A C E F G M N P R S T V

A

aalabels - Static variable in class EDU.bmrb.rtfgen.rtf
amino-acid labels (3-letter)
aasymbols - Static variable in class EDU.bmrb.rtfgen.rtf
amino-acid labels (1-letter)

C

cd - Static variable in class EDU.bmrb.rtfgen.rtf
C-delta
cd1 - Static variable in class EDU.bmrb.rtfgen.rtf
C-delta 1
cd2 - Static variable in class EDU.bmrb.rtfgen.rtf
C-delta 2
ce - Static variable in class EDU.bmrb.rtfgen.rtf
C-epsilon
ce1 - Static variable in class EDU.bmrb.rtfgen.rtf
C-epsilon 1
ce2 - Static variable in class EDU.bmrb.rtfgen.rtf
C-epsilon 2
ce3 - Static variable in class EDU.bmrb.rtfgen.rtf
C-epsilon 3
cg - Static variable in class EDU.bmrb.rtfgen.rtf
C-gamma
cg1 - Static variable in class EDU.bmrb.rtfgen.rtf
C-gamma 1
cg2 - Static variable in class EDU.bmrb.rtfgen.rtf
C-gamma 2
ch2 - Static variable in class EDU.bmrb.rtfgen.rtf
C-eta 2
compare(Object, Object) - Method in interface EDU.bmrb.rtfgen.VectorSorter.Comparer
Compare objects, return a value that indicates their relative order: if (a > b) return > 0; if (a == b) return 0; if (a < b) return < 0.
compare(Object, Object) - Method in class EDU.bmrb.rtfgen.triple
comparator function for sorting
cz - Static variable in class EDU.bmrb.rtfgen.rtf
C-zeta
cz2 - Static variable in class EDU.bmrb.rtfgen.rtf
C-zeta 2
cz3 - Static variable in class EDU.bmrb.rtfgen.rtf
C-zeta 3

E

EDU.bmrb.rtfgen - package EDU.bmrb.rtfgen
RTF generator.
emptyrow - Static variable in class EDU.bmrb.rtfgen.rtf
empty row

F

fileheader - Static variable in class EDU.bmrb.rtfgen.rtf
file header
filetail - Static variable in class EDU.bmrb.rtfgen.rtf
end of file
findAA(Vector, Vector, pair) - Method in class EDU.bmrb.rtfgen.rtfgen
convert vector of shiftdata into a pair of strings: label, sequence code and a vector of pairs: atomname, chemical shift value
findItem(Vector, String) - Method in class EDU.bmrb.rtfgen.rtfgen
find what in alist, return the match and remove the entry from alist.

G

getAAsymbol() - Method in class EDU.bmrb.rtfgen.triple
return residue label.
getAtomName() - Method in class EDU.bmrb.rtfgen.shiftdata
returns atom name.
getChemShift() - Method in class EDU.bmrb.rtfgen.shiftdata
returns chemical shift value.
getLabel() - Method in class EDU.bmrb.rtfgen.pair
returns first string
getResLabel() - Method in class EDU.bmrb.rtfgen.shiftdata
returns residue label.
getRtfRow() - Method in class EDU.bmrb.rtfgen.triple
returns RTF table row.
getSeqCode() - Method in class EDU.bmrb.rtfgen.shiftdata
returns sequence code
getSeqCode() - Method in class EDU.bmrb.rtfgen.triple
returns sequence code.
getSeqCode() - Method in class EDU.bmrb.rtfgen.pair
returns second string

M

main(String[]) - Static method in class EDU.bmrb.rtfgen.rtfgen
program entry point.
makeRow(Vector, Vector, String, pair, boolean, int) - Method in class EDU.bmrb.rtfgen.rtfgen
make a row in rtf table.
matchAA(String) - Static method in class EDU.bmrb.rtfgen.rtf
converts 3-letter amino-acid label to 1-letter label.

