private void button3_Click(object sender, EventArgs e)
{
if (jury1DSetup1.Enabled)
{
ProfileTree t = ProfileAutomatic.AnalyseProfileFile(profileFile, SIMDIST.SIMILARITY);
if (t != null)
{
string profileName = "automatic_similarity.profile";
t.SaveProfiles(profileName);
jury1DSetup1.profileName = profileName;
}
else
{
MessageBox.Show("Could not create automatic profile");
}
}
if (distanceControl1.Enabled)
{
if (distanceControl1.distDef == DistanceMeasures.HAMMING)
{
ProfileTree t = ProfileAutomatic.AnalyseProfileFile(profileFile, SIMDIST.DISTANCE);
string profileName = "automatic_distance.profile";
t.SaveProfiles(profileName);
distanceControl1.profileName = profileName;
}
if (distanceControl1.reference)
{
ProfileTree t = ProfileAutomatic.AnalyseProfileFile(profileFile, SIMDIST.SIMILARITY);
string profileName = "automatic_similarity.profile";
t.SaveProfiles(profileName);
distanceControl1.referenceProfile = profileName;
}
}
}
private JToken ToJson(ProfileTree tree, string[] prefix)
{
string[] newPrefix = prefix
.Concat(new[] { tree.NameString })
.ToArray();
switch (tree)
{
case ProfileTreeNode node:
return(hiddenKeys.Contains(newPrefix.ToQualifiedName())
? (JToken) new JArray(node.Children
.Select(child =>
ToJson(
child,
newPrefix)).ToArray())
: new JObject(node.Children
.Select(child =>
new JProperty(
child.NameString,
ToJson(
child,
newPrefix)))
.ToArray()));
case ProfileTreeLeaf leaf:
return(ToJsonValue(leaf.Value, newPrefix));
default:
throw new NotSupportedException();
}
}
private string LabelActiveProfiles(string fileName)
{
string outStr = "";
ProfileTree tree = new ProfileTree();
try
{
tree.LoadProfiles(fileName);
}
catch (Exception)
{
label2.Text = "";
return(null);
}
inputMode = tree.GetModes();
List <profileNode> active = tree.GetActiveProfiles();
outStr = "Active profiles: ";
if (active != null)
{
for (int i = 0; i < active.Count; i++)
{
outStr += active[i].profName;
if (i < active.Count - 1)
{
outStr += ", ";
}
}
}
return(outStr);
}
public ProfileForm(string fileName, string alignFile, filterOPT filter)
{
InitializeComponent();
if (fileName == null || fileName.Length == 0)
{
this.Text = "Profile not defined";
}
else
{
this.Text = fileName;
this.fileName = fileName;
}
this.filter = filter;
//profilesView.DrawMode = TreeViewDrawMode.OwnerDrawText;
treeProfiles = new ProfileTree();
if (fileName != null && fileName.Length > 0)
{
if (File.Exists(fileName))
{
treeProfiles.LoadProfiles(fileName);
}
}
ShowTree();
//profilesView.
