Navigation Banner
 

OpenDataPanel Batch language command
  This function is used to save and restore states of data panel windows in HyPhy GUI. It is not recommended for direct invokation by the user.
Syntax  OpenDataPanel (dataSetID,"species order","display settings","partition settings"), likefunc ID);
Notes
  • dataSetID: identifier of an existing dataset
  • "species order": a string in the same format used by CreateFilter, used to select what species from dataSetID should be included in the data panel. Leave empty to include all.
  • "display settings": a string, containing 7 comma separated numbers, which control additional features of data display.
    The first number is a flag with the following meaning:
    • Flag has bit 1 turned on (i.e. (flag & 0x01) == 1): show consensus sequence
    • Flag has bit 3 turned on (i.e. (flag & 0x04) == 1): show translated sequence. The index of the sequence to translate is parameter 3 (of 7).
    • Flag has bit 4 turned on (i.e. (flag & 0x08) == 1): show reference sequence. The index of the sequence to translate is parameter 2 (of 7).
  • The fourth number is unused.
  • The fifth number selects the format for sequence names. 0: no names dispayed, 1: first 10 characters displayed, 2: full names displayed.
  • The sixth number selects the format for repeated characters in a site. 0: display actual character, 1: display dots for repeats of the character in sequence 1.
  • The seventh number selects the size of a character group. 9: every 9 sites are grouped (suggested for codon data). 10: every 10 sites are grouped (suggested for nucleotide and aminoacid data).
  • "partition settings": a string containing semicolon separated settings for each partition. Each partition specification is a string with 5 comma separated entries.
    • First entry is the name of the model attached to the partition. "-1" indicates that no model is attached.
    • First entry is the name of the model attached to the partition. "-1" indicates that no model is attached.
    • Second entry selects model options for the partition. Bits 16-19 select parameter options, 0 for local, 1 for global, 2 for global with rate variation, 3 for model specified. Bits 20-23 choose equilibrium frequency options, 0 for partition, 1 for dataset, 2 for equal, 3 for estimate, 4 for model specified. Bits 24-31 specify the number of rate classes, if applicable. Bits 0-15 are not used.
    • Third entry contains partition data settings. The only meaningful value there is the genetic code: bits 16-23 are the internal index of the genetic code table to use.
    • Fourth entry is the RGB color for the partitions: bits 0-7 for blue, 8-15 for green and 16-23 for red.
    • Fifth entry is the identifier of the tree to attach to the partition. "No_tree" specifies that no tree be attached.
  • The last optional parameter is the identifier of the likelihood function to build based on the info provided in other parameters. If the parameter is not included, no LF is built.
Examples
DATA_PANEL_SOURCE_PATH="::data:three.seq";
DataSet three2 = ReadDataFile (DATA_PANEL_SOURCE_PATH);
DataSetFilter beginning = CreateFilter (three2,3,"0-161,165-167","","AGA,AGG,TAA,TAG");
DataSetFilter end = CreateFilter (three2,1,"170-368","");
Tree three_tree2=(a,b,og);
Tree three_tree24=(a,b,og);
OpenDataPanel(three2,"","0,0,0,0,2,0,10", "MG94,65537,720896,14443523,three_tree2;F81,1,0,212,three_tree24", three2_LF);

 Last modified: 8/19/2002

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002