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There is no direct wrapper for FlannBasedMatcher. The only solution for Java is to create Matcher using common matcher factory and set parameters separately using yml configuration file for example. See [OpenCV_source]/modules/java/android_test/src/org/opencv/test/features2d/FlannBasedDescriptorMatcherTest.java test in OpenCV source code as an example of such initialization. Alternatively, you can wrap this functionality manually.