}
public async Task Write(ProfileTree tree, CancellationToken cancellationToken)
{
cancellationToken.ThrowIfCancellationRequested();
var errors = tree
.GetAllChildren()
.Select(tuple => tuple.tree)
.OfType <ProfileTreeError>()
.OrderBy(pair => pair.SourceMark)
.ToList();
if (errors.Count > 0)
{
foreach (var error in errors)
{
logger.Error(new
{
message = "Error reading input",
error = error.Error,
fileName = error.SourceMark.FileName,
line = error.SourceMark.LineNumber
});
}
throw new ApplicationException();
}
using (var stream = outputStreamFactory())
await DoWrite(tree, stream, cancellationToken);
}
private void button3_Click(object sender, EventArgs e)
{
ProfileTree t = ProfileAutomatic.AnalyseProfileFile(profileFile, SIMDIST.SIMILARITY);
string profileName = "automatic_similarity.profile";
t.SaveProfiles(profileName);
jury1DSetup1.profileName = profileName;
}
protected override async Task DoWrite(ProfileTree tree, Stream stream, CancellationToken cancellationToken)
{
using (var writer = new StreamWriter(stream))
using (var jsonWriter = new JsonTextWriter(writer)
{
Formatting = Formatting.Indented
})
await ToJson(tree, new string[0])
.WriteToAsync(jsonWriter);
}
protected override async Task DoWrite(ProfileTree tree, Stream stream, CancellationToken cancellationToken)
{
using (var writer = new StreamWriter(stream))
foreach (var line in tree
.GetLeafs()
.OrderBy(pair => pair.leaf.SourceMark)
.SelectMany(pair => FormatEntry(pair.prefix, pair.leaf)))
{
await writer.WriteLineAsync(line.ToCharArray(), cancellationToken);
}
}
private static bool IsArray(ProfileTree tree)
{
if (!(tree is ProfileTreeNode node))
{
return(false);
}
var cnt = node.Children.Count(child => child.Name.Tokens.Count == 1 && child.Name.Tokens[0] is TextNameToken token && token.Text.All(char.IsDigit));
return(cnt > 0 && cnt == node.Children
.Count(child => !(child.Name.Tokens.Count == 1 && child.Name.Tokens[0] is SubstituteNameToken)));
}
protected override async Task DoWrite(ProfileTree tree, Stream stream, CancellationToken cancellationToken)
{
var serializer = new SerializerBuilder()
.WithEventEmitter(nextEmitter => new QuoteStringEventEmitter(nextEmitter))
.Build();
using (var writer = new StreamWriter(stream))
await writer.WriteAsync(
serializer
.Serialize(ToObject(tree, new string[0]))
.ToCharArray(),
cancellationToken);
}
public void Prepare(List<KeyValuePair<string,string>> profilesStr,string profName,string profFile)
{
r = new ProfileTree();
r.LoadProfiles(profFile);
foreach(var item in profilesStr)
{
List<string> aux = new List<string>(item.Value.Length);
for (int i = 0; i < item.Value.Length; i++)
aux.Add(item.Value[i].ToString());
r.AddItemsCombineStates(item.Key,aux);
}
}
private void MakeViewCopy(ProfileTree tr, TreeNode node)
{
foreach (TreeNode item in node.Nodes)
{
string Path = item.FullPath;
Path = PathRemoveRoot(Path);
Path = ParentPath(Path);
tr.AdddNode(Path, new profileNode((profileNode)item.Tag));
if (item.Nodes.Count > 0)
{
MakeViewCopy(tr, item);
}
}
}
private void GetNodes(TreeNode node, ProfileTree tree)
{
profileNode nodeP;
string parentPath = node.FullPath;
Regex reg = new Regex("^Profiles");
parentPath = reg.Replace(parentPath, "");
foreach (TreeNode item in node.Nodes)
{
string Path = item.FullPath;
Path = reg.Replace(Path, "");
nodeP = treeProfiles.FindNode(Path);
tree.AdddNode(parentPath, new profileNode(nodeP));
if (item.Nodes != null)
{
GetNodes(item, tree);
}
}
}
protected override async Task DoWrite(ProfileTree tree, Stream stream, CancellationToken cancellationToken)
