Uses of Interface
org.strbio.mol.lib.PSIBlast

Packages that use PSIBlast
org.strbio.local These classes are for running or exchanging data with local programs (other programs installed on your computer). 
org.strbio.mol.lib These classes represent conceptual objects used in structural biology algorithms. 
org.strbio.net These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page). 
 

Uses of PSIBlast in org.strbio.local
 

Classes in org.strbio.local that implement PSIBlast
 class PSIBlastP
          Runs a local copy of psiblast.
 class PSIBlastP2
          Runs a local copy of psiblast.
 

Uses of PSIBlast in org.strbio.mol.lib
 

Fields in org.strbio.mol.lib declared as PSIBlast
protected  PSIBlast JMCThreadMethod2.blast
           
protected  PSIBlast JMCThreadMethod.blast
           
 

Constructors in org.strbio.mol.lib with parameters of type PSIBlast
JMCThreadMethod(FoldLibrary lib, PSIBlast b)
          Use a user-specified library and psiblast method
JMCThreadMethod(PSIBlast b)
          Use a user-specified psiblast method
JMCThreadMethod2(FoldLibrary baseLib, FoldLibrary extraLib, PSIBlast b)
          Use a user-specified base library, extra library and psiblast method.
JMCThreadMethod2(FoldLibrary lib, PSIBlast b)
          Use a user-specified library and psiblast method
JMCThreadMethod2(PSIBlast b)
          Use a user-specified psiblast method
 

Uses of PSIBlast in org.strbio.net
 

Classes in org.strbio.net that implement PSIBlast
 class PSIBlastNCBI
          Does a PSI-BLAST search in the NR database at NCBI, using the main web gateway.
 class PSIBlastWeb
          Does a PSI-BLAST search in the NR database over the web.