/// <summary>
/// Specific API
/// 从Aird文件中读取,但是不要将m/z数组的从Integer改为Float
/// <para>
/// Read from aird, but not convert the m/z array from integer to float
///
/// </para>
/// </summary>
/// <param name="index"> 索引序列号 block index </param>
/// <param name="rt"> 光谱产出时刻 retention time for the spectrum </param>
/// <param name="compressor"> 压缩方式 compression method 0: ZDPD 1: S-ZDPD, default compressor = 0 </param>
/// <returns> 该时刻产生的光谱信息, 其中mz数据以int类型返回 the target rt's spectrum with integer mz array </returns>
public virtual MzIntensityPairs getSpectrumAsInteger(BlockIndex index, float rt, int compressor)
{
if (compressor == 0)
{
return(getSpectrumAsInteger(index, rt));
}
else if (compressor == 1)
{
IList <float> rts = index.rts;
int position = rts.IndexOf(rt);
MzIntensityPairs mzIntensityPairs = getSpectrumByIndex(index, position);
int[] mzArray = new int[mzIntensityPairs.getMzArray().Length];
for (int i = 0; i < mzArray.Length; i++)
{
mzArray[i] = (int)(mzIntensityPairs.getMzArray()[i] * mzPrecision);
}
return(new MzIntensityPairs(mzArray, mzIntensityPairs.getIntensityArray()));
}
else
{
Console.WriteLine("No such compressor.");
}
return(null);
}
public virtual SpectrumDetail getSpectrumDetail(int index)
{
IList <BlockIndex> indexList = getAirdInfo().indexList;
for (int i = 0; i < indexList.Count; i++)
{
BlockIndex blockIndex = indexList[i];
if (blockIndex.nums.Contains(index))
{
int targetIndex = blockIndex.nums.IndexOf(index);
MzIntensityPairs pairs = getSpectrumByIndex(blockIndex, targetIndex);
}
}
return(null);
}
/// <summary>
/// 返回值是一个map,其中key为rt,value为这个rt对应点原始谱图信息
/// 特别需要注意的是,本函数在使用完raf对象以后并不会直接关闭该对象,需要使用者在使用完DIAParser对象以后手动关闭该对象
/// <para>
/// the result key is rt,value is the spectrum(mz-intensity pairs)
/// In particular, this function will not close the RAF object directly after using it.
/// Users need to close the object manually after using the diaparser object
///
/// </para>
/// </summary>
/// <param name="startPtr"> 起始指针位置 start point </param>
/// <param name="endPtr"> 结束指针位置 end point </param>
/// <param name="rtList"> rt列表,包含所有的光谱产出时刻 the retention time list </param>
/// <param name="mzSizeList"> mz块的大小列表 the mz block size list </param>
/// <param name="intSizeList"> intensity块的大小列表 the intensity block size list </param>
/// <returns> 每一个时刻对应的光谱信息 the spectrum of the target retention time </returns>
public virtual SortedDictionary <float, MzIntensityPairs> getSpectrums(long startPtr, long endPtr, IList <float> rtList, IList <long> mzSizeList, IList <long> intSizeList)
{
try
{
SortedDictionary <float, MzIntensityPairs> map = new SortedDictionary <float, MzIntensityPairs>();
airdFile.Seek(startPtr, SeekOrigin.Begin);
long delta = endPtr - startPtr;
byte[] result = new byte[(int)delta];
airdFile.Read(result, 0, (int)delta);
Debug.Assert(rtList.Count == mzSizeList.Count);
Debug.Assert(mzSizeList.Count == intSizeList.Count);
int start = 0;
for (int i = 0; i < rtList.Count; i++)
{
float[] intensityArray = null;
float[] mzArray = getMzValues(result, start, ((int)mzSizeList[i]));
start = start + ((int)mzSizeList[i]);
if (intCompressor.methods.Contains(Compressor.METHOD_LOG10))
{
intensityArray = getLogedIntValues(result, start, ((int)intSizeList[i]));
}
else
{
intensityArray = getIntValues(result, start, ((int)intSizeList[i]));
}
start = start + ((int)intSizeList[i]);
map[rtList[i]] = new MzIntensityPairs(mzArray, intensityArray);
}
return(map);
}
catch (Exception e)
{
Console.WriteLine(e.ToString());
Console.Write(e.StackTrace);
}
return(null);
}
/// <summary>
/// 根据特定BlockIndex取出对应SortedDictionary
/// </summary>
/// <param name="file">filereader</param>
/// <param name="blockIndex"> the block index read from the index file </param>
/// <returns> 解码内容, key为rt, value为光谱中的键值对 </returns>
/// <exception cref="Exception"> 读取文件异常 </exception>
public virtual SortedDictionary <double, MzIntensityPairs> parseBlockValue(FileStream file, BlockIndex blockIndex)
