===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
artemis-18.1.0+dfsg/etc/options-1180-   SGN_gene \
artemis-18.1.0+dfsg/etc/options:1181:   SGN_germplasm \
artemis-18.1.0+dfsg/etc/options-1182-   SGN_ref \
##############################################
artemis-18.1.0+dfsg/etc/results_to_netscape-48-# sanger hack:
artemis-18.1.0+dfsg/etc/results_to_netscape:49:file_arg=`echo $file_arg | sed 's@^/tmp_mnt/nfs/@/nfs/@' | sed 's@^/tmp_mnt/tmp_nfs/@/nfs/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape-50-# fix for pcs3:
artemis-18.1.0+dfsg/etc/results_to_netscape:51:file_arg=`echo $file_arg | sed 's@^/yeastpub4/@/nfs/disk222/yeastpub4/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape-52-# fix for pcs4:
artemis-18.1.0+dfsg/etc/results_to_netscape:53:file_arg=`echo $file_arg | sed 's@^/.automount/pcs3/root/nfs/@/nfs/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape:54:file_arg=`echo $file_arg | sed 's@^/.automount/evs-users2/root/@/nfs/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape-55-
##############################################
artemis-18.1.0+dfsg/etc/results_to_netscape-66-# sanger fix for /nfs/repository which isn't mounted on workstations:
artemis-18.1.0+dfsg/etc/results_to_netscape:67:REPOSITORY=`echo $new_file | sed -n  -e 's|^\/nfs\/repository\/\(.*\)\(\/\)\(.*\)$|\3|p'`
artemis-18.1.0+dfsg/etc/results_to_netscape-68-
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-28-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_blastn:29:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_blastn-30-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-49-	
artemis-18.1.0+dfsg/etc/run_blastn:50:	EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_blastn-51-	
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-67-
artemis-18.1.0+dfsg/etc/run_blastn:68:      	DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_blastn-69-
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-121-then
artemis-18.1.0+dfsg/etc/run_blastn:122:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_blastn-123-    do
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-28-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_blastp:29:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_blastp-30-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-49-	
artemis-18.1.0+dfsg/etc/run_blastp:50:	EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_blastp-51-	
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-67-
artemis-18.1.0+dfsg/etc/run_blastp:68:      	DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_blastp-69-
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-120-then
artemis-18.1.0+dfsg/etc/run_blastp:121:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_blastp-122-    do
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_blastx:30:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_blastx-31-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-50-	
artemis-18.1.0+dfsg/etc/run_blastx:51:	EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_blastx-52-	
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-68-
artemis-18.1.0+dfsg/etc/run_blastx:69:      	DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_blastx-70-
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-121-then
artemis-18.1.0+dfsg/etc/run_blastx:122:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_blastx-123-    do
##############################################
artemis-18.1.0+dfsg/etc/run_hth-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_hth:30:EXPANDED_PARAMETERS=`echo "echo $PARAMETERS" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_hth-31-
##############################################
artemis-18.1.0+dfsg/etc/run_hth-71-then
artemis-18.1.0+dfsg/etc/run_hth:72:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_hth-73-    do
##############################################
artemis-18.1.0+dfsg/etc/run_hth-82-then
artemis-18.1.0+dfsg/etc/run_hth:83:    PEPFILES=`cat $1`
artemis-18.1.0+dfsg/etc/run_hth-84-else
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-10-
artemis-18.1.0+dfsg/etc/run_netblastp:11:PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
artemis-18.1.0+dfsg/etc/run_netblastp-12-
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-31-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_netblastp:32:EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_netblastp-33-
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-44-    
artemis-18.1.0+dfsg/etc/run_netblastp:45:    EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_netblastp-46-    
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-94-then
artemis-18.1.0+dfsg/etc/run_netblastp:95:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_netblastp-96-    do
##############################################
artemis-18.1.0+dfsg/etc/run_pepstats-66-then
artemis-18.1.0+dfsg/etc/run_pepstats:67:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_pepstats-68-    do
##############################################
artemis-18.1.0+dfsg/etc/run_sigcleave-67-then
artemis-18.1.0+dfsg/etc/run_sigcleave:68:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_sigcleave-69-    do
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_tblastn:30:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_tblastn-31-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-50-	
artemis-18.1.0+dfsg/etc/run_tblastn:51:	EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_tblastn-52-	
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-68-
artemis-18.1.0+dfsg/etc/run_tblastn:69:      	DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_tblastn-70-
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-121-then
artemis-18.1.0+dfsg/etc/run_tblastn:122:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_tblastn-123-    do
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_tblastx:30:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_tblastx-31-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-50-	
artemis-18.1.0+dfsg/etc/run_tblastx:51:	EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_tblastx-52-	
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-68-
artemis-18.1.0+dfsg/etc/run_tblastx:69:      	DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_tblastx-70-
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-120-then
artemis-18.1.0+dfsg/etc/run_tblastx:121:    for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_tblastx-122-    do
##############################################
artemis-18.1.0+dfsg/etc/writedb_entry-30-	then
artemis-18.1.0+dfsg/etc/writedb_entry:31:		PROXY_SETTINGS="${PROXY_SETTINGS} -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/etc/writedb_entry-32-	fi
##############################################
artemis-18.1.0+dfsg/etc/writedb_entry-70-
artemis-18.1.0+dfsg/etc/writedb_entry:71:JAVA_VERSION=`${JAVA} -version 2>&1`
artemis-18.1.0+dfsg/etc/writedb_entry-72-echo ${JAVA_VERSION}
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Cv.xml-20-  <select id="selectCv" resultMap="select-cv">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Cv.xml:21:    SELECT * FROM cv WHERE cv_id=$cvId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Cv.xml-22-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Db.xml-32-  <select id="getDbByDbId" resultClass="Db">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Db.xml:33:    SELECT * FROM db WHERE db_id=$db_id$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Db.xml-34-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-37-  <select id="getDbXRefByDbXRefIdLazy" resultMap="select-dbxref-lazy">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml:38:    SELECT * FROM dbxref WHERE dbxref_id=$dbXRefId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-39-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-41-  <select id="getDbXRefByDbXRefId" resultMap="select-dbxref">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml:42:	SELECT * FROM dbxref LEFT JOIN db ON dbxref.db_id=db.db_id WHERE dbxref_id=$dbXRefId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-43-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-360-	FROM feature f
