/// <summary>
/// Read-in all available annotations.
/// </summary>
/// <param name="baseNames"></param>
/// <param name="types"></param>
/// <param name="files"></param>
/// <param name="badFiles">all files which couldn't be read</param>
/// <returns></returns>
public static string[][] GetAvailableAnnots(out string[] baseNames, out AnnotType[][] types, out string[] files, out List<string> badFiles )
{
var _files = GetAnnotFiles().ToList();
badFiles = new List<string>();
var _baseNames = new List<string>();
var _types = new List<AnnotType[]>();
var names = new List<string[]>();
foreach (var file in _files)
{
try
{
string baseName;
AnnotType[] type;
var name = GetAvailableAnnots(file, out baseName, out type);
names.Add(name);
_baseNames.Add(baseName);
_types.Add(type);
}
catch (Exception exception)
{
badFiles.Add(file);
}
}
foreach (var badFile in badFiles)
{
_files.Remove(badFile);
}
files = _files.ToArray();
baseNames = _baseNames.ToArray();
types = _types.ToArray();
return names.ToArray();
}
public static string[][] GetAvailableAnnots(out string[] baseNames, out AnnotType[][] types, out string[] files)
{
files = GetAnnotFiles();
baseNames = new string[files.Length];
types = new AnnotType[files.Length][];
string[][] names = new string[files.Length][];
for (int i = 0; i < names.Length; i++)
{
names[i] = GetAvailableAnnots(files[i], out baseNames[i], out types[i]);
}
return(names);
}
private static string[] GetAvailableAnnots(string file, out string baseName, out AnnotType[] types)
{
StreamReader reader = FileUtils.GetReader(file);
string line = reader.ReadLine();
string[] header = line.Split('\t');
line = reader.ReadLine();
string[] desc = line.Split('\t');
reader.Close();
baseName = header[0];
string[] result = ArrayUtils.SubArray(header, 1, header.Length);
types = new AnnotType[desc.Length - 1];
for (int i = 0; i < types.Length; i++)
{
types[i] = FromString1(desc[i + 1]);
}
return(result);
}
public static string[][] GetAvailableAnnots(out string[] baseNames, out AnnotType[][] types, out string[] files)
{
List<string> badFiles;
return GetAvailableAnnots(out baseNames, out types, out files, out badFiles);
}
private static string[] GetAvailableAnnots(string file, out string baseName, out AnnotType[] types)
{
StreamReader reader = FileUtils.GetReader(file);
string line = reader.ReadLine();
string[] header = line.Split('\t');
line = reader.ReadLine();
string[] desc = line.Split('\t');
reader.Close();
baseName = header[0];
string[] result = ArrayUtils.SubArray(header, 1, header.Length);
types = new AnnotType[desc.Length - 1];
for (int i = 0; i < types.Length; i++){
types[i] = FromString1(desc[i + 1]);
}
return result;
}
