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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: Prosite Patterns ############################  -->
    <bean id="jobPrositePatterns" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description"
                  value="PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them"/>
        <property name="analysis" value="true"/>
        <property name="libraryRelease" ref="signatureLibraryReleasePrositePatterns"/>
        <property name="active" value="true"/>
    </bean>

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

    <!-- STEP 1 -->
    <bean id="stepPrositePatternWriteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
          parent="abstractPrositePatternStep">
        <!-- 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="stepPrositePatternRunBinary"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.prosite.RunPsScanStep"
          parent="abstractPrositePatternStep">
        <!-- In example command line below, replace _ with -
          Prosite Profiles:
          /ebi/sp/pro1/interpro/binaries/scripts/ps_scan.pl -d /ebi/sp/pro1/interpro/data/members/prosite/20.105/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/20.105/prosite.dat _-pfscan  /ebi/sp/pro1/interpro/binaries/64_bit_Linux/pfscan -r -b /ebi/sp/pro1/interpro/data/members/prosite/20.105/evaluator.dat -s -o ipro -->
        <property name="dependsUpon" ref="stepPrositePatternWriteFastaFile"/>
        <property name="stepDescription" value="Run ps_scan.pl and pfscan Binary for selected proteins"/>
        <property name="binarySwitches" value="${psscan.prositepatterns.binary.switches}"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="fullPathToPsScanPerlScript" value="${binary.prosite.psscan.pl.path}"/>
        <property name="modelFile" value="${prosite.models.path}"/>
        <property name="fullPathToPfscanBinary" value="${binary.prosite.pfscan.path}"/>
        <property name="fullPathToPfsearchBinary" value="${binary.prosite.pfsearch.path}"/>
        <property name="fullPathToConfirmatoryProfiles" value="${prosite.evaluator.models.path}"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <bean id="stepPrositePatternDeleteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractPrositePatternStep">
        <property name="dependsUpon" ref="stepPrositePatternRunBinary"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of Prosite Profiles."/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
    </bean>

    <!-- STEP 3 -->
    <bean id="stepPrositePatternParseRawOutput"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.prosite.ParsePrositeGffOutputStep"
          parent="abstractPrositePatternStep">
        <property name="dependsUpon" ref="stepPrositePatternRunBinary"/>
        <property name="stepDescription" value="Parse the output from the Prosite binary"/>
        <property name="serialGroup" value="PARSE_PROSITE_PATTERNS"/>
        <property name="retries" value="3"/>
        <property name="outputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="rawMatchDAO" ref="prositePatternRawMatchDAO"/>
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.prosite.PrositePatternMatchParser">
                <constructor-arg ref="prositePatternsSignatureLibraryReleaseVersion"/>
                <property name="cigarEncoder">
                    <bean class="uk.ac.ebi.interpro.scan.model.raw.alignment.CigarAlignmentEncoder"/>
                </property>
            </bean>
        </property>
    </bean>

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

    <bean id="stepPrositePatternPostProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.prosite.PrositePatternsPostProcessingStep"
          parent="abstractPrositePatternStep">

        <property name="dependsUpon" ref="stepPrositePatternParseRawOutput"/>
        <property name="serialGroup" value="PROFILE_SCAN_POST_PROCESSING"/>
        <property name="stepDescription" value="Filter Prosite Patterns matches and persist filtered results"/>
        <property name="signatureLibraryRelease" ref="prositePatternsSignatureLibraryReleaseVersion"/>
        <property name="postProcessor">
            <bean class="uk.ac.ebi.interpro.scan.business.postprocessing.prosite.PatternPostProcessing">
                <property name="passLevels">
                    <list>
                        <value>STRONG</value>
                    </list>
                </property>
            </bean>
        </property>
        <property name="filteredMatchDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.PrositePatternFilteredMatchDAO"/>
        </property>
        <property name="rawMatchDAO" ref="prositePatternRawMatchDAO"/>
    </bean>

    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: PrositeProfiles !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->

    <!-- ######################## Dependencies ############################  -->
    <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="signatureLibraryReleasePrositePatterns"
          class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="PROSITE_PATTERNS"/>
        <constructor-arg type="java.lang.String" ref="prositePatternsSignatureLibraryReleaseVersion"/>
    </bean>

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