{
SortedDictionary <double, MzIntensityPairs> map = new SortedDictionary <double, MzIntensityPairs>();
IList <float> rts = blockIndex.rts;
file.Seek(blockIndex.startPtr, SeekOrigin.Begin);
long delta = blockIndex.endPtr - blockIndex.startPtr;
byte[] result = new byte[(int)delta];
file.Read(result, 0, (int)delta);
IList <long> mzSizes = blockIndex.mzs;
IList <long> intensitySizes = blockIndex.ints;
int start = 0;
for (int i = 0; i < mzSizes.Count; i++)
{
var mz = new byte[(int)mzSizes[i]];
Buffer.BlockCopy(result, start, mz, 0, ((int)mzSizes[i]));
start = start + ((int)mzSizes[i]);
var intensity = new byte[(int)intensitySizes[i]];
Buffer.BlockCopy(result, start, intensity, 0, ((int)intensitySizes[i]));
start = start + ((int)intensitySizes[i]);
try
{
MzIntensityPairs pairs = new MzIntensityPairs(getMzValues(mz), getIntValues(intensity));
map[rts[i] / 60d] = pairs;
}
catch (Exception e)
{
throw e;
}
}
return(map);
}
/// <summary>
/// 返回值是一个map,其中key为rt,value为这个rt对应点原始谱图信息
/// 特别需要注意的是,本函数在使用完raf对象以后并不会直接关闭该对象,需要使用者在使用完DIAParser对象以后手动关闭该对象
/// <para>
/// the result key is rt,value is the spectrum(mz-intensity pairs)
/// In particular, this function will not close the RAF object directly after using it.
/// Users need to close the object manually after using the diaparser object
///
/// </para>
/// </summary>
/// <param name="startPtr"> 起始指针位置 start point </param>
/// <param name="endPtr"> 结束指针位置 end point </param>
/// <param name="rtList"> rt列表,包含所有的光谱产出时刻 the retention time list </param>
/// <param name="mzSizeList"> mz块的大小列表 the mz block size list </param>
/// <param name="tagSizeList"> tag块的大小列表 the tag block size list </param>
/// <param name="intSizeList"> intensity块的大小列表 the intensity block size list </param>
/// <returns> 每一个时刻对应的光谱信息 the spectrum of the target retention time </returns>
public virtual SortedDictionary <float, MzIntensityPairs> getSpectrums(long startPtr, long endPtr, IList <float> rtList, IList <long> mzSizeList, IList <long> tagSizeList, IList <long> intSizeList)
{
try
{
SortedDictionary <float, MzIntensityPairs> map = new SortedDictionary <float, MzIntensityPairs>();
airdFile.Seek(startPtr, SeekOrigin.Begin);
long delta = endPtr - startPtr;
byte[] result = new byte[(int)delta];
airdFile.Read(result, 0, (int)delta);
Debug.Assert(tagSizeList.Count == mzSizeList.Count);
Debug.Assert(mzSizeList.Count == intSizeList.Count);
int start = 0;
int maxTag = (int)Math.Pow(2, mzCompressor.digit);
for (int i = 0; i < mzSizeList.Count; i++)
{
float[] mzArray = getMzValues(result, start, ((int)mzSizeList[i]));
start = start + ((int)mzSizeList[i]);
int[] tagArray = getTags(result, start, ((int)tagSizeList[i]));
start += ((int)tagSizeList[i]);
Dictionary <int, int> tagMap = new Dictionary <int, int>();
foreach (int tag in tagArray)
{
if (tagMap.ContainsKey(tag))
{
tagMap[tag]++;
}
else
{
tagMap.Add(tag, 1);
}
}
IList <float[]> mzGroup = new List <float[]>();
int layerNum = tagMap.Keys.Count;
for (int j = 0; j < layerNum; j++)
{
mzGroup.Add(new float[tagMap[j]]);
}
int[] p = new int[layerNum];
for (int j = 0; j < tagArray.Length; j++)
{
mzGroup[tagArray[j]][p[tagArray[j]]++] = mzArray[j];
}
float[] intensityArray = null;
if (intCompressor.methods.Contains(Compressor.METHOD_LOG10))
{
intensityArray = getLogedIntValues(result, start, ((int)intSizeList[i]));
}
else
{
intensityArray = getIntValues(result, start, ((int)intSizeList[i]));
}
start = start + ((int)intSizeList[i]);
IList <float[]> intensityGroup = new List <float[]>();
int initFlag = 0;
for (int j = 0; j < layerNum; j++)
{
intensityGroup.Add(intensityArray.Skip(initFlag).Take(tagMap[j]).ToArray());
initFlag += tagMap[j];
}
for (int j = 0; j < layerNum; j++)
{
map[rtList[i * maxTag + j]] = new MzIntensityPairs(mzGroup[j], intensityGroup[j]);
}
}
return(map);
}
catch (Exception e)
{
Console.WriteLine(e.ToString());
Console.Write(e.StackTrace);
}
return(null);
}
