y
calcRelY(float). Method in class BaseGraph
calcTolerated(float). Method in class IMassGraph
calcTolerated(float). Method in class IMassZoom
calcTolerated(String). Method in class IMassGraph
calculate the tolerance vector
calcTolerated(String). Method in class IMassZoom
we're interested in matching masses, so using a tolerance, calculate the matching masses in order to plot them later
Centered. Variable in class DragText
clearPept(). Method in class PeptVect
reset max and min, remove all peptides and reset mean values and sums
cmdPanel. Variable in class BioGraph
Count(). Method in class PeptVect
number of elements in the Peptide vector (obvious, huh?)

D

decalList. Variable in class IMassGraph
the attached displacement list for peptide masses
delPept(PeptElt). Method in class PeptVect
remove a peptide element, if used - TODO: adjust mean/average min and max values
destroy(). Method in class BioGraph
DragCanvas(). Constructor for class DragCanvas
draggableCanvas. Static variable in class BioGraph
Dragging. Variable in class DragCanvas
dragPosition. Variable in class BioGraph
key and mouse draggable canvas services
DragText(String, int, int, int, Color). Constructor for class DragText
construct a text (s) at position (x,y) of size(sis) and color(c)
dragXPos. Variable in class DragCanvas
dragging/not dragging and drag position
drawPeekPoint(Graphics, float, float). Method in class BaseGraph
draw a rounded Peek
drawPeptLegend(Graphics, int, String). Method in class IMassGraph
draw the Peptide Mass plot legend
drawPoint(Graphics, float, float, Color). Method in class BaseGraph
draw a point, dot if Peeks, join if Wire and fill otherwise

E

ex. Variable in class BaseGraph
ey. Variable in class BaseGraph

F

FaverageIntensity. Variable in class PeptVect
FColor. Variable in class BaseGraph
Fdx1. Variable in class PeptElt
Fdx1 and Fdx2 define respectively the left and the right mass margin we get due to a mistake made by a spectrometer
Fdx2. Variable in class PeptElt
FFactor. Variable in class BaseMassGraph
FFactor. Variable in class PeptVect
multiply factor, used to equalize two vector intensities, each intensity is returned with intensity*FFactor
FIntDecal. Variable in class PeptVect
FIntDecal: value added to all intensities returned
FIntensity. Variable in class PeptElt
Relative intensity of a Peptide after a spectrometer digestion (relative to Carbon-12 (? not very sure))
FLog. Variable in class IMassGraph
FLog. Variable in class PeptVect
FMass. Variable in class PeptElt
FMassDecal. Variable in class PeptVect
FMassDecal: value that should be added to all masses returned
FmaxDX. Variable in class PeptVect
FmaxIntensity. Variable in class PeptVect
FmaxMass. Variable in class PeptVect
the highest mass of peptides
FMc. Variable in class PeptElt
FMcDesc. Variable in class PeptElt
FminDX. Variable in class PeptVect
the smallest value of margins, the leftmost mass to plot is actually defined by FminDX and not FminMass
FminIntensity. Variable in class PeptVect
the smallest intensity of peptides note that when an intensity is unknown, 0 should be used for more coherence
FminMass. Variable in class PeptVect
the smallest mass of peptides
FPeptVector. Variable in class IMassZoom
we look at two vectors only, see note in BaseMassGraph for implementation options
FPosition. Variable in class PeptElt
FSecVector. Variable in class IMassZoom
FSelected. Variable in class PeptVect
FSequence. Variable in class PeptElt
FsumIntensity. Variable in class PeptVect
sum of intensities of all available elements in the peptide vector, used to calculate the mean value of intensities
FTolerated. Variable in class IMassGraph
calculate the tolerance vector (explained above)
FTolValue. Variable in class IMassZoom
fv. Variable in class BaseGraph

