private void button1_Click(object sender, EventArgs e)
{
IntList intlist = new IntList();
intlist.Add(1);
intlist.Add(2);
intlist.Add(3);
MessageBox.Show(intlist[0].ToString());
泛型.StringList slist = new StringList();
slist.Add("100");
MyList <int> glist = new MyList <int>();
glist.Add(200);
MessageBox.Show(glist.ToString());
MyList <string> glist1 = new MyList <string>();
glist1.Add("200");
MessageBox.Show(glist1.ToString());
//缓存泛型方法的调用演示
Pig pig = CacheMgr.GetData <Pig>("pigkey");
}
public void TestRemove()
{
IntList list = new IntList();
for (int j = 0; j < 1000; j++)
{
list.Add(j);
}
for (int j = 0; j < 1000; j++)
{
Assert.AreEqual(j, list.Remove(0));
Assert.AreEqual(999 - j, list.Count);
}
for (int j = 0; j < 1000; j++)
{
list.Add(j);
}
for (int j = 0; j < 1000; j++)
{
Assert.AreEqual(999 - j, list.Remove(999 - j));
Assert.AreEqual(999 - j, list.Count);
}
try
{
list.Remove(0);
Assert.Fail("should have caught IndexOutOfBoundsException");
}
catch (IndexOutOfRangeException)
{
// as expected
}
}
public void GivenAPopulatedList_WhenCallWithInvalidIndex_ThenThrowInvalidListIndexException()
{
IntList l = new IntList();
l.Add(1);
l.Add(2);
l.Add(3);
Assert.Throws <InvalidListIndexException>(() => l.Get(10));
}
/// <summary>
/// Adds a new range from one of the merged sequences or from the common
/// predecessor.
/// </summary>
/// <remarks>
/// Adds a new range from one of the merged sequences or from the common
/// predecessor. This method can add conflicting and non-conflicting ranges
/// controlled by the conflictState parameter
/// </remarks>
/// <param name="srcIdx">
/// determines from which sequence this range comes. An index of
/// x specifies the x+1 element in the list of sequences
/// specified to the constructor
/// </param>
/// <param name="begin">
/// the first element from the specified sequence which should be
/// included in the merge result. Indexes start with 0.
/// </param>
/// <param name="end">
/// specifies the end of the range to be added. The element this
/// index points to is the first element which not added to the
/// merge result. All elements between begin (including begin) and
/// this element are added.
/// </param>
/// <param name="conflictState">
/// when set to NO_CONLICT a non-conflicting range is added.
/// This will end implicitly all open conflicts added before.
/// </param>
public virtual void Add(int srcIdx, int begin, int end, MergeChunk.ConflictState
conflictState)
{
chunks.Add((int)(conflictState));
chunks.Add(srcIdx);
chunks.Add(begin);
chunks.Add(end);
if (conflictState != MergeChunk.ConflictState.NO_CONFLICT)
{
containsConflicts = true;
}
}
public void GivenAnNonEmptyList_WhenCallCount_ThenReturnCountOfItems()
{
IntList l = new IntList();
l.Add(1);
l.Add(2);
l.Add(3);
l.Add(4);
l.Add(5);
Assert.Equal(5, l.Count);
}
static void Main(string[] args)
{
IntList il = new IntList();
il.Add(1);
il.Add(2);
il.Add(3);
il.Add(4);
foreach (int i in il.BidirectionalSubrange(false, 1, 3))
{
Console.WriteLine(i);
}
}
public void GivenAnEmptyList_WhenCallAddMultipleTimes_ThenCallPopWithIndexReturnCorrectItem()
{
IntList l = new IntList();
l.Add(1);
l.Add(2);
l.Add(3);
l.Add(4);
l.Add(5);
Assert.Equal(5, l.Count);
Assert.Equal(1, l.Pop(0));
Assert.Equal(4, l.Count);
Assert.Equal(2, l.Pop(0));
Assert.Equal(3, l.Count);
}
public void TestConstructors()
{
IntList list = new IntList();
Assert.IsTrue(list.IsEmpty());
list.Add(0);
list.Add(1);
IntList list2 = new IntList(list);
//Assert.AreEqual(list, list2);
Assert.IsTrue(list.Equals(list2));
IntList list3 = new IntList(2);
Assert.IsTrue(list3.IsEmpty());
}
public void TestRetainAll()
{
IntList list = new IntList();
for (int j = 0; j < 1000; j++)
{
list.Add(j);
