EDU.bmrb.rtfgen
Class rtfgen
java.lang.Object
|
+--EDU.bmrb.rtfgen.rtfgen
- public class rtfgen
- extends java.lang.Object
Converts chemical shift table from NMR-STAR loop to RTF.
Constructor Summary |
rtfgen()
default constructor. |
Method Summary |
boolean |
findAA(java.util.Vector shifts,
java.util.Vector alist,
pair aa)
convert vector of shiftdata into a pair of strings: label, sequence code
and a vector of pairs: atomname, chemical shift value |
java.lang.String |
findItem(java.util.Vector alist,
java.lang.String what)
find what in alist , return the match and remove
the entry from alist . |
static void |
main(java.lang.String[] args)
program entry point. |
boolean |
makeRow(java.util.Vector dest,
java.util.Vector alist,
java.lang.String symbol,
pair aa,
boolean is_spec,
int fn_count)
make a row in rtf table. |
void |
run()
Main function. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
rtfgen
public rtfgen()
- default constructor.
main
public static void main(java.lang.String[] args)
- program entry point.
Command-line arguments: input file, sort order, output file (order is
important). Sort order can be "1" to sort by shift sequence number or "2"
to sort by amino acid. If output file is "-", result is written to stdout.
- Parameters:
args
- command-line arguments.
run
public void run()
- Main function.
findAA
public boolean findAA(java.util.Vector shifts,
java.util.Vector alist,
pair aa)
- convert vector of shiftdata into a pair of strings: label, sequence code
and a vector of pairs: atomname, chemical shift value
- Parameters:
shifts:
- source vectoralist:
- target (vector of pair), atom names + chemical shift valuesaa:
- target (pair), amino acid label + sequence code- Returns:
- false on error, true otherwise
findItem
public java.lang.String findItem(java.util.Vector alist,
java.lang.String what)
- find
what
in alist
, return the match and remove
the entry from alist
.
- Parameters:
alist:
- list of AA label/sequence code pairswhat:
- AA label to search for
makeRow
public boolean makeRow(java.util.Vector dest,
java.util.Vector alist,
java.lang.String symbol,
pair aa,
boolean is_spec,
int fn_count)
- make a row in rtf table.
(don't be scared: this code was copy-pasted from original rtfgen.c++. NMF)
- Parameters:
alist:
- source vectorsymbol:
- 1-char AA code- Returns:
- true, false on error (? -- there are no error conditions)