G

getAddVector(). Method in class IMassGraph
getAppletInfo(). Method in class BioGraph
getAverageIntensity(). Method in class PeptVect
getAxis(). Method in class BaseGraph
getBorder(). Method in class BaseGraph
getBorderColor(). Method in class BaseGraph
getColor(). Method in class BaseGraph
getDecalList(). Method in class IMassGraph
getDx1(). Method in class PeptElt
getDx1(int). Method in class PeptVect
get displaced left margin of a given peptide
getDx2(). Method in class PeptElt
getDx2(int). Method in class PeptVect
get the displaced right margin of a given peptide
getFactor(). Method in class BaseMassGraph
getFactor(). Method in class PeptVect
getGrid(). Method in class BaseGraph
getIntDecal(float). Method in class PeptVect
getIntensity(). Method in class PeptElt
getIntensity(int). Method in class PeptVect
get the displaced and log-ed intensity of a given peptide, besides, we use FFactor to equalize vectors of peptides
getLegend(). Method in class BaseGraph
getLog(). Method in class PeptVect
getMass(). Method in class PeptElt
getMass(int). Method in class PeptVect
get displaced mass of a peptide defined by index
getMassDecal(float). Method in class PeptVect
getMassVector(). Method in class IMassGraph
getMaxDX(). Method in class PeptVect
FmaxDX defines the rightnmost mass as we consider margin values, if not, use getMinMass and getMaxMass
getMaxIntensity(). Method in class PeptVect
getMaxMass(). Method in class PeptVect
getMc(). Method in class PeptElt
getMc(int). Method in class PeptVect
get the amount of missed cleavages, only if available
getMcDesc(). Method in class PeptElt
getMcDesc(int). Method in class PeptVect
get the annotation of the missed cleavage site for a given peptide
getMinDX(). Method in class PeptVect
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
getMinIntensity(). Method in class PeptVect
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)
getMinMass(). Method in class PeptVect
real smallest mass displaced and 10% less for plotting
getOrtho(). Method in class BaseGraph
getPeeks(). Method in class BaseGraph
getPept(int). Method in class PeptVect
return an element from the vector, keep private (see warning above)
getPosition(). Method in class PeptElt
getPosition(int). Method in class PeptVect
get the position of a peptide defined by index in the resulting protein
getRealDx1(int). Method in class PeptVect
get real left margin of a given peptide
getRealDx2(int). Method in class PeptVect
get real right margin of a given peptide
getRealIntensity(int). Method in class PeptVect
real intensity of a peptide, with no displacement
getRealMass(int). Method in class PeptVect
real mass of a peptide, with no displacement (no range checking, we know what our prog does, right?:)
getScale(). Method in class BaseGraph
getSelected(). Method in class PeptVect
getSequence(). Method in class PeptElt
getSequence(int). Method in class PeptVect
get the peptide genetic sequence
getTolerated(). Method in class IMassGraph
getWire(). Method in class BaseGraph
getZoomListEnd(). Method in class IMassZoom
getZoomListStart(). Method in class IMassZoom
Grid. Variable in class BaseGraph

H

Height. Variable in class DragCanvas
hx. Variable in class BaseGraph
hy. Variable in class BaseGraph

I

i. Variable in class BaseGraph
IMassGraph(int, int, int, int). Constructor for class IMassGraph
IMassZoom(int, int, int, int). Constructor for class IMassZoom
init(). Method in class BioGraph
Applet input can be a series of PeaksX (Peaks1, Peaks2, etc...) of PeptVect readable values (check PeptVect annotations) with PeaksXName for graph annotations
Intersects(int, int). Method in class DragCanvas
point(x,y) intersects current object?
Intersects(int, int). Method in class DragText
point(x,y) intersects current object?
isDragging. Variable in class BioGraph
isDragging(). Method in class DragCanvas
isFetched. Variable in class BioGraph
Italic. Variable in class DragText

J

j. Variable in class BaseGraph

K

k. Variable in class BaseGraph
keyDown(Event, int). Method in class BioGraph

L

l4. Variable in class BaseGraph
Legend. Variable in class BaseGraph
ll. Variable in class BaseGraph