}
IntList listCopy = new IntList(list);
IntList listOdd = new IntList();
IntList listEven = new IntList();
for (int j = 0; j < 1000; j++)
{
if (j % 2 == 0)
{
listEven.Add(j);
}
else
{
listOdd.Add(j);
}
}
list.RetainAll(listOdd);
//Assert.AreEqual(list, listOdd);
Assert.IsTrue(list.Equals(listOdd));
list.RetainAll(listEven);
Assert.IsTrue(list.IsEmpty());
listCopy.RetainAll(listEven);
//Assert.AreEqual(listCopy, listEven);
Assert.IsTrue(listCopy.Equals(listEven));
listCopy.RetainAll(listOdd);
Assert.IsTrue(listCopy.IsEmpty());
}
public void TestSet()
{
IntList list = new IntList();
for (int j = 0; j < 1000; j++)
{
list.Add(j);
}
for (int j = 0; j < 1001; j++)
{
try
{
list.Set(j, j + 1);
if (j == 1000)
{
Assert.Fail("Should have gotten exception");
}
Assert.AreEqual(j + 1, list.Get(j));
}
catch (IndexOutOfRangeException)
{
if (j != 1000)
{
Assert.Fail("premature exception");
}
}
}
}
public void CompleteTests()
{
var array = new IntList();
Assert.Equal(0, array.Count);
array = AddArray(1, 2, 3, 4);
Assert.Equal(4, array.Count);
array.Add(5);
Assert.Equal(5, array.Count);
Assert.Equal(5, array[4]);
array[4] = 220;
Assert.Equal(220, array[4]);
Assert.True(array.Contains(3));
Assert.False(array.Contains(10));
Assert.Equal(-1, array.IndexOf(100));
array.Insert(5, 100);
Assert.Equal(5, array.IndexOf(100));
Assert.Equal(6, array.Count);
array.Remove(100);
Assert.Equal(-1, array.IndexOf(100));
Assert.Equal(5, array.Count);
array.RemoveAt(4);
Assert.Equal(4, array[3]);
Assert.Equal(4, array.Count);
}
public void TestGet()
{
IntList list = new IntList();
for (int j = 0; j < 1000; j++)
{
list.Add(j);
}
for (int j = 0; j < 1001; j++)
{
try
{
Assert.AreEqual(j, list.Get(j));
if (j == 1000)
{
Assert.Fail("should have gotten exception");
}
}
catch (IndexOutOfRangeException)
{
if (j != 1000)
{
Assert.Fail("unexpected IndexOutOfBoundsException");
}
}
}
}
private IntList LineMap(int ptr, int end)
{
// Experimentally derived from multiple source repositories
// the average number of bytes/line is 36. Its a rough guess
// to initially size our map close to the target.
//
IntList map = new IntList((end - ptr) / 36);
map.FillTo(1, int.MinValue);
for (; ptr < end; ptr = NextLF(ptr))
{
map.Add(ptr);
}
map.Add(end);
return(map);
}
static void NoReallocationTime()
{
int size = 512 * 424 * 1000;
IntList list = new IntList(size);
Stopwatch sw = new Stopwatch();
sw.Start();
for (int c = 0; c < size; c++)
{
list.Add(c);
}
sw.Stop();
Console.WriteLine("IntList Time: " + sw.ElapsedMilliseconds / 1000.0f + " ms");
List <int> list2 = new List <int>(size);
Stopwatch sw2 = new Stopwatch();
sw2.Start();
for (int c = 0; c < size; c++)
{
list2.Add(c);
}
sw2.Stop();
Console.WriteLine("List<int> Time: " + sw2.ElapsedMilliseconds / 1000.0f + "ms");
}
public void GivenAnEmptyList_WhenCallAppend_ThenCallPopReturnAppendedItem()
{
IntList l = new IntList();
l.Add(5);
Assert.Equal(5, l.Pop());
}
public void Test_Add_Should_Correctly_Add_One_Element_For_One_Integer_Array()
{
var array = new IntList();
array.Add(1);
Assert.Equal(1, array.Count);
}
public void SerializeParameters(UIElementCollection parameterGrid, string shaderName)
{
ShaderName = shaderName;
ClearLists();
foreach (var p in parameterGrid)
{
if (p is BoolView)
{
var vm = (p as BoolView).DataContext as BoolViewModel;
BoolList.Add(new SerializeHolder <bool>(vm.ShaderName, vm.ContentValue));
}
else if (p is IntView)
{
var vm = (p as IntView).DataContext as IntViewModel;
IntList.Add(new SerializeHolder <int>(vm.ShaderName, vm.ContentValue));
}
else if (p is FloatView)
{
var vm = (p as FloatView).DataContext as FloatViewModel;
FloatList.Add(new SerializeHolder <float>(vm.ShaderName, vm.ContentValue));
}
else if (p is Float2View)
