Change to wiki page

foisys · andreasprlic · commit 77177ddf10f2 · 2016-04-09T10:59:09.000-07:00
diff --git a/_wikis/BioJava:CookBook3:NCBIQBlastService.md b/_wikis/BioJava:CookBook3:NCBIQBlastService.md
@@ -23,16 +23,19 @@ requests, grab the requests ID and fetch the results at a later time.
 To use QBlast, you use a NCBIQBlastService object (which implements
 RemotePairwiseAlignmentService) to manage the connection to the QBlast
 service, submission of requests and fetching of results. To do so, it
-needs a sequence (represented by either a string, a RichSequence object
-or a GID) and a NCBIQBlastAlignmentProperties object. This class
-implements RemotePairwiseAlignmentProperties and it is use to set which
-program and which database to use for the analysis. Right now, it can't
-much make use of other parameters of the QBlast service but the methods
-are in development to fix this situation. One would recover results
-using the same RemoteQBlastService object, which hold submission
-information, and an object of type NCBIQBlastOutputProperties to
-specifiy the informations to recover and the format to present to the
-submitter.
+needs a sequence (represented by either a string or a Sequence object;
+search by GID will be added in a future release) and a
+NCBIQBlastAlignmentProperties object. Submitting a Sequence object is
+the preferred method since it allows for some basic sanity checks
+related to the sequence type-to-program selection. The
+NCBIQBlastAlignmentProperties class implements
+RemotePairwiseAlignmentProperties and it is use to set which program and
+which database to use for the analysis. Right now, it can't much make
+use of other parameters of the QBlast service but the methods are in
+development to fix this situation. One would recover results using the
+same NCBIQBlastService object, which hold submission information, and an
+object of type NCBIQBlastOutputProperties to specify the informations to
+recover and the format to present to the submitter.
 
 Using the interfaces found in package org.biojava3.ws.alignment should
 allow extensions to other remote alignment services like FASTA and Blast
@@ -47,7 +50,7 @@ high in the TO DO list.
 on a ProteinSequence object...
 
 - Do not use multiple threads to send loads of requests to NCBI. This
-would only get you into trouble, up to getting blacklisted by NCBI.
+would only get you into trouble, up to getting you blacklisted by NCBI.
 
 <java>
 
diff --git a/_wikis/BioJava:CookBook3:NCBIQBlastService.mediawiki b/_wikis/BioJava:CookBook3:NCBIQBlastService.mediawiki
@@ -4,7 +4,7 @@ BioJava now has some ability to use remote bioinformatics services to execute ta
 
 The QBlast BioJava classes implement a serie of interfaces: RemotePairwiseAlignmentService, RemotePairwiseAlignmentProperties and RemotePairwiseAlignmentOutputProperties. These interfaces are designed in such a fashion that setting the parameters for alignement, submitting the results and fetching the results in a desired format are done independently from each other. This allows a program to send a bunch of requests, grab the requests ID and fetch the results at a later time.
 
-To use QBlast, you use a NCBIQBlastService object (which implements RemotePairwiseAlignmentService) to manage the connection to the QBlast service, submission of requests and fetching of results. To do so, it needs a sequence (represented by either a string, a RichSequence object or a GID) and a NCBIQBlastAlignmentProperties object. This class implements RemotePairwiseAlignmentProperties and it is use to set which program and which database to use for the analysis. Right now, it can't much make use of other parameters of the QBlast service but the methods are in development to fix this situation. One would recover results using the same RemoteQBlastService object, which hold submission information, and an object of type NCBIQBlastOutputProperties to specifiy the informations to recover and the format to present to the submitter.
+To use QBlast, you use a NCBIQBlastService object (which implements RemotePairwiseAlignmentService) to manage the connection to the QBlast service, submission of requests and fetching of results. To do so, it needs a sequence (represented by either a string or a Sequence object; search by GID will be added in a future release) and a NCBIQBlastAlignmentProperties object. Submitting a Sequence object is the preferred method since it allows for some basic sanity checks related to the sequence type-to-program selection. The NCBIQBlastAlignmentProperties class implements RemotePairwiseAlignmentProperties and it is use to set which program and which database to use for the analysis. Right now, it can't much make use of other parameters of the QBlast service but the methods are in development to fix this situation. One would recover results using the same NCBIQBlastService object, which hold submission information, and an object of type NCBIQBlastOutputProperties to specify the informations to recover and the format to present to the submitter.
 
 Using the interfaces found in package org.biojava3.ws.alignment should allow extensions to other remote alignment services like FASTA and Blast at EBI, which use web services.
 
@@ -14,7 +14,7 @@ WARNING (as of early February 2011):
 
 - Basic sanity checks are in place so that you won't try to use blastn on a ProteinSequence object...
 
-- Do not use multiple threads to send loads of requests to NCBI. This would only get you into trouble, up to getting blacklisted by NCBI. 
+- Do not use multiple threads to send loads of requests to NCBI. This would only get you into trouble, up to getting you blacklisted by NCBI. 
 
 <java>
 
