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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="classpath:/spring/persistence/persistence-config-context.xml"/>

    <!-- ######################## JOB: Pfam-A ############################  -->
    <bean id="jobPfam" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description"
                  value="A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)"/>
        <property name="analysis" value="true"/>

        <property name="libraryRelease" ref="signatureLibraryReleasePfamA"/>
    </bean>

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

    <!-- STEP 1 -->
    <bean id="stepPfamWriteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
          parent="abstractPfamStep">
        <!-- 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="stepPfamRunHmmer3"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer.RunHmmerBinaryStep"
          parent="abstractPfamStep">
        <property name="dependsUpon" ref="stepPfamWriteFastaFile"/>
        <property name="stepDescription" value="Run HMMER 3 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.pfama} ${hmmer3.hmmsearch.cpu.switch.pfama}"/>
        <property name="fullPathToHmmFile" value="${pfam-a.hmm.path}"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="usesFileOutputSwitch" value="true"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="requiresDatabaseAccess" value="false"/>

    </bean>

    <bean id="stepPfamDeleteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractPfamStep">
        <property name="dependsUpon" ref="stepPfamRunHmmer3"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of HMMER3"/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="deleteWorkingDirectoryOnCompletion" value="${delete.temporary.directory.on.completion}"/>
    </bean>

    <!-- STEP 3 -->
    <bean id="stepPfamParseHmmerOutput"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.PfamA.ParsePfam_A_HMMER3OutputStep"
          parent="abstractPfamStep">
        <property name="dependsUpon" ref="stepPfamRunHmmer3"/>
        <property name="stepDescription" value="Parse the output from HMMER3"/>

        <!-- TODO - Apparently not being used for anything ... ?  Need to test. -->
        <!--<property name="fullPathToHmmFile" value="${Pfam-A.hmm.path}"/>-->
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3SearchMatchParser">
                <property name="parserSupport">
                    <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Pfam_A_Hmmer3Hmmer3ParserSupport">
                        <property name="gaValuesRetriever">
                            <bean class="uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever">
                                <constructor-arg value="${pfam-a.hmm.path}"/>
                            </bean>
                        </property>
                        <property name="signatureLibraryRelease" ref="pfamSignatureLibraryReleaseVersion"/>
                        <property name="signatureLibrary" value="PFAM"/>
                    </bean>
                </property>
            </bean>
        </property>
        <property name="serialGroup" value="PARSE_PFAM_A"/>
        <property name="rawMatchDAO" ref="pfamRawMatchDAO"/>
        <property name="retries" value="3"/>
        <property name="outputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
    </bean>

    <bean id="stepPfamDeleteHmmerOutput"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractPfamStep">
        <property name="dependsUpon" ref="stepPfamParseHmmerOutput"/>
        <property name="stepDescription" value="Delete the hmmer output file following successful parsing"/>
        <property name="fileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="deleteWorkingDirectoryOnCompletion" value="${delete.temporary.directory.on.completion}"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <!-- STEP 4 -->
    <bean id="stepPfamPostProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.PfamA.Pfam_A_PostProcessingStep"
          parent="abstractPfamStep">
        <property name="dependsUpon" ref="stepPfamParseHmmerOutput"/>
        <property name="stepDescription" value="Performs post processing on Pfam data (Hmmer 3 based)"/>
        <property name="postProcessor">
            <bean class="uk.ac.ebi.interpro.scan.business.postprocessing.pfam_A.PfamHMMER3PostProcessing">
                <property name="clanFileParser">
                    <bean class="uk.ac.ebi.interpro.scan.business.postprocessing.pfam_A.ClanFileParser">
                        <property name="pfamASeedFile" value="${pfam-a.seed.path}"/>
                        <property name="pfamCFile" value="${pfam-clans.path}"/>
                    </bean>
                </property>
                <property name="pfamHmmDataPath" value="${pfam-a.dat.path}"/>
            </bean>
        </property>
        <property name="serialGroup" value="HMMER3_POST_PROCESSING"/>
        <property name="signatureLibraryRelease" ref="pfamSignatureLibraryReleaseVersion"/>
        <property name="signatureLibrary" value="PFAM"/>
        <property name="rawMatchDAO" ref="pfamRawMatchDAO"/>
        <property name="filteredMatchDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.PfamFilteredMatchDAOImpl"/>
        </property>
    </bean>
    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: Pfam-A !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->

    <!-- ######################## Dependencies ############################  -->
    <bean id="pfamRawMatchDAO" class="uk.ac.ebi.interpro.scan.persistence.raw.PfamHmmer3RawMatchDAOImpl"/>

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

    <bean id="pfamSignatureLibraryReleaseVersion" class="java.lang.String">
        <constructor-arg value="${pfam-a.signature.library.release}"/>
    </bean>
    <!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
</beans>