--------------------------------------------
v1.0 patched emma__v1_0__patched20101004.zip
date: 2010-10-06
--------------------------------------------

+ Reader for DCD files ( NiceDCDReader ) not throwing "Unsupported
Exception" when querying getTimeOfFrame().
  The returned value is always 0.0 . Currently the time is not used by
any algorithm. Future version will support proper readout.

+ Fixed bug in CommandLineParser / IOption.Options: 
  Options "-positivediagonal" "-symmetrizable" and "-countreversible"
were always evaluated to true, even if not present. 
  Concerned were commands "mm_timescales" and "mm_countmatrixEstimation"

+ Output format of all commands is changed to sparse matrix format.

+ mm_transitionMatrixAnalysis now writes out results of analysis.

+ Slow usage of String concatenation operator "+=" replaced by for all
file writers and output operations.