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InterProScan JMS Implementation Module
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<?xml version="1.0" encoding="UTF-8" ?>
<beans xmlns="http://www.springframework.org/schema/beans"
       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:schemaLocation="http://www.springframework.org/schema/beans
                           http://www.springframework.org/schema/beans/spring-beans-4.2.xsd">

    <import resource="../persistence/persistence-config-context.xml"/>

    <!-- ######################## JOB: HAMAP ############################  -->
    <bean id="jobHAMAP-180510" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description" value="High-quality Automated and Manual Annotation of Microbial Proteomes"/>
        <property name="analysis" value="true"/>
        <property name="libraryRelease" ref="signatureLibraryReleaseHAMAP-180510"/>
    </bean>

    <bean id="abstractHamapStep-180510" abstract="true" class="uk.ac.ebi.interpro.scan.management.model.Step">
        <property name="job" ref="jobHAMAP-180510"/>
        <property name="maxProteins" value="${analysis.max.sequence.count.HAMAP}"/>
        <property name="createStepInstancesForNewProteins" value="true"/>
        <property name="retries" value="0"/>
        <property name="nfsDelayMilliseconds" value="${nfs.delay.milliseconds}"/>
    </bean>

    <!-- STEP 1 -->
    <bean id="stepHamapWriteFastaFile-180510"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
          parent="abstractHamapStep-180510">
        <!-- This step has no dependencies, so will be scheduled first for its associated job. -->
        <property name="stepDescription" value="Create fasta file."/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <!--<property name="serialGroup"                        value="WRITE_FASTA_FILE"/>-->
        <property name="proteinDAO" ref="proteinDAO"/>
    </bean>

    <!-- STEP 2 -->
    <bean id="stepHamapRunBinary-180510"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.prosite.RunPsScanStep"
          parent="abstractHamapStep-180510">
        <!-- In example command line below, replace _ with -
          /ebi/sp/pro1/interpro/binaries/scripts/ps_scan.pl -d /ebi/production/interpro/data/members/hamap/180510/hamap.prf _-pfscan /ebi/sp/pro1/interpro/binaries/64_bit_Linux/pfscan -l -1 -o gff
          (PROSITE for comparison:)
          Prosite Profiles:
          /ebi/sp/pro1/interpro/binaries/scripts/ps_scan.pl -d /ebi/sp/pro1/interpro/data/members/prosite/20.52/prosite.dat _-pfscan /ebi/sp/pro1/interpro/binaries/64_bit_Linux/pfscan -s -m -o gff
          Prosite Patterns:
          /ebi/sp/pro1/interpro/binaries/scripts/ps_scan.pl -d /ebi/sp/pro1/interpro/data/members/prosite/20.52/prosite.dat _-pfscan  /ebi/sp/pro1/interpro/binaries/64_bit_Linux/pfscan -r -b /ebi/sp/pro1/interpro/data/members/prosite/20.52/evaluator.dat -s -o ipro -->
        <property name="dependsUpon" ref="stepHamapWriteFastaFile-180510"/>
        <property name="stepDescription" value="Run fingerprintscan Binary for selected proteins"/>
        <property name="binarySwitches" value="-l -1 -o gff"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="fullPathToPsScanPerlScript" value="${binary.prosite.psscan.pl.path}"/>
        <property name="modelFile" value="${hamap.profile.models.path.180510}"/>
        <property name="fullPathToPfscanBinary" value="${binary.prosite.pfscan.path}"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <bean id="stepHamapDeleteFastaFile-180510"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractHamapStep-180510">
        <property name="dependsUpon" ref="stepHamapRunBinary-180510"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of FPS"/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
    </bean>

    <!-- STEP 3 -->
    <bean id="stepHamapParseRawOutput-180510"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.prosite.ParsePrositeGffOutputStep"
          parent="abstractHamapStep-180510">
        <property name="dependsUpon" ref="stepHamapRunBinary-180510"/>
        <property name="stepDescription" value="Parse the output from the ProSite binary"/>
        <property name="serialGroup" value="PARSE_HAMAP"/>
        <property name="retries" value="3"/>
        <property name="outputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="rawMatchDAO" ref="hamapRawMatchDAO-180510"/>
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.prosite.HamapMatchParser">
                <constructor-arg value="180510"/>
                <property name="cigarEncoder">
                    <bean class="uk.ac.ebi.interpro.scan.model.raw.alignment.CigarAlignmentEncoder"/>
                </property>
            </bean>
        </property>
    </bean>

    <bean id="stepHamapDeleteRawOutput-180510"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractHamapStep-180510">
        <property name="dependsUpon" ref="stepHamapParseRawOutput-180510"/>
        <property name="stepDescription" value="Delete the hmmer output file following successful parsing"/>
        <property name="fileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
    </bean>

    <bean id="stepHamapPostProcessing-180510"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hamap.HamapPostProcessingStep"
          parent="abstractHamapStep-180510">

        <property name="dependsUpon" ref="stepHamapParseRawOutput-180510"/>
        <property name="serialGroup" value="PROFILE_SCAN_POST_PROCESSING"/>
        <property name="stepDescription" value="Filter HAMAP matches and persist filtered results"/>
        <property name="signatureLibraryRelease" value="180510"/>
        <property name="postProcessor">
            <bean class="uk.ac.ebi.interpro.scan.business.postprocessing.prosite.ProfilePostProcessing">
                <property name="passLevels">
                    <list>
                        <value>ONE</value>
                        <value>ZERO</value>
                    </list>
                </property>
            </bean>
        </property>
        <property name="filteredMatchDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.HamapFilteredMatchDAOImpl"/>
        </property>
        <property name="rawMatchDAO" ref="hamapRawMatchDAO-180510"/>
    </bean>

    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: HAMAP !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->

    <!-- ######################## Dependencies ############################  -->
    <bean id="hamapRawMatchDAO-180510" class="uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl">
        <constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.HamapRawMatch"/>
    </bean>
    <bean id="signatureLibraryReleaseHAMAP-180510" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="HAMAP"/>
        <constructor-arg type="java.lang.String" value="180510"/>
    </bean>
    <!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
</beans>