N

nd1 - Static variable in class EDU.bmrb.rtfgen.rtf
N-delta 1
nd2 - Static variable in class EDU.bmrb.rtfgen.rtf
N-delta 2
ne - Static variable in class EDU.bmrb.rtfgen.rtf
N-epsilon
ne1 - Static variable in class EDU.bmrb.rtfgen.rtf
N-epsilon 1
ne2 - Static variable in class EDU.bmrb.rtfgen.rtf
N-epsilon 2
nh1 - Static variable in class EDU.bmrb.rtfgen.rtf
N-eta 1
nh2 - Static variable in class EDU.bmrb.rtfgen.rtf
N-eta 2
nz - Static variable in class EDU.bmrb.rtfgen.rtf
N-zeta

P

pair - class EDU.bmrb.rtfgen.pair.
Pair of strings class
pair() - Constructor for class EDU.bmrb.rtfgen.pair
creates new pair.
pair(String, String) - Constructor for class EDU.bmrb.rtfgen.pair
creates new pair.

R

rowheader - Static variable in class EDU.bmrb.rtfgen.rtf
row header
rowtail - Static variable in class EDU.bmrb.rtfgen.rtf
end of row
rtf - class EDU.bmrb.rtfgen.rtf.
RTF constants.
rtf() - Constructor for class EDU.bmrb.rtfgen.rtf
 
rtfgen - class EDU.bmrb.rtfgen.rtfgen.
Converts chemical shift table from NMR-STAR loop to RTF.
rtfgen() - Constructor for class EDU.bmrb.rtfgen.rtfgen
default constructor.
run() - Method in class EDU.bmrb.rtfgen.rtfgen
Main function.

S

setAAsymbol(String) - Method in class EDU.bmrb.rtfgen.triple
changes residue label.
setAtomName(String) - Method in class EDU.bmrb.rtfgen.shiftdata
changes atom name.
setChemShift(String) - Method in class EDU.bmrb.rtfgen.shiftdata
changes chemical shift value.
setLabel(String) - Method in class EDU.bmrb.rtfgen.pair
Changes first string
setResLabel(String) - Method in class EDU.bmrb.rtfgen.shiftdata
changes residue label.
setRtfRow(String) - Method in class EDU.bmrb.rtfgen.triple
changes RTF table row.
setSeqCode(int) - Method in class EDU.bmrb.rtfgen.triple
changes sequence code.
setSeqCode(String) - Method in class EDU.bmrb.rtfgen.shiftdata
changes sequence code.
setSeqCode(String) - Method in class EDU.bmrb.rtfgen.pair
Changes second string
shiftdata - class EDU.bmrb.rtfgen.shiftdata.
Class that contains raw chemical shift data.
shiftdata() - Constructor for class EDU.bmrb.rtfgen.shiftdata
creates new shiftdata
sort(Vector, int, int, boolean, VectorSorter.Comparer) - Static method in class EDU.bmrb.rtfgen.VectorSorter
Sort a portion of a vector, using the comparison defined by the Comparer object c.
sort(Vector, Vector, int, int, boolean, VectorSorter.Comparer) - Static method in class EDU.bmrb.rtfgen.VectorSorter
This is the main sort() routine.
sort(Vector, VectorSorter.Comparer) - Static method in class EDU.bmrb.rtfgen.VectorSorter
Sort a vector of arbitrary objects into ascending order, using the comparison defined by the Comparer object c
sort(Vector, Vector, VectorSorter.Comparer) - Static method in class EDU.bmrb.rtfgen.VectorSorter
 

T

tableheader - Static variable in class EDU.bmrb.rtfgen.rtf
table header
tabletitle - Static variable in class EDU.bmrb.rtfgen.rtf
table title -- start
tabletitletail - Static variable in class EDU.bmrb.rtfgen.rtf
table title -- end
toString() - Method in class EDU.bmrb.rtfgen.shiftdata
returns this object as string
toString() - Method in class EDU.bmrb.rtfgen.pair
returns this object as string.
triple - class EDU.bmrb.rtfgen.triple.
Structure that holds amino-acid symbol, sequence code and an RTF formatted table row.
triple() - Constructor for class EDU.bmrb.rtfgen.triple
creates new triple.
triple(String, int) - Constructor for class EDU.bmrb.rtfgen.triple
creates new triple.
triple(String, int, String) - Constructor for class EDU.bmrb.rtfgen.triple
creates new triple.

V

VectorSorter - class EDU.bmrb.rtfgen.VectorSorter.
This class defines a bunch of static methods for efficiently sorting Vectors.
VectorSorter.Comparer - interface EDU.bmrb.rtfgen.VectorSorter.Comparer.
This interface defines the compare() method used to compare two objects.
VectorSorter() - Constructor for class EDU.bmrb.rtfgen.VectorSorter
 

A C E F G M N P R S T V