From: Alexander Sherstnev <asherstnev@main-laptop2>
Date: Fri, 29 Mar 2013 12:37:48 +0000 (+0000)
Subject: different corrections
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=acd285b98c4cfa54d2123861ffc30f2d42e86b20;p=jabaws.git

different corrections
---

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index 37710f0..9fccaaf 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -262,7 +262,6 @@
     <web-resource-collection>
     	<web-resource-name>Administrator pages</web-resource-name>
    		<!-- Prohibit access to any resources -->
-    	<url-pattern>/</url-pattern>
     	<url-pattern>/DisplayStat</url-pattern>
     	<url-pattern>/Joblist</url-pattern>
     	<url-pattern>/AnnualStat</url-pattern>
@@ -309,4 +308,4 @@
     <role-name>admin</role-name>
   </security-role>
   
-</web-app>
\ No newline at end of file
+</web-app>
diff --git a/conf/Executable.properties b/conf/Executable.properties
index 114ac18..4caf6c8 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -142,7 +142,8 @@ probcons.parameters.file=conf/settings/ProbconsParameters.xml
 #local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
 #local.jronn.bin=/sw/java/latest/bin/java
 #cluster.jronn.bin=/sw/java/latest/bin/java
-jronn.jar.file=binaries/windows/jronn3.1.jar
+#ERROR! jronn.jar.file=binaries/windows/jronn3.1.jar
+jronn.jar.file=binaries/windows/bj3.0.4p-jronn.jar
 #jronn.limits.file=conf/settings/JronnLimits.xml
 ## Jronn can use multiple CPUs
 ## This parameter specifies the number of CPU to use
diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index 6c3e943..39a93f1 100644
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -24,8 +24,6 @@ import java.util.Iterator;
 import java.util.Scanner;
 import java.util.regex.MatchResult;
 
-import javax.vecmath.MismatchedSizeException;
-
 import compbio.util.Util;
 
 /**