void mixLists(
LinkedList<Integer> left,
LinkedList<Integer> right,
ArrayList<LinkedList<Integer>> mix,
LinkedList<Integer> before) {
if (before.isEmpty() || right.isEmpty()) {
LinkedList<Integer> l = new LinkedList<>();
l = (LinkedList<Integer>) before.clone();
l.addAll(left);
l.addAll(right);
mix.add(l);
return;
}
int hl = left.removeFirst();
before.addLast(hl);
mixLists(left, right, mix, before);
before.removeLast();
left.addFirst(hl);
int hr = right.removeFirst();
before.addLast(hr);
mixLists(left, right, mix, before);
before.removeLast();
right.addFirst(hr);
}
/*
case_label =
{constant} case minus? integer_constant |
{default} default;
*/
public void outAConstantCaseLabel(AConstantCaseLabel node) {
String s = (String) mProductions.removeLast();
int sign = 1;
if (node.getMinus() != null) sign = -1;
if (s.endsWith("L")) {
mProductions.addLast(LongConstant.v(sign * Long.parseLong(s.substring(0, s.length() - 1))));
} else mProductions.addLast(IntConstant.v(sign * Integer.parseInt(s)));
}
public void outAIntegerConstant(AIntegerConstant node) {
String s = (String) mProductions.removeLast();
StringBuffer buf = new StringBuffer();
if (node.getMinus() != null) buf.append('-');
buf.append(s);
s = buf.toString();
if (s.endsWith("L")) {
mProductions.addLast(LongConstant.v(Long.parseLong(s.substring(0, s.length() - 1))));
} else mProductions.addLast(IntConstant.v(Integer.parseInt(s)));
}
private void resolveLocalFileHeaderData(
final Map<ZipEntry, NameAndComment> entriesWithoutUTF8Flag) throws IOException {
for (final Entry ze : this.entries) {
final OffsetEntry offsetEntry = ze.getOffsetEntry();
final long offset = offsetEntry.headerOffset;
this.archive.seek(offset + 26L);
this.archive.readFully(this.SHORT_BUF);
final int fileNameLen = ZipShort.getValue(this.SHORT_BUF);
this.archive.readFully(this.SHORT_BUF);
final int extraFieldLen = ZipShort.getValue(this.SHORT_BUF);
int skipped;
for (int lenToSkip = fileNameLen; lenToSkip > 0; lenToSkip -= skipped) {
skipped = this.archive.skipBytes(lenToSkip);
if (skipped <= 0) {
throw new IOException("failed to skip file name in local file header");
}
}
final byte[] localExtraData = new byte[extraFieldLen];
this.archive.readFully(localExtraData);
ze.setExtra(localExtraData);
offsetEntry.dataOffset = offset + 26L + 2L + 2L + fileNameLen + extraFieldLen;
if (entriesWithoutUTF8Flag.containsKey(ze)) {
final NameAndComment nc = entriesWithoutUTF8Flag.get(ze);
ZipUtil.setNameAndCommentFromExtraFields(ze, nc.name, nc.comment);
}
final String name = ze.getName();
LinkedList<ZipEntry> entriesOfThatName = this.nameMap.get(name);
if (entriesOfThatName == null) {
entriesOfThatName = new LinkedList<ZipEntry>();
this.nameMap.put(name, entriesOfThatName);
}
entriesOfThatName.addLast(ze);
}
}
public void outAInvokeStatement(AInvokeStatement node) {
Value op = (Value) mProductions.removeLast();
Unit u = Jimple.v().newInvokeStmt(op);
mProductions.addLast(u);
}
public void outALocalImmediate(ALocalImmediate node) {
String local = (String) mProductions.removeLast();
Local l = (Local) mLocals.get(local);
if (l == null) throw new RuntimeException("did not find local: " + local);
mProductions.addLast(l);
}
/**
* Add a new <code>SourceJob</code> for the <code>Source source</code>, with AST <code>ast</code>.
* A new job will be created if needed. If the <code>Source source</code> has already been
* processed, and its job discarded to release resources, then <code>null</code> will be returned.
*/
public SourceJob addJob(Source source, Node ast) {
Object o = jobs.get(source);
SourceJob job = null;
if (o == COMPLETED_JOB) {
// the job has already been completed.