M

M_WIDTH. Static variable in class IMassZoom
MassAbout. Variable in class BioGraph
MassGraph. Variable in class BioGraph
MassListEnd. Variable in class IMassZoom
selectors from min and max masses for zoom
MassListStart. Variable in class IMassZoom
selectors from min and max masses for zoom
MassNames. Variable in class BioGraph
MassNames. Variable in class IMassGraph
massSet. Variable in class IMassZoom
MassTitle. Variable in class BioGraph
MassVector. Variable in class BioGraph
MassVector. Variable in class IMassGraph
the current petide vector
MassVectors. Variable in class BioGraph
MassVectors. Variable in class IMassGraph
all plotted vectors with their respective names
MassZoom. Variable in class BioGraph
MatchLabel. Variable in class BioGraph
maxcol. Variable in class BaseGraph
maxlig. Variable in class BaseGraph
mouseDown(Event, int, int). Method in class BioGraph
mouseDrag(Event, int, int). Method in class BioGraph
mouseMove(Event, int, int). Method in class BioGraph
mouseMove(Event, int, int). Method in class DragCanvas
mouseUp(Event, int, int). Method in class BioGraph
MouseX. Variable in class DragCanvas
last mouse move position
MouseY. Variable in class DragCanvas
Multiline. Variable in class DragText

O

Ortho. Variable in class BaseGraph

P

paint(Graphics). Method in class BioGraph
since we do double-buffer, this should be empty
paint(Graphics). Method in class DragCanvas
frame the current object, place location information if framed, etc
paint(Graphics). Method in class DragText
paint text, for shaded, simply paint twice with a displacement
paint(Graphics). Method in class IMassGraph
paint the object # adjust the multiply factor # set the wire option depending on the location of the vector # paint legend
paint(Graphics). Method in class IMassZoom
glob paint loop, axis, frame, etc...
paintAddVector(Graphics). Method in class IMassZoom
paint the second vector
paintAll(Graphics). Method in class BioGraph
paintAxis(Graphics). Method in class BaseGraph
paint X and Y axis
paintComponents(Graphics). Method in class BioGraph
paintCurrentMPept(PeptVect, Graphics). Method in class BaseMassGraph
paint a Peptide tooltip (the small yellow box with relevant info)
paintMassVector(Graphics). Method in class IMassGraph
paint the current mass vector
paintText(Graphics, String, int, int, int, boolean). Method in class DragText
calculate line width, etc, paint line by line if needed - nothing exciting ...
paintTolVector(Graphics). Method in class IMassGraph
paint the tolVector, a tolerance vector is a series of peptide masses matching between the first and the second peptide vector in the mass series
paintTolVector(Graphics). Method in class IMassZoom
show points that have matched the tolerance
paintZoomVector(Graphics). Method in class IMassZoom
paint the zoom vector
Peaks. Variable in class BioGraph
Peeks. Variable in class BaseGraph
PeptAnnotation. Variable in class BioGraph
PeptElt(). Constructor for class PeptElt
void constructor for vectorisation and listing
PeptElt(float, float, float, float, int, String, String, String). Constructor for class PeptElt
constructing a peptide with all information, when some information should be omitted, use "?" for string values and 0 for integer or float values
peptides. Variable in class PeptVect
the vector of peptides itself, keep private (see warning above)
PeptVect(). Constructor for class PeptVect
PrevPoint. Variable in class BaseGraph
prevVector. Static variable in class PeptVect
print(Graphics). Method in class BioGraph
printAll(Graphics). Method in class BioGraph
printComponents(Graphics). Method in class BioGraph
unfortunately this does not work under Java 1.0, when run with full Java 1.1 api, printing works just fine in BioGraph
px. Variable in class BaseGraph
py. Variable in class BaseGraph

R

r. Variable in class BaseGraph
ReadPeakVector(String). Method in class PeptVect
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
resetDragging(boolean). Method in class DragCanvas
drag modifiers, standard method as used in Win32 API
Reshape(). Method in class BioGraph
Reshape(). Method in class IMassZoom
run(). Method in class BioGraph