{
var xmlNamespaces = (from pair in tree.GetLeafs()
where pair.leaf.NameString.StartsWith("xmlns:")
select new { Key = pair.leaf.NameString.Substring(6), pair.leaf.Value })
.ToDictionary(x => x.Key, x => XNamespace.Get(x.Value));
using (var writer = new StreamWriter(stream))
using (var xmlWriter = XmlWriter.Create(writer, new XmlWriterSettings
{
Async = true,
Indent = (xmlOptions & XmlOptions.NoIndent) == XmlOptions.None,
NewLineOnAttributes = (xmlOptions & XmlOptions.NewLineOnAttributes) == XmlOptions.NewLineOnAttributes
}))
await ApplyOutputPrefix(
(XElement)ToXml(tree, new string[0], "", xmlNamespaces)
.Single()
.node)
.WriteToAsync(xmlWriter, cancellationToken);
}
private void button5_Click(object sender, EventArgs e)
{
DialogResult res = openFileDialog1.ShowDialog();
if (res == DialogResult.OK)
{
localNode.profName = textBox1.Text;
ProfileTree t = ProfileAutomatic.AnalyseProfileFile(openFileDialog1.FileName, SIMDIST.SIMILARITY);
if (t.masterNode.ContainsKey(localNode.profName))
{
dataGridView1.Rows.Clear();
foreach (var item in t.masterNode[localNode.profName].states.Keys)
{
dataGridView1.Rows.Add(1);
dataGridView1.Rows[dataGridView1.Rows.Count - 2].Cells[0].Value = item;
dataGridView1.Rows[dataGridView1.Rows.Count - 2].Cells[1].Value = item;
}
}
}
}
public ProfileForm(string fileName,string alignFile,filterOPT filter)
{
InitializeComponent();
if (fileName == null || fileName.Length == 0)
this.Text = "Profile not defined";
else
{
this.Text = fileName;
this.fileName = fileName;
}
this.filter = filter;
//profilesView.DrawMode = TreeViewDrawMode.OwnerDrawText;
treeProfiles = new ProfileTree();
if(fileName!=null && fileName.Length>0)
if(File.Exists(fileName))
treeProfiles.LoadProfiles(fileName);
ShowTree();
//profilesView.
}
public ProfileForm(string fileName, string alignFile, filterOPT filter)
{
InitializeComponent();
if (fileName == null || fileName.Length == 0)
{
this.Text = "Profile not defined";
}
else
{
this.Text = fileName;
this.fileName = fileName;
}
this.filter = filter;
//profilesView.DrawMode = TreeViewDrawMode.OwnerDrawText;
treeProfiles = new ProfileTree();
if (fileName != null && fileName.Length > 0)
{
if (File.Exists(fileName))
{
treeProfiles.LoadProfiles(fileName);
if (treeProfiles.combine == profileCombination.JOIN_STATES)
{
toolStripButton1.Enabled = false;
toolStripButton4.Enabled = true;
}
else
{
toolStripButton1.Enabled = true;
toolStripButton4.Enabled = false;
}
}
}
ShowTree();
//profilesView.
}
private object ToObject(ProfileTree tree, string[] prefix)
{
string[] newPrefix = prefix
.Concat(new[] { tree.NameString })
.ToArray();
switch (tree)
{
case ProfileTreeNode node:
return(hiddenKeys.Contains(newPrefix.ToQualifiedName())
? (object)node.Children.Select(
child => ToObject(child, newPrefix)).ToArray()
: node.Children.ToDictionary(
child => child.NameString,
child => ToObject(child, newPrefix)));
case ProfileTreeLeaf leaf:
return(ToObjectValue(leaf.Value, newPrefix));
default:
throw new NotSupportedException();
}
}
protected override async Task DoWrite(ProfileTree tree, Stream stream, CancellationToken cancellationToken)
{
using (var memoryStream = new MemoryStream())
using (var writer = new StreamWriter(stream))
{
var parser = new IniStreamParser();
var data = new IniData();
foreach (var(prefix, leaf) in tree.GetLeafs())
{
var names = prefix.Parts
.Select(part => part.Tokens.Cast <TextNameToken>().Single().Text)
.Skip(1);
if (outputPrefix != null)
{
names = outputPrefix.Concat(names);
}
if (delimiter == ".")