// We don't need to add a job
return null;
} else if (o == null) {
// No appropriate job yet exists, we will create one.
job = this.createSourceJob(source, ast);
// record the job in the map and the worklist.
jobs.put(source, job);
worklist.addLast(job);
if (Report.should_report(Report.frontend, 3)) {
Report.report(3, "Adding job for " + source + " at the " + "request of job " + currentJob);
}
} else {
job = (SourceJob) o;
}
// if the current source job caused this job to load, record the
// dependency.
if (currentJob instanceof SourceJob) {
((SourceJob) currentJob).addDependency(source);
}
return job;
}
public void defaultCase(Node node) {
if (node instanceof TQuotedName
|| node instanceof TFullIdentifier
|| node instanceof TIdentifier
|| node instanceof TStringConstant
|| node instanceof TIntegerConstant
|| node instanceof TFloatConstant
|| node instanceof TAtIdentifier) {
if (debug) G.v().out.println("Default case -pushing token:" + ((Token) node).getText());
String tokenString = ((Token) node).getText();
if (node instanceof TStringConstant || node instanceof TQuotedName) {
tokenString = tokenString.substring(1, tokenString.length() - 1);
}
if (node instanceof TIdentifier
|| node instanceof TFullIdentifier
|| node instanceof TQuotedName
|| node instanceof TStringConstant) {
try {
tokenString = StringTools.getUnEscapedStringOf(tokenString);
} catch (RuntimeException e) {
G.v().out.println(tokenString);
throw e;
}
}
mProductions.addLast(tokenString);
}
}
@Override
public synchronized void write(byte[] ba, int str, int len) {
try {
curLength += len;
if (bytesEndWith(ba, str, len, LINE_SEP)) {
lineLengths.addLast(new Integer(curLength));
curLength = 0;
if (lineLengths.size() > maxLines) {
textArea.replaceRange(null, 0, lineLengths.removeFirst().intValue());
}
}
for (int xa = 0; xa < 10; xa++) {
try {
textArea.append(new String(ba, str, len));
break;
} catch (
Throwable
thr) { // sometimes throws a java.lang.Error: Interrupted attempt to aquire write
// lock
if (xa == 9) {
thr.printStackTrace();
}
}
}
textArea.setCaretPosition(textArea.getText().length());
} catch (Throwable thr) {
CharArrayWriter caw = new CharArrayWriter();
thr.printStackTrace(new PrintWriter(caw, true));
textArea.append(System.getProperty("line.separator", "\n"));
textArea.append(caw.toString());
}
}
public void outAFullIdentNonvoidType(AFullIdentNonvoidType node) {
String typeName = (String) mProductions.removeLast();
Type t = RefType.v(typeName);
int dim = node.getArrayBrackets().size();
if (dim > 0) t = ArrayType.v(t, dim);
mProductions.addLast(t);
}
public void outAAssignStatement(AAssignStatement node) {
Value rvalue = (Value) mProductions.removeLast();
Value variable = (Value) mProductions.removeLast();
Unit u = Jimple.v().newAssignStmt(variable, rvalue);
mProductions.addLast(u);
}
public void outALookupswitchStatement(ALookupswitchStatement node) {
List lookupValues = new ArrayList();
List targets = new ArrayList();
UnitBox defaultTarget = null;
if (node.getCaseStmt() != null) {
int size = node.getCaseStmt().size();
for (int i = 0; i < size; i++) {
Object valueTargetPair = mProductions.removeLast();
if (valueTargetPair instanceof UnitBox) {
if (defaultTarget != null)
throw new RuntimeException("error: can't ;have more than 1 default stmt");
defaultTarget = (UnitBox) valueTargetPair;
} else {
Object[] pair = (Object[]) valueTargetPair;
lookupValues.add(0, pair[0]);
targets.add(0, pair[1]);
}
}
} else {
throw new RuntimeException("error: switch stmt has no case stmts");
}
Value key = (Value) mProductions.removeLast();
Unit switchStmt = Jimple.v().newLookupSwitchStmt(key, lookupValues, targets, defaultTarget);
mProductions.addLast(switchStmt);
}
public void totalExport() {
File expf = new File("export");
if (expf.exists()) rmrf(expf);
expf.mkdirs();
for (int sto = 0; sto < storeLocs.size(); sto++) {
try {
String sl =
storeLocs.get(sto).getAbsolutePath().replaceAll("/", "-").replaceAll("\\\\", "-");
File estore = new File(expf, sl);
estore.mkdir();
File log = new File(estore, LIBRARY_NAME);
PrintWriter pw = new PrintWriter(log);
for (int i = 0; i < store.getRowCount(); i++)
if (store.curStore(i) == sto) {
File enc = store.locate(i);
File dec = sec.prepareMainFile(enc, estore, false);
pw.println(dec.getName());
pw.println(store.getValueAt(i, Storage.COL_DATE));
