How can I set proxy settings programatically for JMeter without running it using command line

Given you run JMeter from a separate Java program you need to pass proxy arguments to this Java program. There are several ways on how this could be done, check our Java Networking and Proxies article for comprehensive information, you seem to be a fan of doing everything through the code so just add the following lines before launching a JMeter test:

System.setProperty("http.proxyHost","your_proxy_host");
System.setProperty("http.proxyPort", "your_proxy_port");
System.setProperty("https.proxyHost","your_proxy_host");
System.setProperty("https.proxyPort","your_proxy_port");
System.setProperty("http.nonProxyHosts","");

Just in case complete code demonstrating how you can run an existing JMeter test using JMeter API through JMeter's HTTP(S) Test Script Recorder as a proxy

import org.apache.jmeter.engine.StandardJMeterEngine;
import org.apache.jmeter.reporters.ResultCollector;
import org.apache.jmeter.reporters.Summariser;
import org.apache.jmeter.save.SaveService;
import org.apache.jmeter.util.JMeterUtils;
import org.apache.jorphan.collections.HashTree;

import java.io.File;

public class JMeterFromCode {

    public static void main(String[] argv) throws Exception {


        //Define JVM Proxy Settings
        System.setProperty("http.proxyHost", "localhost");
        System.setProperty("http.proxyPort", "8888");
        System.setProperty("https.proxyHost", "localhost");
        System.setProperty("https.proxyPort", "8888");
        System.setProperty("http.nonProxyHosts", "");

        // JMeter Engine
        StandardJMeterEngine jmeter = new StandardJMeterEngine();

        // Initialize Properties, logging, locale, etc.
        JMeterUtils.loadJMeterProperties("/tmp/jmeter/bin/jmeter.properties");
        JMeterUtils.setJMeterHome("/tmp/jmeter");
        JMeterUtils.initLocale();


        // Initialize JMeter SaveService
        SaveService.loadProperties();

        // Load existing .jmx Test Plan
        HashTree testPlanTree = SaveService.loadTree(new File("/tmp/jmeter/bin/test.jmx"));

        Summariser summer = null;
        String summariserName = JMeterUtils.getPropDefault("summariser.name", "summary");
        if (summariserName.length() > 0) {
            summer = new Summariser(summariserName);
        }

        ResultCollector logger = new ResultCollector(summer);
        logger.setFilename("/tmp/jmeter/test.jtl");
        testPlanTree.add(testPlanTree.getArray()[0], logger);


        // Run JMeter Test
        jmeter.configure(testPlanTree);
        jmeter.run();
    }
}