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:361:    WHERE f.feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-362-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-380-	LEFT JOIN db ON dbxref.db_id=db.db_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:381:    WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-382-  </select>	
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-407-        (  SELECT feature_id FROM featureloc WHERE srcfeature_id IN 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:408:         ( SELECT feature_id  FROM featureloc WHERE srcfeature_id=$value$) )
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-409-    ORDER BY f.feature_id
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-469-	LEFT JOIN feature ON cvterm.cvterm_id=feature.type_id 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:470:	WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-471-	  residues notnull AND residues != '' AND
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-483-	JOIN featureprop using (feature_id) 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:484:	WHERE  <isNotNull> feature.organism_id=$value$ AND </isNotNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-485-	  featureprop.type_id in (
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-529-      <isNotNull property="timeLastModified"> , timelastmodified=#timeLastModified# </isNotNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:530:    WHERE feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-531-  </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-576-            seqlen=(seqLen+$seqLen$)
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:577:            WHERE feature_id=$featureLoc.featureBySrcFeatureId.featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-578-   </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-584-    DELETE FROM feature
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:585:    WHERE uniquename=#uniqueName# AND type_id=$cvTerm.cvTermId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-586-  </delete>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-590-    DELETE FROM feature
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:591:    WHERE feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-592-  </delete>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-64-        WHERE feature_id IN 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml:65:		(SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-66-	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-76-        WHERE feature_id IN 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml:77:		(SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-78-	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-131-      SET rank=$rank$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml:132:      WHERE feature_cvterm_id=$featureCvTermId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-133-    </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-42-	   WHERE feature_id IN 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml:43:       (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-44-	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-54-       LEFT JOIN db ON db.db_id=dbx.db_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml:55:       WHERE feature_cvterm_id=$feature_cvterm_id$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-56-    </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermPub.xml-39-       WHERE feature_id IN 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermPub.xml:40:       (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermPub.xml-41-	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-41-        <isGreaterThan property="featureId" compareValue="0">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml:42:          WHERE dbx_f.feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-43-        </isGreaterThan>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-53-    <!-- RIGHT JOIN feature f ON dbx_f.feature_id=f.feature_id -->
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml:54:    WHERE dbx_f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-55-    ORDER BY dbx_f.feature_id
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-66-	LEFT JOIN db ON db.db_id=dbx.db_id    
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml:67:	WHERE srcfeature_id = $featureId$ 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-68-	  <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-46-       FROM  featureloc
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml:47:       WHERE featureloc.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-48-     </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-95-       </isNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml:96:      WHERE fmin >= $startBase$ AND srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-97-    </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-59-       LEFT JOIN cvterm ON fp.type_id=cvterm_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml:60:	   WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-61-     </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-66-      SET value=#value#   
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml:67:      WHERE rank=$rank$ AND type_id=$cvTerm.cvTermId$ AND 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-68-            feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#)
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-40-        WHERE f.feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml:41:        (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-42-	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-56-        <isGreaterThan property="featureId" compareValue="0">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml:57:          WHERE f.feature_id = $featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-58-        </isGreaterThan>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureRelationship.xml-133-                             LEFT JOIN cvterm AS fr2_cvterm ON fr2_cvterm.cvterm_id=fr2.type_id 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureRelationship.xml:134:                             WHERE subject_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate> 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureRelationship.xml-135-		                     AND (fr2_cvterm.name='derives_from' OR fr2_cvterm.name='part_of' OR fr2_cvterm.name='proper_part_of'))  
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-87-	  LEFT JOIN featureloc fl ON fl.feature_id=fs.feature_id AND srcfeature_id=$featureId$  
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml:88:	  WHERE srcfeature_id=$featureId$		
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-89-	  <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-97-      WHERE f.feature_id IN 
