option explicit   
Dim compo, compoxml, fso, f, ts, filename, lines, filepath, filenametarget, g, gso, gs, haeppchen, targetpath, targetmgf,t, headerexist, latestAnalysis   
Dim compString, LineArray, IsTitleline, myanalysis,answer, isMSScan, MSScan, isMSMSScan, MSMSScan   
filepath = Analysis.path   
filename = Analysis.name   
filenametarget = split (filename,".d",-1,1)   
'targetpath = Split(filepath, filename,-1,1)    
targetpath = filepath   
 
analysis.save 
'analysis.export filepath&"\"&filenametarget(0)&".mzXML",damzXML"'
analysis.chromatograms.add daBPC,daAllMS,"50-1221; 1225-3000", daBoth  
create_mgf 
   
       
     
form.close   
   
Sub create_mgf   
    Dim i, hso, h, b   
    
       Analysis.ProcessAutoMSn   
       
        create_combined_file "Proteinanalysisresults.mgf", filenametarget(0)&".mgf"  
        
  
   
End Sub            
   
Sub copy_to_supervised (filename,targetfolder)   
    Dim hso   
    Set hso = CreateObject("Scripting.FileSystemObject")   
    hso.copyFile targetpath &"\"& filename, targetfolder    
End Sub   
   
Sub create_combined_file (mgf_filename, targetfile)   
    Dim i, rt, rtparts   
    headerexist=false   
       
       
    Set fso = CreateObject("Scripting.FileSystemObject")    
    Set f = fso.GetFile(filepath &"\"& mgf_filename)    
    Set ts = f.openAsTextStream(1,0)    
    'targetpath = Split(filepath, filename,-1,1)    
   ' If ts.read(6)= "CHARGE" Then lines = 14 Else lines = 13   
   ' ts.close   
    Set f = fso.GetFile(filepath &"\" & mgf_filename)    
    Set ts = f.openAsTextStream(1,0)    
    Set gso = CreateObject("Scripting.FileSystemObject")    
       
    If gso.fileexists(targetpath&"\"&targetfile) Then   
        gso.deletefile (targetpath&"\"&targetfile)   
    End IF 'Else    
         
    gso.CreateTextFile (targetpath&"\"&targetfile)    
    Set g = gso.GetFile (targetpath&"\"&targetfile)    
    Set gs = g.OpenAsTextStream(8,0)  
       
    while left(ts.readline,3) <> "###" 
        ts.skipline 
    wend    
    
    while ts.atendofstream <> true   
        compString = ts.readline  
        isMSScan = Instr(1,compstring, "###MS:" ,1) 
            If isMSScan <> 0 then MSScan = right(compstring, len(compstring)-6)  
        isMSMSScan = Instr(1,compstring, "###MSMS:" ,1) 
            If isMSMSScan <> 0 then MSMSScan = right(compstring, len(compstring)-8) 
        isTitleline = Instr(1,compstring, "TITLE" ,1)       
        If isTitleline <> 0 Then    
         
           LineArray = Split(CompString,"=", -1, 1)    
            
            
           rtparts = split(Compstring,chr(32),-1,1)   
           '  msgbox rtparts(3) 
                if rtparts(5) = "s" then  
                    rt = cdbl(rtparts(4))   
                else   
                    rt = cdbl(rtparts(4) * 60)  
                end if                          
 
           gs.writeline "RTINSECONDS="&rt 
           gs.writeline "SCANS=MS:" &MSSCAN&" MSMS:" &MSMSScan 
            compstring = LineArray(0)&"="& LineArray(1)& " MS:"&MSSCAN&" MSMS:"&MSMSScan    
             
        End If   
        gs.writeline (compstring)          
    wend     
        
    ts.close   
    gs.close    
   
End Sub