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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: TIGRFAM ############################  -->
    <bean id="jobTIGRFAM" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description" value="TIGRFAMs are protein families based on Hidden Markov Models or HMMs"/>
        <property name="analysis" value="true"/>
        <property name="libraryRelease" ref="signatureLibraryReleaseTigrfam"/>
    </bean>

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

    <!-- STEP 1 -->
    <bean id="stepTIGRFAMWriteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
          parent="abstractTIGRFAMStep">
        <!-- 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="proteinDAO" ref="proteinDAO"/>
    </bean>


    <!--TODO - The run binary step for HMMER should choose between search or scan, depending
        TODO - upon the number of proteins being searched.  True for both HMMER2 & 3.
        TODO - PROBLEM - HMMER2 hmmsearch ONLY ACCEPTS ONE MODEL AT A TIME. -->

    <!-- STEP 2 -->
    <bean id="stepTIGRFAMRunHmmer3"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer.RunHmmerBinaryStep"
          parent="abstractTIGRFAMStep">
        <!-- In example command line below, replace _ with -
        
        /ebi/production/interpro/binaries/64_bit_Linux/HMMER3.1b1/hmmsearch -Z 4023 _-cut_tc  /ebi/production/interpro/data/members/tigrfam/15.0/TIGRFAMs_15.0_HMM.LIB  -->
        <property name="dependsUpon" ref="stepTIGRFAMWriteFastaFile"/>
        <property name="stepDescription" value="Run fingerprintscan Binary for selected proteins"/>
        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
        <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.tigrfam} ${hmmer3.hmmsearch.cpu.switch.tigrfam}"/>
        <property name="usesFileOutputSwitch" value="true"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="fullPathToHmmFile" value="${tigrfam.hmm.path}"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <bean id="stepTIGRFAMDeleteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractTIGRFAMStep">
        <property name="dependsUpon" ref="stepTIGRFAMRunHmmer3"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of FPS"/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
    </bean>


    <bean id="stepTIGRFAMStoreRawMatches"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.ParseTigrFamHMMER3OutputStep"
          parent="abstractTIGRFAMStep">
        <property name="dependsUpon" ref="stepTIGRFAMRunHmmer3"/>
        <property name="stepDescription" value="Parse the TigrFam binary output and store as Filtered matches."/>
        <property name="serialGroup" value="PARSE_TIGRFAM"/>
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3MatchParser">
                <property name="useHmmsearch" value="true"/>
                <property name="parserSupport">
                    <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.TigrFamHmmer3ParserSupport">
                        <property name="signatureLibraryRelease" ref="tigrfamSignatureLibraryReleaseVersion"/>
                        <property name="hmmKey" value="ACCESSION"/>
                    </bean>
                </property>
            </bean>
        </property>
        <property name="outputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="rawMatchDAO" ref="tigrfamRawMatchDAO"/>
    </bean>

    <bean id="stepTIGRFAMDeleteRawOutput"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractTIGRFAMStep">
        <property name="dependsUpon" ref="stepTIGRFAMStoreRawMatches"/>
        <property name="stepDescription"
                  value="Delete the raw output file following successful parsing and persistence"/>
        <property name="fileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
    </bean>

    <!-- TODO - Check for changes - presumably now using different objects to store the results? -->
    <bean id="stepTIGRFamPostProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.TigrFamHmmer3FilterStep"
          parent="abstractTIGRFAMStep">
        <property name="dependsUpon" ref="stepTIGRFAMStoreRawMatches"/>
        <property name="signatureLibraryRelease" ref="tigrfamSignatureLibraryReleaseVersion"/>
        <property name="stepDescription" value="Stores raw matches as filtered matches."/>
        <property name="filteredMatchDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.TigrFamHmmer3FilteredMatchDAOImpl"/>
        </property>
        <property name="serialGroup" value="HMMER3_POST_PROCESSING"/>
        <property name="rawMatchDAO" ref="tigrfamRawMatchDAO"/>
        <property name="signatureLibrary" value="TIGRFAM"/>
        <property name="filter">
            <bean class="uk.ac.ebi.interpro.scan.business.filter.AllPassRawMatchFilter"/>
        </property>
    </bean>

    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: TIGRFAM !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->

    <!-- ######################## Dependencies ############################  -->
    <bean id="tigrfamRawMatchDAO"
          class="uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl">
        <constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.TigrFamHmmer3RawMatch"/>
    </bean>

    <!--<bean id="prositePatternRawMatchDAO" class="uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl">-->
    <!--<constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.ProSitePatternRawMatch"/>-->
    <!--</bean>-->

    <bean id="signatureLibraryReleaseTigrfam" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="TIGRFAM"/>
        <constructor-arg type="java.lang.String" ref="tigrfamSignatureLibraryReleaseVersion"/>
    </bean>


    <bean id="tigrfamSignatureLibraryReleaseVersion" class="java.lang.String">
        <constructor-arg value="${tigrfam.signature.library.release}"/>
    </bean>

    <!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
</beans>