pw.println(store.getValueAt(i, Storage.COL_TAGS));
synchronized (jobs) {
jobs.addLast(expJob(enc, dec));
}
}
pw.close();
} catch (IOException exc) {
exc.printStackTrace();
JOptionPane.showMessageDialog(frm, "Exporting Failed");
return;
}
}
JOptionPane.showMessageDialog(frm, "Exporting to:\n " + expf.getAbsolutePath());
}
public void outANonstaticInvokeExpr(ANonstaticInvokeExpr node) {
List args;
if (node.getArgList() != null) args = (List) mProductions.removeLast();
else args = new ArrayList();
SootMethodRef method = (SootMethodRef) mProductions.removeLast();
String local = (String) mProductions.removeLast();
Local l = (Local) mLocals.get(local);
if (l == null) throw new RuntimeException("did not find local: " + local);
Node invokeType = (Node) node.getNonstaticInvoke();
Expr invokeExpr;
if (invokeType instanceof ASpecialNonstaticInvoke) {
invokeExpr = Jimple.v().newSpecialInvokeExpr(l, method, args);
} else if (invokeType instanceof AVirtualNonstaticInvoke) {
invokeExpr = Jimple.v().newVirtualInvokeExpr(l, method, args);
} else {
if (debug)
if (!(invokeType instanceof AInterfaceNonstaticInvoke))
throw new RuntimeException("expected interface invoke.");
invokeExpr = Jimple.v().newInterfaceInvokeExpr(l, method, args);
}
mProductions.addLast(invokeExpr);
}
public void outAIdentityNoTypeStatement(AIdentityNoTypeStatement node) {
mProductions.removeLast(); // get rid of @caughtexception string presently on top of the stack
Value local =
(Value) mLocals.get(mProductions.removeLast()); // the local ref from it's identifier
Unit u = Jimple.v().newIdentityStmt(local, Jimple.v().newCaughtExceptionRef());
mProductions.addLast(u);
}
public void outABinopExpr(ABinopExpr node) {
Value right = (Value) mProductions.removeLast();
BinopExpr expr = (BinopExpr) mProductions.removeLast();
Value left = (Value) mProductions.removeLast();
expr.setOp1(left);
expr.setOp2(right);
mProductions.addLast(expr);
}
public void outAArrayRef(AArrayRef node) {
Value immediate = (Value) mProductions.removeLast();
String identifier = (String) mProductions.removeLast();
Local l = (Local) mLocals.get(identifier);
if (l == null) throw new RuntimeException("did not find local: " + identifier);
mProductions.addLast(Jimple.v().newArrayRef(l, immediate));
}
/*
case_stmt =
case_label colon goto_stmt;
*/
public void outACaseStmt(ACaseStmt node) {
String labelName = (String) mProductions.removeLast();
UnitBox box = Jimple.v().newStmtBox(null);
addBoxToPatch(labelName, box);
Value labelValue = null;
if (node.getCaseLabel() instanceof AConstantCaseLabel)
labelValue = (Value) mProductions.removeLast();
// if labelValue == null, this is the default label.
if (labelValue == null) mProductions.addLast(box);
else {
Object[] valueTargetPair = new Object[2];
valueTargetPair[0] = labelValue;
valueTargetPair[1] = box;
mProductions.addLast(valueTargetPair);
}
}
public void outAGotoStatement(AGotoStatement node) {
String targetLabel = (String) mProductions.removeLast();
UnitBox box = Jimple.v().newStmtBox(null);
Unit branch = Jimple.v().newGotoStmt(box);
addBoxToPatch(targetLabel, box);
mProductions.addLast(branch);
}
public void outALocalFieldRef(ALocalFieldRef node) {
SootFieldRef field = (SootFieldRef) mProductions.removeLast();
String local = (String) mProductions.removeLast();
Local l = (Local) mLocals.get(local);
if (l == null) throw new RuntimeException("did not find local: " + local);
mProductions.addLast(Jimple.v().newInstanceFieldRef(l, field));
}
public void parseInputFile(File inputFile) throws IOException {
geneFeatures.clear();
otherRecords.clear();
try {
GFFEntrySet gffEntries = GFFTools.readGFF(inputFile);
Iterator itr = gffEntries.lineIterator();
int count = 0;
int intronFeatures = 0;
LinkedList<GFFRecord> cdsRecs = new LinkedList<GFFRecord>();
while (itr.hasNext()) {
Object val = itr.next();
if (val instanceof GFFRecord) {
GFFRecord rec = (GFFRecord) val;
count += 1;
if (rec.getFeature().endsWith("gene")) {
GeneFeatures gf = new GeneFeatures(rec);
geneFeatures.put(gf.id, gf);
} else if (rec.getFeature().equals("CDS")) {
cdsRecs.addLast(rec);
} else {
otherRecords.add(rec);
}
}
}
for (GFFRecord rec : cdsRecs) {
Map<String, List<String>> attrs = decodeAttrMap(rec);
if (geneFeatures.containsKey(attrs.get("Parent").get(0))) {