{
var vm = (p as Float2View).DataContext as Float2ViewModel;
Float2List.Add(new SerializeHolder <Float2>(vm.ShaderName, vm.ContentValue));
}
else if (p is Float3View)
{
var vm = (p as Float3View).DataContext as Float3ViewModel;
Float3List.Add(new SerializeHolder <Float3>(vm.ShaderName, vm.ContentValue));
}
else if (p is Float4View)
{
var vm = (p as Float4View).DataContext as Float4ViewModel;
Float4List.Add(new SerializeHolder <Float4>(vm.ShaderName, vm.ContentValue));
}
else if (p is Texture2DView)
{
var vm = (p as Texture2DView).DataContext as Texture2DViewModel;
Texture2DList.Add(new SerializeHolder <string>(vm.ShaderName, vm.FileName));
}
}
var ofd = new SaveFileDialog();
string baseDirectory = System.AppDomain.CurrentDomain.BaseDirectory;
ofd.InitialDirectory = baseDirectory;
ofd.DefaultExt = ".xml";
ofd.Filter = "XML files (.xml)|*.xml";
if (ofd.ShowDialog() == true)
{
using (var f = File.Create(ofd.FileName))
{
XmlSer.Serialize(f, this);
}
}
}
public void OnButtonClicked()
{
IntList unlockedLevels = AssetBundleManager.Instance.GetAsset <IntList>("configs", "Unlocked Levels");
if (!unlockedLevels.Contains(0))
{
unlockedLevels.Add(0);
}
if (!unlockedLevels.Contains(1))
{
unlockedLevels.Add(1);
}
if (!unlockedLevels.Contains(2))
{
unlockedLevels.Add(2);
}
}
public void AddDbcell(int cell)
{
if (field_5_dbcells == null)
{
field_5_dbcells = new IntList();
}
field_5_dbcells.Add(cell);
}
public void GivenAnEmptyList_WhenCallAddMultipleTimes_ThenCallGetWithIndexReturnCorrectItemAndMaintainOriginalCount()
{
IntList l = new IntList();
l.Add(1);
l.Add(2);
l.Add(3);
l.Add(4);
l.Add(5);
Assert.Equal(5, l.Count);
Assert.Equal(1, l.Get(0));
Assert.Equal(2, l.Get(1));
Assert.Equal(3, l.Get(2));
Assert.Equal(4, l.Get(3));
Assert.Equal(5, l.Get(4));
Assert.Equal(5, l.Count);
}
public static void Main()
{
IntList list = new IntList();
list.Add(1);
list.Add(55);
list.Add(43);
foreach (int value in list)
{
Console.WriteLine("Value = {0}", value);
}
foreach (int value in list)
{
Console.WriteLine("Value = {0}", value);
list.Add(124);
}
}
public Grid()
{
Numbers = new IntList();
for (int i = 1; i < 10; i++)
Numbers.Add(i);
for (int i = 0; i < 9; i++)
for (int j = 0; j < 9; j++)
Possibilities[i, j] = new IntList(Numbers);
}
public IntList CompareTo(string other)
{
var results = new IntList();
foreach (var v in this)
{
results.Add(string.CompareOrdinal(v.ToString(), other));
}
return(results);
}
private IntList CreateTestList()
{
var list = new IntList();
for (var i = 0; i < 25; i++)
{
list.Add(i);
}
return(list);
}
public void TestContainsAll()
{
IntList list = new IntList();
Assert.IsTrue(list.ContainsAll(list));
for (int j = 0; j < 10; j++)
{
list.Add(j);
}
IntList list2 = new IntList(list);
Assert.IsTrue(list2.ContainsAll(list));
Assert.IsTrue(list.ContainsAll(list2));
list2.Add(10);
Assert.IsTrue(list2.ContainsAll(list));
Assert.IsTrue(!list.ContainsAll(list2));
list.Add(11);
Assert.IsTrue(!list2.ContainsAll(list));
Assert.IsTrue(!list.ContainsAll(list2));
}
private IntList AddArray(params int[] values)
{
IntList array = new IntList();
foreach (var value in values)
{
array.Add(value);
}
return(array);
}
protected IntList AddedArray(params int[] numbers)
{
IntList array = new IntList();
foreach (var number in numbers)
{
array.Add(number);
}
return(array);
}
public void TestClear()
{
IntList list = new IntList();
for (int j = 0; j < 500; j++)
{
list.Add(j);
}
Assert.AreEqual(500, list.Count);
list.Clear();
Assert.AreEqual(0, list.Count);
for (int j = 0; j < 500; j++)
{
list.Add(j + 1);
}
Assert.AreEqual(500, list.Count);
for (int j = 0; j < 500; j++)
{
Assert.AreEqual(j + 1, list.Get(j));
}
}
public void GivenAnEmptyList_WhenCallAppendMultipleTimes_ThenCallPopReturnAppendedItemsInReverseOrder()
