Beispiel #1
0
        /// <summary>
        /// If the object has already been loaded, it returns the typed, parsed object.  If the object has not yet been loaded, it returns a base AssetsObject with unparsed data so that it's faster to write and doesn't pull in all the pointer refs
        /// </summary>
        public AssetsObject GetObjectForWrite()
        {
            if (_object != null)
            {
                return(_object);
            }

            lock (ParentFile)
            {
                using (var reader = ParentFile.GetReaderAtDataOffset())
                {
                    return(new AssetsObject(this, reader));
                }
            }
        }
Beispiel #2
0
 public DissociationType GetDissociationType()
 {
     if (_dissociationType == DissociationType.UnKnown)
     {
         if (ParentFile.IsOpen)
         {
             _dissociationType = ParentFile.GetDissociationType(SpectrumNumber);
         }
         else
         {
             throw new ArgumentException("The parent data file is closed");
         }
     }
     return(_dissociationType);
 }
Beispiel #3
0
 public virtual int GetPrecursorCharge()
 {
     if (_precursorCharge == 0)
     {
         if (ParentFile.IsOpen)
         {
             _precursorCharge = ParentFile.GetPrecusorCharge(SpectrumNumber, MsnOrder);
         }
         else
         {
             throw new ArgumentException("The parent data file is closed");
         }
     }
     return(_precursorCharge);
 }
Beispiel #4
0
 public DoubleRange GetIsolationRange()
 {
     if (_isolationRange == null)
     {
         if (ParentFile.IsOpen)
         {
             _isolationRange = ParentFile.GetIsolationRange(SpectrumNumber);
         }
         else
         {
             throw new ArgumentException("The parent data file is closed");
         }
     }
     return(_isolationRange);
 }
Beispiel #5
0
 public double GetPrecursorMz()
 {
     if (double.IsNaN(_precursorMz))
     {
         if (ParentFile.IsOpen)
         {
             _precursorMz = ParentFile.GetPrecursorMz(SpectrumNumber, MsnOrder);
         }
         else
         {
             throw new ArgumentException("The parent data file is closed");
         }
     }
     return(_precursorMz);
 }
Beispiel #6
0
 public virtual double GetInjectionTime()
 {
     if (_injectionTime >= 0)
     {
         return(_injectionTime);
     }
     if (ParentFile.IsOpen)
     {
         _injectionTime = ParentFile.GetInjectionTime(SpectrumNumber);
     }
     else
     {
         throw new ArgumentException("The parent data file is closed");
     }
     return(_injectionTime);
 }
Beispiel #7
0
 public virtual int GetParentSpectrumNumber()
 {
     if (_parentScanNumber >= 0)
     {
         return(_parentScanNumber);
     }
     if (ParentFile.IsOpen)
     {
         _parentScanNumber = ParentFile.GetParentSpectrumNumber(SpectrumNumber);
     }
     else
     {
         throw new ArgumentException("The parent data file is closed");
     }
     return(_parentScanNumber);
 }
Beispiel #8
0
        public void StoreChanges()
        {
            byte[] Data = ParentFile.GetFileData();

            Helpers.WriteString(ref Data, Offset, _Name, 8);
            Helpers.Overwrite32(ref Data, Offset + 0x08, _Parameters);
            Helpers.Overwrite32(ref Data, Offset + 0x0C, BitConverter.ToUInt32(BitConverter.GetBytes(_Position.X), 0));
            Helpers.Overwrite32(ref Data, Offset + 0x10, BitConverter.ToUInt32(BitConverter.GetBytes(_Position.Y), 0));
            Helpers.Overwrite32(ref Data, Offset + 0x14, BitConverter.ToUInt32(BitConverter.GetBytes(_Position.Z), 0));
            Helpers.Overwrite16(ref Data, Offset + 0x18, (ushort)(_Rotation.X * 182.04444444444444f));
            Helpers.Overwrite16(ref Data, Offset + 0x1A, (ushort)(_Rotation.Y * 182.04444444444444f));
            Helpers.Overwrite16(ref Data, Offset + 0x1C, (ushort)(_Rotation.Z * 182.04444444444444f));
            Helpers.Overwrite16(ref Data, Offset + 0x1E, _Unknown);

            ParentFile.SetFileData(Data);
        }
Beispiel #9
0
 private void LoadObject()
 {
     lock (ParentFile)
     {
         using (var reader = ParentFile.GetReaderAtDataOffset())
         {
             try
             {
                 _object = (T)Activator.CreateInstance(typeof(T), this, reader);
             } catch (System.MissingMethodException)
             {
                 // Try with bool param
                 _object = (T)Activator.CreateInstance(typeof(T), this, reader, false);
             }
         }
     }
 }
Beispiel #10
0
 public override int GetHashCode()
 {
     return(ParentFile.GetHashCode() ^ SpectrumNumber);
 }
Beispiel #11
0
 // TODO: kill DX80s/SWs?
 public ZipArchive GetZipArchive()
 {
     return(new(ParentFile.GetLumpStream(Paklump)));
 }
Beispiel #12
0
        protected AirdInfo buildBasicInfo()
        {
            AirdInfo airdInfo = new AirdInfo();
            List <DomainsCore.Aird.Software> softwares = new List <DomainsCore.Aird.Software>();
            List <ParentFile> parentFiles = new List <ParentFile>();

            //Basic Job Info
            airdInfo.airdPath       = jobInfo.airdFilePath;
            airdInfo.fileSize       = fileSize;
            airdInfo.createDate     = new DateTime();
            airdInfo.type           = jobInfo.type;
            airdInfo.totalScanCount = msd.run.spectrumList.size();
            airdInfo.creator        = jobInfo.jobParams.creator;
            airdInfo.activator      = activator;
            airdInfo.energy         = energy;
            airdInfo.rtUnit         = rtUnit;
            airdInfo.msType         = msType;
            airdInfo.polarity       = polarity;
            //Scan index and window range info
            airdInfo.rangeList = ranges;

