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FIX Antenna Java gives the ability to set up a custom FIX dictionary for FIX sessions. 

To support it, please first specify 'customFIXVersions' section in FIX Antenna configuration file (fixengine.properties). 

fixengine.properties
# comma separated list of custom FIX dictionary aliases
customFixVersions=FIX44Custom,FIX50Custom

# pair of 'fixVersion' and 'fileName' for each FIX dictionary alias with pattern:
# customFixVersion.<custom FIX version alias>.fixVersion=<base standard FIX version>
# customFixVersion.<custom FIX version alias>.fileName=<custom FIX dictionary file name>

# example of custom FIX dictionary based on FIX.4.4
customFixVersion.FIX44Custom.fixVersion=FIX.4.4
customFixVersion.FIX44Custom.fileName=classpath:fixdic44-custom.xml

# examples of custom FIX dictionary based on FIX.5.0
customFixVersion.FIX50Custom.fixVersion=FIX.5.0
customFixVersion.FIX50Custom.fileName=classpath:fixdic50-custom.xml

The next step is to set defined dictionary aliases as a session's fixVersion or appVersion in a configuration file:

# comma separated list of configured sessions
sessionIDs=session1,session2,session3

# session1 configured with default 'FIX.4.4' dictionary
sessions.session1.sessionType=acceptor
sessions.session1.fixVersion=FIX.4.4
sessions.session1.senderCompID=senderCompID1
sessions.session1.targetCompID=targetCompID1

# session2 configured with custom 'FIX44Custom' dictionary
sessions.session2.sessionType=acceptor
sessions.session2.fixVersion=FIX44Custom
sessions.session2.senderCompID=senderCompID2
sessions.session2.targetCompID=targetCompID2

# session3 configured with custom 'FIX50Custom' dictionary
sessions.session3.sessionType=acceptor
sessions.session3.fixVersion=FIXT.1.1
sessions.session3.appVersion=FIX50Custom
sessions.session3.senderCompID=senderCompID3
sessions.session3.targetCompID=targetCompID3

The same can be done in the application code:

// creating connection parameters
SessionParameters sessionParameters = new SessionParameters();
sessionParameters.setFixVersion(FIXVersion.FIXT11);
// configured with custom 'FIX50Custom' dictionary
sessionParameters.setAppVersion("FIX50Custom");
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