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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
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