improved the -src option to also accpet source directories

build.gradle

@@ -89,6 +89,9 @@ dependencies {
     compile 'net.sourceforge.findbugs:annotations:1.3.2'
     compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.7.5'
 
+	// https://mvnrepository.com/artifact/org.checkerframework/checker-qual
+	compile group: 'org.checkerframework', name: 'checker-qual', version: '2.1.10'
+
     compile fileTree(dir: 'lib', include: '*.jar')    
     testCompile "junit:junit:4.11"  // Or whatever version
 }

src/main/java/bixie/Main.java

@@ -9,6 +9,8 @@
 import java.io.PrintWriter;
 
 import bixie.checker.reportprinter.JSONReportPrinter;
+
+import org.checkerframework.checker.nullness.qual.NonNull;
 import org.kohsuke.args4j.CmdLineException;
 import org.kohsuke.args4j.CmdLineParser;
 
@@ -74,7 +76,7 @@ public void run(String input, String output) {
 		if (input != null && input.endsWith(".bpl")) {
 			try {
 				ProgramFactory pf = new ProgramFactory(input);
-				ReportPrinter jp = runChecker(pf);
+				@NonNull ReportPrinter jp = runChecker(pf);
 				report2File(jp);
 			} catch (Exception e) {
 				// TODO Auto-generated catch block
@@ -112,7 +114,7 @@ public void translateAndRun(String input, String classpath, String output) {
 
 	private ReportPrinter reportPrinter = null;
 
-	protected ReportPrinter getReportPrinter() {
+	protected @NonNull ReportPrinter getReportPrinter() {
 		if (reportPrinter==null) {
 			if (bixie.Options.v().getHtmlDir()!=null) {
 				File dir = new File(bixie.Options.v().getHtmlDir());
@@ -149,12 +151,12 @@ protected ReportPrinter getReportPrinter() {
 		return reportPrinter;
 	}
 
-	public ReportPrinter translateAndRun(String input, String classpath) {
+	public @NonNull ReportPrinter translateAndRun(String input, String classpath) {
 		return translateAndRun(input, classpath, getReportPrinter());
 	}
 
-	public ReportPrinter translateAndRun(String input, String classpath,
-			ReportPrinter reportPrinter) {
+	public @NonNull ReportPrinter translateAndRun(String input, String classpath,
+			@NonNull ReportPrinter reportPrinter) {
 		bixie.util.Log.info("Translating. This may take a while.");
 
 		bixie.translation.Main.setClassPath(classpath);
@@ -164,18 +166,18 @@ public ReportPrinter translateAndRun(String input, String classpath,
 		bixie.util.Log.info("... translation finished.");
 		if (pf == null) {
 			bixie.util.Log.error("Internal Error: Parsing failed");
-			return null;
+			return reportPrinter;
 		}
 		ReportPrinter jp = runChecker(pf, reportPrinter);
 		return jp;
 	}
 
-	public ReportPrinter runChecker(ProgramFactory pf) {
+	public @NonNull ReportPrinter runChecker(ProgramFactory pf) {
 		return runChecker(pf, getReportPrinter());
 	}
 
-	public ReportPrinter runChecker(ProgramFactory pf,
-			ReportPrinter reportPrinter) {
+	public @NonNull ReportPrinter runChecker(ProgramFactory pf,
+			@NonNull ReportPrinter reportPrinter) {
 		bixie.util.Log.info("Checking");
 		try {
 			ProgramAnalysis.runFullProgramAnalysis(pf, reportPrinter);

src/main/java/bixie/Options.java

@@ -9,6 +9,9 @@
 import java.util.HashSet;
 import java.util.Set;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.kohsuke.args4j.Option;
 
 /**
@@ -64,7 +67,7 @@ public String getJSONDir() {
 	/**
 	 * Location of the source files for reporting.
 	 */
-	@Option(name = "-src", usage = "List of all source files")
+	@Option(name = "-src", usage = "List of all source files separated by colon, or list of root folders.")
 	private String srcFilesString=null;
 	private Set<String> sourceFiles = null;
 	public Set<String> getSrcFilesString() {
@@ -73,15 +76,37 @@ public Set<String> getSrcFilesString() {
 			sourceFiles = new HashSet<String>();
 			if (files!=null) {
 				for (String s : files) {
-					sourceFiles.add(s);
+					File f = new File(s);
+					if (f.exists()) {
+						if (f.isFile()) {
+							sourceFiles.add(f.getAbsolutePath());
+						} else if (f.isDirectory()) {
+							sourceFiles.addAll(findFilesRecursively(f, ".java"));
+						}
+					} else {
+						//log error
+					}
 				}
 			}
 		}
 		return sourceFiles;
 	}
 
-	@Option(name = "-serverityLimit", usage = "Maximum serverity level for warnings.")
-	public int serverityLimit = 2;
+	private List<String> findFilesRecursively(File f, String ending) {
+		List<String> res = new ArrayList<String>();
+		if (f.isDirectory()) {
+			for (File c : f.listFiles()) {
+				res.addAll(findFilesRecursively(c, ending));
+			}
+		} else if (f.isFile() && f.getAbsolutePath().endsWith(ending)) {
+			res.add(f.getAbsolutePath());
+		}
+		return res;
+	}
+
+
+	@Option(name = "-severityLimit", usage = "Maximum severity level for warnings.")
+	public int severityLimit = 2;
 
 
 	@Option(name = "-exportStubs", usage = "Write all used stubs to file")

src/main/java/bixie/checker/reportprinter/BasicReportPrinter.java

@@ -73,7 +73,7 @@ public String printSummary() {
 			//TODO: don't hard code the keys.
 			sb.append("In File: " + fname+"\n");
 			cirtical+= printReportForFileBySeverity(sb, fname, 0, "** Critical **");
-			if (bixie.Options.v().serverityLimit>0){
+			if (bixie.Options.v().severityLimit>0){
 				unreachable += printReportForFileBySeverity(sb, fname, 1, " - Unreachable -");
 			}
 		}

src/main/java/bixie/checker/reportprinter/HtmlReportPrinter.java

@@ -107,7 +107,7 @@ public String printSummary() {
 				bodyText.append("<p>Nothing found</p>\n");
 			}
 			cirtical += count;
-			if (bixie.Options.v().serverityLimit > 0) {
+			if (bixie.Options.v().severityLimit > 0) {
 				bodyText.append("<h6>Unreachability warnings</h6>\n");
 				count = createSnippet(fname, bodyText, jsText, 1);
 				if (count == 0) {

src/main/java/bixie/checker/reportprinter/JSONReportPrinter.java

@@ -64,7 +64,7 @@ public String printSummary() {
 
 	protected void consumeReport(Report r) {
 		for (Entry<Integer, List<Report.FaultExplanation>> entry : r.getReports().entrySet()) {
-			if (entry.getKey()>bixie.Options.v().serverityLimit) {
+			if (entry.getKey()>bixie.Options.v().severityLimit) {
 				// suppress warnings above threshold.
 				continue;
 			}