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
 

Constructor Detail

rtfgen

public rtfgen()
default constructor.
Method Detail

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 vector
alist: - target (vector of pair), atom names + chemical shift values
aa: - 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 pairs
what: - 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 vector
symbol: - 1-char AA code
Returns:
true, false on error (? -- there are no error conditions)