zmapApp - main program

Configuration of sequence and control of ZMap

Sequence options

Historically there have been two options inthe [Zmap] stanza that controlled how ZMap started up and loaded data:

[ZMap]
show-main-window = false
default-sequence = chr6-18_12314500-12344230
The main window is normally hidden when ZMap is run and controlled via Otterlace and visible when run from the command line, and if the default-sequence is specified then it is loaded automatically. This is not specified when Zmap is run from Otterlace, and Otterlace requests the sequence to be loaded via an XRemote message. If the main window is hidden then if a ZMap is closed ZMap does not exit.

This is a little clumsy and the following changes are introduced:

Note that the above implies that Otterlace will also include the dataset name eitehr in the sequence name or as a separate XML field.