{
IntList l = new IntList();
l.Add(1);
l.Add(2);
l.Add(3);
l.Add(4);
l.Add(5);
Assert.Equal(5, l.Count);
Assert.Equal(5, l.Pop());
Assert.Equal(4, l.Count);
Assert.Equal(4, l.Pop());
Assert.Equal(3, l.Count);
Assert.Equal(3, l.Pop());
Assert.Equal(2, l.Count);
Assert.Equal(2, l.Pop());
Assert.Equal(1, l.Count);
Assert.Equal(1, l.Pop());
Assert.Equal(0, l.Count);
Assert.Throws <EmptyListException>(() => l.Pop());
}
public void Test_Insert_Should_Correctly_Insert_Element_Array_Has_Exactly_3_elements()
{
//Given
IntList array = AddedArray(1, 2, 3);
//When
array.Insert(1, 100);
//Then
array.Add(10);
Assert.Equal(1, array.IndexOf(100));
Assert.Equal(3, array.IndexOf(3));
Assert.Equal(5, array.Count);
}
static public int Add(IntPtr l)
{
try {
IntList self = (IntList)checkSelf(l);
System.Int32 a1;
checkType(l, 2, out a1);
self.Add(a1);
pushValue(l, true);
return(1);
}
catch (Exception e) {
return(error(l, e));
}
}
private static void allTests(Ice.Communicator communicator)
{
Console.Out.Write("testing equals() for Slice structures... ");
Console.Out.Flush();
//
// Define some default values.
//
C def_cls = new C(5);
S1 def_s = new S1("name");
string[] def_ss = new string[]{ "one", "two", "three" };
IntList def_il = new IntList();
def_il.Add(1);
def_il.Add(2);
def_il.Add(3);
Dictionary<string, string> def_sd = new Dictionary<string, string>();
def_sd.Add("abc", "def");
Ice.ObjectPrx def_prx = communicator.stringToProxy("test");
S2 def_s2 = new S2(true, (byte)98, (short)99, 100, 101, (float)1.0, 2.0, "string", def_ss, def_il, def_sd,
def_s, def_cls, def_prx);
//
// Compare default-constructed structures.
//
{
test(new S2().Equals(new S2()));
}
//
// Change one primitive member at a time.
//
{
S2 v;
v = (S2)def_s2.Clone();
test(v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.bo = false;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.by--;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.sh--;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.i--;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.l--;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.f--;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.d--;
test(!v.Equals(def_s2));
v = (S2)def_s2.Clone();
v.str = "";
test(!v.Equals(def_s2));
}
//
// String member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.str = (string)def_s2.str.Clone();
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.str = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.str = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.str = null;
v2.str = null;
test(v1.Equals(v2));
}
//
// Sequence member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.ss = (string[])def_s2.ss.Clone();
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.ss = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.ss = null;
test(!v1.Equals(v2));
}
//
// Custom sequence member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.il = (IntList)def_s2.il.Clone();
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v1.il = new IntList();
test(!v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.il = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.il = null;
test(!v1.Equals(v2));
}
//
// Dictionary member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.sd = new Dictionary<string, string>(def_s2.sd);
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v1.sd = new Dictionary<string, string>();
test(!v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.sd = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.sd = null;
test(!v1.Equals(v2));
}
//
// Struct member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.s = (S1)def_s2.s.Clone();