{
names = names.Select(name => name.Replace(".", "\\."));
}
data[names.First()][string.Join(delimiter, names.Skip(1))] = leaf.Value;
}
parser.WriteData(writer, data);
await writer.FlushAsync();
memoryStream.Seek(0, SeekOrigin.Begin);
await memoryStream.CopyToAsync(stream);
}
}
private void button3_Click(object sender, EventArgs e)
{
ProfileTree t = ProfileAutomatic.AnalyseProfileFile(profileFile, SIMDIST.SIMILARITY);
if (t != null)
{
string profileName = "automatic_similarity.profile";
t.SaveProfiles(profileName);
userHash1.profRefFile = profileName;
userHash1.profRegFile = profileName;
distanceControl1.referenceProfile = profileName;
if (distanceControl1.distDef == DistanceMeasures.HAMMING)
{
t = ProfileAutomatic.AnalyseProfileFile(profileFile, SIMDIST.DISTANCE);
profileName = "automatic_distance.profile";
t.SaveProfiles(profileName);
distanceControl1.profileName = profileName;
}
}
else
{
MessageBox.Show("Profile cannot be generated");
}
}
public Alignment()
{
r = new ProfileTree();
}
private string LabelActiveProfiles(string fileName)
{
string outStr = "";
ProfileTree tree = new ProfileTree();
if (fileName.Length > 0)
tree.LoadProfiles(fileName);
else
return null;
inputMode = tree.GetModes();
List<profileNode> active = tree.GetActiveProfiles();
outStr = "Active profiles: ";
if(active!=null)
for (int i = 0; i < active.Count; i++)
{
outStr += active[i].profName;
if (i < active.Count - 1)
outStr += ", ";
}
return outStr;
}
public async Task Write(ProfileTree tree, CancellationToken cancellationToken) => await inner.Write(tree.Ignore(ignore), cancellationToken);
public static IEnumerable <IProfileEntry> WithImplicitHiddenKeys(this SchemeNode node, ProfileTree tree)
{
var originalPayload = node.GetOriginalPayload().ToList();
var implicitHiddenKeys = (from pair in tree.GetAllChildren()
where IsArray(pair.tree)
select new Payload(
new QualifiedName(pair.prefix.Parts.Append(new NamePart(new[] { new TextNameToken("type") }))),
new[] { new TextValueToken("hiddenKey") }, pair.tree.GetFirstSourceMark())).ToList();
return(originalPayload.Concat(implicitHiddenKeys));
}
public static ProfileTree AnalyseProfileFile(string fileName, SIMDIST similarityFlag, string internalName = null)
{
ProfileTree t = new ProfileTree();
StreamReader wr;
if (fileName == null || !File.Exists(fileName))
{
throw new Exception("File:" + fileName + " not exists");
}
wr = new StreamReader(fileName);
string line = wr.ReadLine();
Dictionary <string, Dictionary <string, int> > dic = new Dictionary <string, Dictionary <string, int> >();
while (line != null)
{
if (line.Contains(">"))
{
line = wr.ReadLine();
while (line != null && line[0] != '>')
{
if (line.Contains("profile") && !line.Contains("SEQ"))
{
string[] tmp = line.Split(new string[] { " profile " }, StringSplitOptions.None);
if (!dic.ContainsKey(tmp[0]))
{
dic.Add(tmp[0], new Dictionary <string, int>());
}
string[] aux;
if (tmp[1].Contains(" "))
{
aux = tmp[1].Split(' ');
}
else
{
aux = new string[tmp[1].Length];
for (int i = 0; i < tmp[1].Length; i++)
{
aux[i] = tmp[1][i].ToString();
}
}
foreach (var item in aux)
{
if (item != "-" && item != "")
{
if (!dic[tmp[0]].ContainsKey(item))
{
dic[tmp[0]].Add(item, 0);
}
}
}
}
line = wr.ReadLine();
}
}
else
{
line = wr.ReadLine();
}
}
wr.Close();
if (dic.Keys.Count == 0)
{