S

Scale. Variable in class BaseGraph
scaleStr. Variable in class BaseGraph
scaleX. Variable in class BaseGraph
scaleY. Variable in class BaseGraph
setAxis(boolean). Method in class BaseGraph
Graph Axis
setBold(boolean). Method in class DragText
setBorder(boolean). Method in class BaseGraph
Graph Border
setBorderColor(Color). Method in class BaseGraph
border color
setCentered(boolean). Method in class DragText
setColor(Color). Method in class BaseGraph
Graph Color
setColor(Color). Method in class DragText
setDPos(int, int, int, int). Method in class DragCanvas
set the relative drag position
setDragging(boolean). Method in class DragCanvas
setDx1(float). Method in class PeptElt
setDx2(float). Method in class PeptElt
setFactor(boolean). Method in class BaseMassGraph
common multiply factor
setFactor(float). Method in class PeptVect
setGrid(boolean). Method in class BaseGraph
Graph Grid
setIntDecal(float). Method in class PeptVect
setIntensity(float). Method in class PeptElt
setItalic(boolean). Method in class DragText
setLegend(boolean). Method in class BaseGraph
Graph Legend
setLog(boolean). Method in class IMassGraph
set the log() factor, explained in PeptVect, do not forget to adjust min/max
setLog(boolean). Method in class IMassZoom
setLog(boolean). Method in class PeptVect
setMass(float). Method in class PeptElt
setMassDecal(float). Method in class IMassGraph
setMassDecal(float). Method in class PeptVect
setMassDecal(String). Method in class IMassGraph
setMassNames(Vector). Method in class IMassGraph
setMassVector(PeptVect). Method in class IMassGraph
setMassVectors(Vector). Method in class IMassGraph
setMc(int). Method in class PeptElt
number of missed cleavage sites for the current Peptide
setMcDesc(String). Method in class PeptElt
Missed Cleavage sites resulting from a non-division of two Peptides (typically returned by PeptIdent at www.expasy.ch) something of a form: NAME:VALUE
setMultiline(boolean). Method in class DragText
setOrtho(boolean). Method in class BaseGraph
Graph Orthonorm (proportional)
setPeeks(boolean). Method in class BaseGraph
Graph Peeks
setPosition(String). Method in class PeptElt
position of a peptide in a protein sequence something of a form "456-789"
setScale(boolean). Method in class BaseGraph
show scaling values
setSelected(int). Method in class PeptVect
setSequence(String). Method in class PeptElt
sequence of the peptide, something of a form AAFFEEBB
setShaded(boolean). Method in class DragText
setText(String). Method in class DragText
setWidth(int). Method in class DragText
setWire(boolean). Method in class BaseGraph
Wire or Fill
setZoom(PeptVect, float, float). Method in class IMassZoom
setZoom(PeptVect, float, float, PeptVect). Method in class IMassZoom
setZoom(PeptVect, String, String). Method in class IMassZoom
(re)set zoom from minMass to maxMass
setZoomVector(PeptVect). Method in class IMassZoom
set a zoom source vector and create two lists with values from peptide masses from that vector
Shaded. Variable in class DragText
Size. Variable in class DragText
start(). Method in class BioGraph
stop(). Method in class BioGraph
sv. Variable in class BaseGraph

T

tenFont. Variable in class DragCanvas
Text. Variable in class DragText
TextColor. Variable in class DragText
textFont. Variable in class DragText
TolVector. Variable in class BaseMassGraph
tolerance vector, we show matching masses using masses from this vector
tv. Variable in class BaseGraph
twelveFont. Variable in class DragCanvas

U

u. Variable in class BaseGraph
Update(). Method in class BioGraph
update(Graphics). Method in class BioGraph
updateFont(). Method in class DragText
updateThread. Variable in class BioGraph
we need a thread to update graphics, thats how games work, gee this is so cool!

V

V_INTERVAL. Static variable in class BioGraph
unless you want to stall the machine, it's useful to sleep once in a while

W

Width. Variable in class DragCanvas
Wire. Variable in class BaseGraph

X

x. Variable in class BaseGraph
xa. Variable in class BaseGraph
Xmax. Variable in class BaseGraph
(Xmin,Ymin) (XMax,YMax) bounds of series of points
Xmin. Variable in class BaseGraph
xPoints. Variable in class BaseGraph
XPos. Variable in class DragCanvas
(XPos,YPos) - leftmost upper corner of the object of Width and Height
XpPoly. Variable in class BaseGraph
xx. Variable in class BaseGraph

Y

y. Variable in class BaseGraph
ya. Variable in class BaseGraph
Ymax. Variable in class BaseGraph
Ymin. Variable in class BaseGraph
yPoints. Variable in class BaseGraph
YPos. Variable in class DragCanvas
YpPoly. Variable in class BaseGraph
yy. Variable in class BaseGraph
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