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v1.s = new S1("name");
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v1.s = new S1("noname");
test(!v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.s = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.s = null;
test(!v1.Equals(v2));
}
//
// Class member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.cls = (C)def_s2.cls.Clone();
test(!v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.cls = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.cls = null;
test(!v1.Equals(v2));
}
//
// Proxy member
//
{
S2 v1, v2;
v1 = (S2)def_s2.Clone();
v1.prx = communicator.stringToProxy("test");
test(v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v1.prx = communicator.stringToProxy("test2");
test(!v1.Equals(def_s2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v1.prx = null;
test(!v1.Equals(v2));
v1 = (S2)def_s2.Clone();
v2 = (S2)def_s2.Clone();
v2.prx = null;
test(!v1.Equals(v2));
}
Console.Out.WriteLine("ok");
}
public void SessionAuthUserAccessTest()
{
SessionAuthUser authUser = new SessionAuthUser("UNIT_TEST", 1, "Tester", "Mr. Tester", 1);
Assert.IsNotNull(authUser);
IntList allAcceessLevelIds = new IntList();
allAcceessLevelIds.Add(CoreConstants.MODULE_ADMINISTRATION_ACCESS_NONE);
allAcceessLevelIds.Add(CoreConstants.MODULE_ADMINISTRATION_ACCESS_READ_ONLY);
allAcceessLevelIds.Add(CoreConstants.MODULE_ADMINISTRATION_ACCESS_EDIT);
allAcceessLevelIds.Add(CoreConstants.MODULE_ADMINISTRATION_ACCESS_FULL);
allAcceessLevelIds.Add(CoreConstants.MODULE_AUTH_ACCESS_NONE);
allAcceessLevelIds.Add(CoreConstants.MODULE_AUTH_ACCESS_READ_ONLY);
allAcceessLevelIds.Add(CoreConstants.MODULE_AUTH_ACCESS_EDIT);
allAcceessLevelIds.Add(CoreConstants.MODULE_AUTH_ACCESS_FULL);
allAcceessLevelIds.Add(CoreConstants.MODULE_BILLING_ACCESS_NONE);
allAcceessLevelIds.Add(CoreConstants.MODULE_BILLING_ACCESS_READ_ONLY);
allAcceessLevelIds.Add(CoreConstants.MODULE_BILLING_ACCESS_EDIT);
allAcceessLevelIds.Add(CoreConstants.MODULE_BILLING_ACCESS_FULL);
allAcceessLevelIds.Add(CoreConstants.MODULE_SAAS_ACCESS_NONE);
allAcceessLevelIds.Add(CoreConstants.MODULE_SAAS_ACCESS_READ_ONLY);
allAcceessLevelIds.Add(CoreConstants.MODULE_SAAS_ACCESS_EDIT);
allAcceessLevelIds.Add(CoreConstants.MODULE_SAAS_ACCESS_FULL);
allAcceessLevelIds.Add(CoreConstants.MODULE_GLOBAL_ACCESS_NONE);
allAcceessLevelIds.Add(CoreConstants.MODULE_GLOBAL_ACCESS_READ_ONLY);
allAcceessLevelIds.Add(CoreConstants.MODULE_GLOBAL_ACCESS_EDIT);
allAcceessLevelIds.Add(CoreConstants.MODULE_GLOBAL_ACCESS_FULL);
IntList acceessLevelIds = new IntList();
authUser.AccessLevels = new IntList();
foreach (int acceessLevelID in acceessLevelIds)
Assert.IsFalse(authUser.IsAuthorized(acceessLevelID), "Default access should be off");
#region Administrator Check
authUser.IsAdministrator = true;
foreach (int acceessLevelID in allAcceessLevelIds)
Assert.IsTrue(authUser.IsAuthorized(acceessLevelID), "IsAdministrator should have access to all");
authUser.IsAdministrator = false;
foreach (int acceessLevelID in allAcceessLevelIds)
Assert.IsFalse(authUser.IsAuthorized(acceessLevelID), "IsAdministrator turned off should disable access to all");
#endregion
#region Limited Access Check
authUser.AccessLevels = new IntList();
authUser.AccessLevels.Add(CoreConstants.MODULE_AUTH_ACCESS_NONE);
authUser.AccessLevels.Add(CoreConstants.MODULE_AUTH_ACCESS_READ_ONLY);
authUser.AccessLevels.Add(CoreConstants.MODULE_AUTH_ACCESS_EDIT);
foreach (int acceessLevelIDtoCheck in allAcceessLevelIds)
{
bool isAuthorized = authUser.IsAuthorized(acceessLevelIDtoCheck);
bool shouldBeAuthorized = (
(acceessLevelIDtoCheck == CoreConstants.MODULE_AUTH_ACCESS_NONE) ||
