different corrections

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index 37710f0..9fccaaf 100644 (file)
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -262,7 +262,6 @@
     <web-resource-collection>\r
        <web-resource-name>Administrator pages</web-resource-name>\r
                <!-- Prohibit access to any resources -->\r
-       <url-pattern>/</url-pattern>\r
        <url-pattern>/DisplayStat</url-pattern>\r
        <url-pattern>/Joblist</url-pattern>\r
        <url-pattern>/AnnualStat</url-pattern>\r
@@ -309,4 +308,4 @@
     <role-name>admin</role-name>\r
   </security-role>\r
   \r
-</web-app>
\ No newline at end of file
+</web-app>\r

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 114ac18..4caf6c8 100644 (file)
--- 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 \r
 #local.jronn.bin=/sw/java/latest/bin/java\r
 #cluster.jronn.bin=/sw/java/latest/bin/java\r
-jronn.jar.file=binaries/windows/jronn3.1.jar\r
+#ERROR! jronn.jar.file=binaries/windows/jronn3.1.jar\r
+jronn.jar.file=binaries/windows/bj3.0.4p-jronn.jar\r
 #jronn.limits.file=conf/settings/JronnLimits.xml\r
 ## Jronn can use multiple CPUs\r
 ## This parameter specifies the number of CPU to use\r

diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index 6c3e943..39a93f1 100644 (file)
--- 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;\r
 import java.util.regex.MatchResult;\r
 \r
-import javax.vecmath.MismatchedSizeException;\r
-\r
 import compbio.util.Util;\r
 \r
 /**\r