From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 4 Oct 2013 12:16:28 +0000 (+0100)
Subject: JWS-68 parameters cannot take multiple option names (this should have
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8907c35efd10d5968c0a64dba6a9524a2545df28;p=jabaws.git

JWS-68 parameters cannot take multiple option names (this should have
been caught via configuration file validation - see JWS-73)
---

diff --git a/conf/settings/GLprobsParameters.xml b/conf/settings/GLprobsParameters.xml
index ee18617..858f81d 100644
--- a/conf/settings/GLprobsParameters.xml
+++ b/conf/settings/GLprobsParameters.xml
@@ -29,7 +29,6 @@
             passes of consistency transformation
         </description>
         <optionNames>-c</optionNames>
-        <optionNames>--consistency</optionNames>
         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>
         <defaultValue>2</defaultValue>
         <validValue>
@@ -45,7 +44,6 @@
             number of passes of iterative-refinement
         </description>
         <optionNames>-ir</optionNames>
-        <optionNames>--iterative-refinement</optionNames>
         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>
         <defaultValue>100</defaultValue>
         <validValue>
diff --git a/conf/settings/MSAprobsParameters.xml b/conf/settings/MSAprobsParameters.xml
index 6ace32c..cc4227e 100644
--- a/conf/settings/MSAprobsParameters.xml
+++ b/conf/settings/MSAprobsParameters.xml
@@ -29,7 +29,6 @@
             passes of consistency transformation
         </description>
         <optionNames>-c</optionNames>
-        <optionNames>--consistency</optionNames>
         <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
         <defaultValue>2</defaultValue>
         <validValue>
@@ -45,7 +44,6 @@
                       number of passes of iterative-refinement
         </description>
         <optionNames>-ir</optionNames>
-        <optionNames>--iterative-refinement</optionNames>
         <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
         <defaultValue>10</defaultValue>
         <validValue>