(acceessLevelIDtoCheck == CoreConstants.MODULE_AUTH_ACCESS_READ_ONLY) ||
(acceessLevelIDtoCheck == CoreConstants.MODULE_AUTH_ACCESS_EDIT)
);
Assert.AreEqual(isAuthorized, shouldBeAuthorized, "Failed to correctly authorize the only set item.");
}
#endregion
}
public static void Main(string[] args)
{
try {
PlatformManager.Services.MaxSequenceSize = int.MaxValue;
PlatformManager.Services.DefaultBufferSize = 4096;
PlatformManager.Services.Is64BitProcessType = true;
if (args.Length > 4) {
Console.WriteLine ("Too many arguments");
DisplayHelp ();
} else if (args.Length < 4) {
Console.WriteLine ("Not enough arguments");
DisplayHelp();
}else if (args [0] == "h" || args [0] == "help" || args [0] == "?" || args [0] == "-h") {
DisplayHelp ();
} else {
string subreads_name = args [0];
string ccs_name = args [1];
string ref_name = args [2];
string zmw = args[3];
// Validate files exist
for(int i = 0; i < 3; i++) {
var fname = args[i];
if (!File.Exists(fname)) {
Console.WriteLine ("Can't find file: " + fname);
return;
}
if (i < 2) {
//TODO: Add code to ensure BAM exists here
}
}
// Validate ZMW Number
int holeNumber;
bool converted = int.TryParse(zmw, out holeNumber);
if (!converted || holeNumber < 0) {
Console.WriteLine("Could not convert " + zmw +" into hole number >= 0");
}
Console.WriteLine("Loading Data ...");
// Get CCS Read
IntList zmws = new IntList();
zmws.Add(holeNumber);
//zmws.Add(133403);
DataSet dt = new DataSet(ccs_name);
var query = new ZmwQuery(zmws, dt);
var ccs = query.FirstOrDefault();
if (ccs == null) {
Console.WriteLine("Could not query hole number " + holeNumber + " from file " + ccs_name);
return;
}
var seq_str = ccs.Sequence();
var sequence = new Sequence(DnaAlphabet.Instance, seq_str);
sequence.ID = ccs.FullName();
//Clean up
query.Dispose(); query = null;
ccs.Dispose(); ccs = null;
dt.Dispose(); dt = null;
Console.WriteLine("Aligning Data ... ");
BWAPairwiseAligner bwa = new BWAPairwiseAligner(ref_name, false);
// Now get initial alignment and variants
BWAPairwiseAlignment aln = bwa.AlignRead(sequence) as BWAPairwiseAlignment;
if (aln == null) {
Console.WriteLine("Consensus read did not align");
return;
}
// Now get all the subreads
dt = new DataSet(subreads_name);
query = new ZmwQuery(zmws, dt);
// We must copy the data right away, or we wind up with a bunch of pointers that all hit the same thing
var subreads = query.Select(s => new Sequence(DnaAlphabet.Instance, s.Sequence()) {ID = s.FullName()}).ToList();
if (subreads.Count == 0 )
{
Console.WriteLine("Did not find any subreads from " + holeNumber + " in file " + subreads_name);
return;
}
subreads.ForEach( s => {
var split = s.ID.Split('/');
s.ID = String.Join("/", split.Skip(1)); });
zmws.Dispose(); zmws = null;
query.Dispose(); query = null;
// Now generate the dataset
var data = new CCSDataSet(sequence, subreads, aln);
Application.Init ();
MainWindow win = new MainWindow (data);
win.Show ();
Application.Run ();
}
}
catch(DllNotFoundException thrown) {
Console.WriteLine ("Error thrown when attempting to generate the CCS results.");
Console.WriteLine("A shared library was not found. To solve this, please add the folder" +
" with the downloaded files *.so and *.dylib " +
"to your environmental variables (LD_LIBRARY_PATH on Ubuntu, DYLD_LIBRARY_PATH on Mac OS X).");
Console.WriteLine ("Error: " + thrown.Message);
Console.WriteLine (thrown.StackTrace);
}
catch(Exception thrown) {
Console.WriteLine ("Error thrown when attempting to generate the CCS results");
Console.WriteLine ("Error: " + thrown.Message);
Console.WriteLine (thrown.StackTrace);
while (thrown.InnerException != null) {
Console.WriteLine ("Inner Exception: " + thrown.InnerException.Message);
thrown = thrown.InnerException;
}
}
}