Christopher Hartl b59948709f Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated. ... A number of functions int he sampleDB looked to be assuming that samples could not share IDs (e.g. sample IDs are unique, so a sample present in two families could not be represented by multiple Sample objects). Added an assertion in the SampleDBBuilder to document/test this assumption. MVLikelihoodRatio now uses the trio methods from SampleDB.		2012-08-25 08:48:27 -07:00
..
Affection.java	Renaming quantitative trait to OtherPhenotype which is now a String not a double	2011-10-05 12:26:33 -07:00
Gender.java	Reorganization of Sample	2011-09-30 15:50:54 -04:00
PedReader.java	Renaming quantitative trait to OtherPhenotype which is now a String not a double	2011-10-05 12:26:33 -07:00
PedigreeValidationType.java	Final PED documentation	2011-10-05 15:17:41 -07:00
Sample.java	Added getParents() -> returns an arrayList containing the sample's parent(s) if available	2011-10-20 12:47:27 +02:00
SampleDB.java	Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.	2012-08-25 08:48:27 -07:00
SampleDBBuilder.java	Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.	2012-08-25 08:48:27 -07:00
Trio.java	Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.	2012-08-25 08:48:27 -07:00