geneFeatures.get(attrs.get("Parent").get(0)).addCDS(rec, attrs);
} else {
System.err.println("Unknown CDS Parent: " + attrs.get("Parent").get(0));
}
}
for (String k : geneFeatures.keySet()) {
GeneFeatures gf = geneFeatures.get(k);
if (gf.cds != null && gf.cds.size() > 1) {
intronFeatures++;
}
}
System.err.println("# GFF Records: " + count);
System.err.println("# Gene Feature Sets: " + geneFeatures.size());
System.err.println("\t# Intron-Features: " + intronFeatures);
} catch (ParserException e) {
e.printStackTrace();
} catch (BioException e) {
e.printStackTrace();
}
}
public void outAIfStatement(AIfStatement node) {
String targetLabel = (String) mProductions.removeLast();
Value condition = (Value) mProductions.removeLast();
UnitBox box = Jimple.v().newStmtBox(null);
Unit u = Jimple.v().newIfStmt(condition, box);
addBoxToPatch(targetLabel, box);
mProductions.addLast(u);
}
public static TreeNode createTree(ArrayList<String> list) {
LinkedList<NodeWithBranch> queue = new LinkedList<>();
TreeNode head = new TreeNode(0);
queue.addLast(new NodeWithBranch(head, 0));
for (String s : list) {
NodeWithBranch node = queue.removeFirst();
if (!s.equals(NULL)) {
if (node.branch == 0) {
node.tree.left = new TreeNode(Integer.parseInt(s));
queue.addLast(new NodeWithBranch(node.tree.left, 0));
queue.addLast(new NodeWithBranch(node.tree.left, 1));
} else {
node.tree.right = new TreeNode(Integer.parseInt(s));
queue.addLast(new NodeWithBranch(node.tree.right, 0));
queue.addLast(new NodeWithBranch(node.tree.right, 1));
}
}
}
return head.left;
}
public void outAReturnStatement(AReturnStatement node) {
Value v;
Stmt s = null;
if (node.getImmediate() != null) {
v = (Value) mProductions.removeLast();
s = Jimple.v().newReturnStmt(v);
} else {
s = Jimple.v().newReturnVoidStmt();
}
mProductions.addLast(s);
}
public void outADeclaration(ADeclaration node) {
List localNameList = (List) mProductions.removeLast();
Type type = (Type) mProductions.removeLast();
Iterator it = localNameList.iterator();
List localList = new ArrayList();
while (it.hasNext()) {
Local l = Jimple.v().newLocal((String) it.next(), type);
mLocals.put(l.getName(), l);
localList.add(l);
}
mProductions.addLast(localList);
}
public void search(Vertex[] nodes, int start) {
LinkedList<Vertex> queue = new LinkedList<>();
nodes[start].numPaths = 1;
nodes[start].minDistance = 0;
queue.addLast(nodes[start]);
while (!queue.isEmpty()) {
Vertex curr = queue.removeFirst();
for (Edge e : curr.edges) {
Vertex other = e.end;
if (!other.checked) {
other.checked = true;
queue.addLast(other);
}
if (curr.minDistance + e.weight < other.minDistance) {
other.minDistance = curr.minDistance + e.weight;
other.numPaths = curr.numPaths;
} else if (curr.minDistance + e.weight == other.minDistance) {
other.numPaths += curr.numPaths;
}
}
}
}
public void outAFieldSignature(AFieldSignature node) {
String className, fieldName;
Type t;
fieldName = (String) mProductions.removeLast();
t = (Type) mProductions.removeLast();
className = (String) mProductions.removeLast();
SootClass cl = mResolver.makeClassRef(className);
SootFieldRef field = Scene.v().makeFieldRef(cl, fieldName, t, false);
mProductions.addLast(field);
}
public void outAStringConstant(AStringConstant node) {
String s = (String) mProductions.removeLast();
mProductions.addLast(StringConstant.v(s));
/*
try {
String t = StringTools.getUnEscapedStringOf(s);
mProductions.push(StringConstant.v(t));
} catch(RuntimeException e) {
G.v().out.println(s);
throw e;
}
*/
}
/*
throws_clause =
throws class_name_list;
*/
public void outAThrowsClause(AThrowsClause node) {
List l = (List) mProductions.removeLast();
Iterator it = l.iterator();
List exceptionClasses = new ArrayList(l.size());
while (it.hasNext()) {
String className = (String) it.next();
exceptionClasses.add(mResolver.makeClassRef(className));
}
mProductions.addLast(exceptionClasses);
}
public void secureExport(int i) {
File expf = getExportTempFile(store.plainName(i));
// check if its already been exported
if (expf.exists()) secureUse(expf);
else { // otherwise add to work queue
File cipf = store.locate(i);
if (cipf != null) {
synchronized (jobs) {
if (priorityExport) jobs.addFirst(expJob(cipf, expf));
else jobs.addLast(expJob(cipf, expf));
}
} else System.err.println("Cannot export, missing encrypted file");
}
updateStatus();
}