throw new Exception("File " + fileName + " is not valid Profile file!");
}
foreach (var item in dic)
{
profileNode node = new profileNode();
node.active = true;
if (internalName != null)
{
node.internalName = internalName;
}
else
{
node.internalName = "User defined profile";
}
node.profName = item.Key;
foreach (var itemK in item.Value)
{
node.AddStateItem(itemK.Key, itemK.Key);
}
node.profWeights = GenerateWeights(new List <string>(item.Value.Keys), similarityFlag);
t.AdddNode("/", node);
}
// t.pr
return(t);
}
public static ProfileTree AnalyseProfileFile(string fileName, SIMDIST similarityFlag)
{
ProfileTree t = new ProfileTree();
StreamReader wr;
if (fileName == null || !File.Exists(fileName))
throw new Exception("File:" + fileName + " not exists");
wr = new StreamReader(fileName);
string line = wr.ReadLine();
Dictionary<string, Dictionary<string, int>> dic = new Dictionary<string, Dictionary<string, int>>();
while (line != null)
{
if (line.Contains(">"))
{
line = wr.ReadLine();
while (line != null && line[0] != '>')
{
if (line.Contains("profile") && !line.Contains("SEQ"))
{
string[] tmp = line.Split(new string[] { " profile " }, StringSplitOptions.None);
if (!dic.ContainsKey(tmp[0]))
dic.Add(tmp[0], new Dictionary<string, int>());
string[] aux;
if (tmp[1].Contains(" "))
aux = tmp[1].Split(' ');
else
{
aux = new string[tmp[1].Length];
for (int i = 0; i < tmp[1].Length; i++)
aux[i] = tmp[1][i].ToString();
}
foreach (var item in aux)
if (item != "-" && item!="")
if (!dic[tmp[0]].ContainsKey(item))
dic[tmp[0]].Add(item, 0);
}
line = wr.ReadLine();
}
}
else
line = wr.ReadLine();
}
wr.Close();
if (dic.Keys.Count == 0)
throw new Exception("File " + fileName + " is not valid Profile file!");
foreach (var item in dic)
{
profileNode node = new profileNode();
node.active = true;
node.internalName = "User defined profile";
node.profName = item.Key;
foreach (var itemK in item.Value)
node.AddStateItem(itemK.Key, itemK.Key);
node.profWeights = GenerateWeights(new List<string>(item.Value.Keys), similarityFlag);
t.AdddNode("/", node);
}
// t.pr
return t;
}
private string LabelActiveProfiles(string fileName)
{
string outStr = "";
ProfileTree tree = new ProfileTree();
try
{
tree.LoadProfiles(fileName);
}
catch(Exception ex)
{
label2.Text = "";
}
inputMode = tree.GetModes();
List<profileNode> active = tree.GetActiveProfiles();
outStr = "Active profiles: ";
if(active!=null)
for (int i = 0; i < active.Count; i++)
{
outStr += active[i].profName;
if (i < active.Count - 1)
outStr += ", ";
}
return outStr;
}
private void MakeViewCopy(ProfileTree tr,TreeNode node)
{
foreach (TreeNode item in node.Nodes)
{
string Path = item.FullPath;
Path = PathRemoveRoot(Path);
Path = ParentPath(Path);
tr.AdddNode(Path, new profileNode((profileNode)item.Tag));
if (item.Nodes.Count > 0)
MakeViewCopy(tr,item);
}
}
protected abstract Task DoWrite(ProfileTree tree, Stream stream, CancellationToken cancellationToken);
private void GetNodes(TreeNode node, ProfileTree tree)
{
profileNode nodeP;
string parentPath = node.FullPath;
Regex reg = new Regex("^Profiles");
parentPath = reg.Replace(parentPath, "");
foreach (TreeNode item in node.Nodes)
{
string Path=item.FullPath;
Path=reg.Replace(Path,"");
nodeP=treeProfiles.FindNode(Path);
tree.AdddNode(parentPath, new profileNode(nodeP));
if (item.Nodes != null)
GetNodes(item, tree);
}
}