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml:98:        (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-99-	  <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-30-  <select id="getGraphs" resultMap="select-graph">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml:31:    SELECT graph_id, feature_id, name, description FROM graph.graph WHERE feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-32-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-34-  <select id="getGraph" resultMap="select-graphdata">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml:35:    SELECT * FROM graph.graph WHERE graph_id=$graphId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-36-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Pub.xml-33-  <select id="selectPub" resultMap="select-pub">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Pub.xml:34:    SELECT * FROM pub WHERE pub_id=$pub_id$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Pub.xml-35-  </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Synonym.xml-42-    <delete id="deleteAlias" parameterClass="FeatureSynonym">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Synonym.xml:43:      DELETE FROM synonym WHERE synonym_id=$synonym.synonymId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Synonym.xml-44-    </delete>
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3658-      EntryGroup entryGroup0 = mock(EntryGroup.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3659:      doReturn("uk.ac.sanger.artemis.FilteredEntryGroup", "1_O!1w+4", "`6uh$GzN\"/V~J:0", "D-fBu$%JA,$", "`6uh$GzN\"/V~J:0").when(entryGroup0).toString();
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3660-      doReturn(entryVector0, (EntryVector) null).when(entryGroup0).getActiveEntries();
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3661-      FeaturePredicate featurePredicate0 = mock(FeaturePredicate.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3662:      FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(entryGroup0, featurePredicate0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3663-      assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3664:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3665-      assertEquals(0, filteredEntryGroup0.refCount());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3668-      FeatureVector featureVector0 = mock(FeatureVector.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3669:      FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, featureVector0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3670-      assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3671:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3672-      assertEquals(0, filteredEntryGroup0.refCount());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3673:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup1.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3674-      assertEquals(0, filteredEntryGroup1.size());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3680-      assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3681:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3682-      assertEquals(0, filteredEntryGroup0.refCount());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3683:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup1.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3684-      assertEquals(0, filteredEntryGroup1.size());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3693-      assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3694:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3695-      assertEquals(0, filteredEntryGroup0.refCount());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3696:      assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup1.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3697-      assertEquals(0, filteredEntryGroup1.size());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-4107-      EntryGroup entryGroup0 = mock(EntryGroup.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:4108:      doReturn("mo!$>TPLf}x`ejqHx", "r0.{'#UE(!", "mo!$>TPLf}x`ejqHx", "", "uk.ac.sanger.artemis.FilteredEntryGroup$2").when(entryGroup0).toString();
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-4109-      doReturn(entryVector0).when(entryGroup0).getActiveEntries();
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-7349-      FeaturePredicate featurePredicate0 = mock(FeaturePredicate.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:7350:      FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(entryGroup0, featurePredicate0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-7351-      FeatureVector featureVector0 = mock(FeatureVector.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:7352:      FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, featureVector0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-7353-      filteredEntryGroup1.features();
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/components/RunBlastAtNCBI_ESTest.java-87-  public void test7()  throws Throwable  {
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/components/RunBlastAtNCBI_ESTest.java:88:      String string0 = RunBlastAtNCBI.constructRequest("$q^+H", "11", "n.ae`3jzQU$Qamd:", "11", "$q^+H", "n.ae`3jzQU$Qamd:", "", (String) null, "k*4*");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/components/RunBlastAtNCBI_ESTest.java-89-      assertEquals("CMD=Put&QUERY=11&DATABASE=n.ae%603jzQU%24Qamd%3A&HITLIST_SIZE=11&FILTER=%24q%5E%2BH&EXPECT=n.ae%603jzQU%24Qamd%3A&FORMAT_TYPE=HTML&PROGRAM=%24q%5E%2BH&CLIENT=web&SERVICE=&GAPCOSTS=null+k*4*", string0);
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-293-      MockFile mockFile0 = new MockFile("${vqx\"ta`Rd=`Rm1R9@");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java:294:      MockFile.createTempFile("${vqx\"ta`Rd=`Rm1R9@", "${vqx\"ta`Rd=`Rm1R9@", (File) mockFile0);
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-295-      ZipFileDocument zipFileDocument0 = new ZipFileDocument(mockFile0, "${vqx\"ta`Rd=`Rm1R9@");
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-314-      MockFile mockFile0 = new MockFile("${vqx\"ta`Rd=`Rm1R9@");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java:315:      MockFile.createTempFile("${vqx\"ta`Rd=`Rm1R9@", "${vqx\"ta`Rd=`Rm1R9@", (File) mockFile0);
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-316-      mockFile0.setReadable(false, false);
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-27--	then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:28:-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-29--	fi
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-117--	then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:118:-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-119--	fi
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-207--	then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:208:-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-209--	fi
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-289--	then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:290:-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-291--	fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/act-54-	then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/act:55:		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/act-56-	fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/art-60-	then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/art:61:		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/art-62-	fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/bamview-22-	then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/bamview:23:		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/bamview-24-	fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/dnaplotter-41-	then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/dnaplotter:42:		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/dnaplotter-43-	fi