            //Block index
            airdInfo.indexList = indexList;

            //Instrument Info
            List <Instrument> instruments = new List <Instrument>();

            foreach (InstrumentConfiguration ic in msd.instrumentConfigurationList)
            {
                Instrument instrument = new Instrument();
                //仪器设备信息
                if (jobInfo.format.Equals("WIFF"))
                {
                    instrument.manufacturer = "SCIEX";
                }
                if (jobInfo.format.Equals("RAW"))
                {
                    instrument.manufacturer = "THERMO";
                }

                //设备信息在不同的源文件格式中取法不同,有些是在instrumentConfigurationList中获取,有些是在paramGroups获取,因此出现了以下比较丑陋的写法
                if (ic.cvParams.Count != 0)
                {
                    foreach (CVParam cv in ic.cvParams)
                    {
                        featuresMap.Add(cv.name, cv.value);
                    }
                    instrument.model = ic.cvParams[0].name;
                }
                else if (msd.paramGroups.Count != 0)
                {
                    foreach (ParamGroup pg in msd.paramGroups)
                    {
                        if (pg.cvParams.Count != 0)
                        {
                            foreach (CVParam cv in pg.cvParams)
                            {
                                if (!featuresMap.ContainsKey(cv.name))
                                {
                                    featuresMap.Add(cv.name, cv.value.ToString());
                                }
                            }
                            instrument.model = pg.cvParams[0].name;
                        }
                    }
                }
                foreach (Component component in ic.componentList)
                {
                    switch (component.type)
                    {
                    case ComponentType.ComponentType_Analyzer:
                        foreach (CVParam cv in component.cvParams)
                        {
                            instrument.analyzer.Add(cv.name);
                        }
                        break;

                    case ComponentType.ComponentType_Source:
                        foreach (CVParam cv in component.cvParams)
                        {
                            instrument.source.Add(cv.name);
                        }
                        break;

                    case ComponentType.ComponentType_Detector:
                        foreach (CVParam cv in component.cvParams)
                        {
                            instrument.detector.Add(cv.name);
                        }
                        break;
                    }
                }
                instruments.Add(instrument);
            }
            airdInfo.instruments = instruments;

            //Software Info
            foreach (Software soft in msd.softwareList)
            {
                DomainsCore.Aird.Software software = new DomainsCore.Aird.Software();
                software.name    = soft.id;
                software.version = soft.version;
                softwares.Add(software);
            }
            DomainsCore.Aird.Software airdPro = new DomainsCore.Aird.Software();
            airdPro.name    = SoftwareInfo.NAME;
            airdPro.version = SoftwareInfo.VERSION;
            airdPro.type    = "DataFormatConversion";
            softwares.Add(airdPro);
            airdInfo.softwares = softwares;

            //Parent Files Info
            foreach (SourceFile sf in msd.fileDescription.sourceFiles)
            {
                ParentFile file = new ParentFile();
                file.name       = sf.name;
                file.location   = sf.location;
                file.formatType = sf.id;
                parentFiles.Add(file);
            }
            airdInfo.parentFiles = parentFiles;

            //Compressor Info
            List <Compressor> coms = new List <Compressor>();
            //mz compressor
            Compressor mzCompressor = new Compressor();

            if (jobInfo.jobParams.useStackZDPD())
            {
                mzCompressor.addMethod(Compressor.METHOD_STACK);
                mzCompressor.digit = jobInfo.jobParams.digit;
            }
            mzCompressor.addMethod(Compressor.METHOD_PFOR);
            mzCompressor.addMethod(Compressor.METHOD_ZLIB);
            mzCompressor.target    = Compressor.TARGET_MZ;
            mzCompressor.precision = (int)(Math.Ceiling(1 / jobInfo.jobParams.mzPrecision));
            coms.Add(mzCompressor);
            //intensity compressor
            Compressor intCompressor = new Compressor();

            if (jobInfo.jobParams.useStackZDPD())
            {
                intCompressor.addMethod(Compressor.METHOD_STACK);
                intCompressor.digit = jobInfo.jobParams.digit;
            }
            if (jobInfo.jobParams.log2)
            {
                intCompressor.addMethod(Compressor.METHOD_LOG10);
                intCompressor.addMethod(Compressor.METHOD_ZLIB);
            }
            else
            {
                intCompressor.addMethod(Compressor.METHOD_ZLIB);
            }

            intCompressor.target    = Compressor.TARGET_INTENSITY;
            intCompressor.precision = 10;  //intensity默认精确到小数点后1位

            coms.Add(intCompressor);
            airdInfo.compressors = coms;

            airdInfo.ignoreZeroIntensityPoint = jobInfo.jobParams.ignoreZeroIntensity;
            //Features Info
            featuresMap.Add(Features.raw_id, msd.id);
            featuresMap.Add(Features.ignore_zero_intensity, jobInfo.jobParams.ignoreZeroIntensity);
            featuresMap.Add(Features.source_file_format, jobInfo.format);
            featuresMap.Add(Features.byte_order, ByteOrder.LITTLE_ENDIAN);
            featuresMap.Add(Features.aird_algorithm, jobInfo.jobParams.getAirdAlgorithmStr());
            airdInfo.features    = FeaturesUtil.toString(featuresMap);
            airdInfo.version     = SoftwareInfo.VERSION;
            airdInfo.versionCode = SoftwareInfo.VERSION_CODE;
            return(airdInfo);
        }