gui: fix missed nodes in hierarchical packages tree

jadx-gui/src/main/java/jadx/gui/treemodel/JPackage.java

@@ -84,11 +84,13 @@ public class JPackage extends JNode implements Comparable<JPackage> {
 
 	@Override
 	public boolean equals(Object o) {
-		if (this == o) return true;
-		if (o == null || getClass() != o.getClass()) return false;
-		JPackage jPackage = (JPackage) o;
-		if (!name.equals(jPackage.name)) return false;
-		return true;
+		if (this == o) {
+			return true;
+		}
+		if (o == null || getClass() != o.getClass()) {
+			return false;
+		}
+		return name.equals(((JPackage) o).name);
 	}
 
 	@Override

jadx-gui/src/main/java/jadx/gui/treemodel/JRoot.java

@@ -10,7 +10,7 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.HashSet;
+import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -47,6 +47,12 @@ public class JRoot extends JNode {
 		}
 	}
 
+	/**
+	 * Convert packages list to hierarchical packages representation
+	 *
+	 * @param packages input packages list
+	 * @return root packages
+	 */
 	List<JPackage> getHierarchyPackages(List<JavaPackage> packages) {
 		Map<String, JPackage> pkgMap = new HashMap<String, JPackage>();
 		for (JavaPackage pkg : packages) {
@@ -63,11 +69,11 @@ public class JRoot extends JNode {
 					pkg.getInnerPackages().addAll(innerPkg.getInnerPackages());
 					pkg.getClasses().addAll(innerPkg.getClasses());
 					pkg.setName(pkg.getName() + "." + innerPkg.getName());
+
 					innerPkg.getInnerPackages().clear();
 					innerPkg.getClasses().clear();
 
 					repeat = true;
-					pkgMap.remove(innerPkg.getName());
 					break;
 				}
 			}
@@ -80,14 +86,16 @@ public class JRoot extends JNode {
 				it.remove();
 			}
 		}
-		// find root packages
-		Set<JPackage> inners = new HashSet<JPackage>();
+
+		// use identity set for collect inner packages
+		Set<JPackage> innerPackages = Collections.newSetFromMap(new IdentityHashMap<JPackage,Boolean>());
 		for (JPackage pkg : pkgMap.values()) {
-			inners.addAll(pkg.getInnerPackages());
+			innerPackages.addAll(pkg.getInnerPackages());
 		}
+		// find root packages
 		List<JPackage> rootPkgs = new ArrayList<JPackage>();
 		for (JPackage pkg : pkgMap.values()) {
-			if (!inners.contains(pkg)) {
+			if (!innerPackages.contains(pkg)) {
 				rootPkgs.add(pkg);
 			}
 		}

jadx-gui/src/test/java/jadx/gui/treemodel/JRootTest.java

@@ -8,10 +8,10 @@ import jadx.api.JavaPackage;
 import jadx.core.dex.nodes.ClassNode;
 import jadx.gui.JadxWrapper;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import org.junit.Before;
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;
@@ -19,19 +19,20 @@ import static org.mockito.Mockito.mock;
 
 public class JRootTest {
 
+	private JRoot root;
+	private Decompiler decompiler;
+
+	@Before
+	public void init() {
+		root = new JRoot(mock(JadxWrapper.class));
+		decompiler = new Decompiler(mock(IJadxArgs.class));
+	}
+
 	@Test
 	public void testHierarchyPackages() {
 		String pkgName = "a.b.c.d.e";
 
-		JadxWrapper wrapper = mock(JadxWrapper.class);
-		JRoot root = new JRoot(wrapper);
-
-		JavaClass cls = Factory.newClass(new Decompiler(mock(IJadxArgs.class)), mock(ClassNode.class));
-		JavaPackage pkg = Factory.newPackage(pkgName, Arrays.asList(cls));
-
-		List<JavaPackage> packages = new ArrayList<JavaPackage>();
-		packages.add(pkg);
-
+		List<JavaPackage> packages = Arrays.asList(newPkg(pkgName));
 		List<JPackage> out = root.getHierarchyPackages(packages);
 
 		assertEquals(out.size(), 1);
@@ -40,4 +41,62 @@ public class JRootTest {
 		assertEquals(jpkg.getClasses().size(), 1);
 	}
 
+	@Test
+	public void testHierarchyPackages2() {
+		List<JavaPackage> packages = Arrays.asList(
+				newPkg("a.b"),
+				newPkg("a.c"),
+				newPkg("a.d")
+		);
+		List<JPackage> out = root.getHierarchyPackages(packages);
+
+		assertEquals(out.size(), 1);
+		JPackage jpkg = out.get(0);
+		assertEquals(jpkg.getName(), "a");
+		assertEquals(jpkg.getClasses().size(), 0);
+		assertEquals(jpkg.getInnerPackages().size(), 3);
+	}
+
+	@Test
+	public void testHierarchyPackages3() {
+		List<JavaPackage> packages = Arrays.asList(
+				newPkg("a.b.p1"),
+				newPkg("a.b.p2"),
+				newPkg("a.b.p3")
+		);
+		List<JPackage> out = root.getHierarchyPackages(packages);
+
+		assertEquals(out.size(), 1);
+		JPackage jpkg = out.get(0);
+		assertEquals(jpkg.getName(), "a.b");
+		assertEquals(jpkg.getClasses().size(), 0);
+		assertEquals(jpkg.getInnerPackages().size(), 3);
+	}
+
+	@Test
+	public void testHierarchyPackages4() {
+		List<JavaPackage> packages = Arrays.asList(
+				newPkg("a.p1"),
+				newPkg("a.b.c.p2"),
+				newPkg("a.b.c.p3"),
+				newPkg("d.e"),
+				newPkg("d.f.a")
+		);
+		List<JPackage> out = root.getHierarchyPackages(packages);
+
+		assertEquals(out.size(), 2);
+		assertEquals(out.get(0).getName(), "a");
+		assertEquals(out.get(0).getInnerPackages().size(), 2);
+		assertEquals(out.get(1).getName(), "d");
+		assertEquals(out.get(1).getInnerPackages().size(), 2);
+	}
+
+	private JavaPackage newPkg(String name) {
+		return Factory.newPackage(name, Arrays.asList(newClass()));
+	}
+
+	private JavaClass newClass() {
+		return Factory.newClass(decompiler, mock(ClassNode.class));
+	}
+
 }