       1 #!/usr/bin/perl -w
       2 #
       3 # $RCSfile: ElementalAnalysisTextFiles.pl,v $
       4 # $Date: 2015/02/28 20:46:19 $
       5 # $Revision: 1.28 $
       6 #
       7 # Author: Manish Sud <msud@san.rr.com>
       8 #
       9 # Copyright (C) 2015 Manish Sud. All rights reserved.
      10 #
      11 # This file is part of MayaChemTools.
      12 #
      13 # MayaChemTools is free software; you can redistribute it and/or modify it under
      14 # the terms of the GNU Lesser General Public License as published by the Free
      15 # Software Foundation; either version 3 of the License, or (at your option) any
      16 # later version.
      17 #
      18 # MayaChemTools is distributed in the hope that it will be useful, but without
      19 # any warranty; without even the implied warranty of merchantability of fitness
      20 # for a particular purpose.  See the GNU Lesser General Public License for more
      21 # details.
      22 #
      23 # You should have received a copy of the GNU Lesser General Public License
      24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
      25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
      26 # Boston, MA, 02111-1307, USA.
      27 #
      28
      29 use strict;
      30 use FindBin; use lib "$FindBin::Bin/../lib";
      31 use Getopt::Long;
      32 use File::Basename;
      33 use Text::ParseWords;
      34 use Benchmark;
      35 use FileUtil;
      36 use TextUtil;
      37 use MolecularFormula;
      38
      39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      40
      41 # Autoflush STDOUT
      42 $| = 1;
      43
      44 # Starting message...
      45 $ScriptName = basename($0);
      46 print "\n$ScriptName: Starting...\n\n";
      47 $StartTime = new Benchmark;
      48
      49 # Get the options and setup script...
      50 SetupScriptUsage();
      51 if ($Options{help} || @ARGV < 1) {
      52   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      53 }
      54
      55 my(@TextFilesList);
      56 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
      57
      58 # Process options...
      59 my(%OptionsInfo);
      60 print "Processing options...\n";
      61 ProcessOptions();
      62
      63 print "Checking input text file(s)...\n";
      64 my(%TextFilesInfo);
      65 RetrieveTextFilesInfo();
      66 RetrieveColumnsAndLabelsInfo();
      67
      68 # Generate output files...
      69 my($FileIndex);
      70 if (@TextFilesList > 1) {
      71   print "\nProcessing text files...\n";
      72 }
      73 for $FileIndex (0 .. $#TextFilesList) {
      74   if ($TextFilesInfo{FileOkay}[$FileIndex]) {
      75     print "\nProcessing file $TextFilesList[$FileIndex]...\n";
      76     PerformElementalAnalysis($FileIndex);
      77   }
      78 }
      79 print "\n$ScriptName:Done...\n\n";
      80
      81 $EndTime = new Benchmark;
      82 $TotalTime = timediff ($EndTime, $StartTime);
      83 print "Total time: ", timestr($TotalTime), "\n";
      84
      85 ###############################################################################
      86
      87 # Perform elemental analysis...
      88 sub PerformElementalAnalysis {
      89   my($Index) = @_;
      90   my($TextFile, $NewTextFile, $FormulaCol, $Line, $NewLine, $FormulaColValue, $InDelim, $ColNum, $Value, $Status, $ErrorMsg, @ColLabels, @LineWords, @ColNumsBeforeNew, @ColNumsAfterNew);
      91
      92   $TextFile = $TextFilesList[$Index];
      93   $InDelim = $TextFilesInfo{InDelim}[$Index];
      94   $NewTextFile = $TextFilesInfo{OutFile}[$Index];
      95   $FormulaCol = $TextFilesInfo{FormulaColNum}[$Index];
      96
      97   @ColNumsBeforeNew = @{$TextFilesInfo{ColNumsBeforeNew}[$Index]};
      98   @ColNumsAfterNew = @{$TextFilesInfo{ColNumsAfterNew}[$Index]};
      99
     100   print "Generating new Text file $NewTextFile...\n";
     101   open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
     102   open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n";
     103
     104   # Skip over column labels from old file...
     105   $Line = GetTextLine(\*TEXTFILE);
     106
     107   # Add column lablels in new file...
     108   @ColLabels = ();
     109   for $ColNum (@ColNumsBeforeNew) {
     110     push @ColLabels, $TextFilesInfo{ColLabels}[$Index][$ColNum];
     111   }
     112   for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
     113     push @ColLabels, $TextFilesInfo{ValueLabelsMap}[$Index]{$Value};
     114   }
     115   for $ColNum (@ColNumsAfterNew) {
     116     push @ColLabels, $TextFilesInfo{ColLabels}[$Index][$ColNum];
     117   }
     118   $NewLine = '';
     119   $NewLine = JoinWords(\@ColLabels, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
     120   print NEWTEXTFILE "$NewLine\n";
     121
     122   # Go over all rows...
     123   my($LineCount, $ElementsRef, $ElementCompositionRef, $CalculationType, $CalculatedValue, @CalculatedValues);
     124
     125   $LineCount = 1;
     126   TEXTLINE: while ($Line = GetTextLine(\*TEXTFILE)) {
     127     @LineWords = quotewords($InDelim, 0, $Line);
     128     $LineCount++;
     129
     130     @CalculatedValues = ();
     131     for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
     132       push @CalculatedValues, '';
     133     }
     134     if ($FormulaCol > @LineWords) {
     135       $ErrorMsg = "Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] not found";
     136       PrintErrorMsg($Line, $ErrorMsg);
     137       ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
     138       next TEXTLINE;
     139     }
     140
     141     # Make sure it's a valid molecular formula...
     142     $FormulaColValue = $LineWords[$FormulaCol];
     143     if ($OptionsInfo{CheckFormula}) {
     144       ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($FormulaColValue);
     145       if (!$Status) {
     146         $ErrorMsg = "Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] value is not valid: $ErrorMsg";
     147         PrintErrorMsg($Line, $ErrorMsg);
     148         ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
     149         next TEXTLINE;
     150       }
     151     }
     152
     153     # Calculate appropriate values and write 'em out...
     154     @CalculatedValues = ();
     155     for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
     156       if ($CalculationType =~ /^ElementalAnalysis$/i) {
     157         ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($FormulaColValue);
     158         $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
     159       }
     160       elsif ($CalculationType =~ /^MolecularWeight$/i) {
     161         $CalculatedValue = MolecularFormula::CalculateMolecularWeight($FormulaColValue);
     162         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
     163       }
     164       elsif ($CalculationType =~ /^ExactMass$/i) {
     165         $CalculatedValue = MolecularFormula::CalculateExactMass($FormulaColValue);
     166         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
     167       }
     168       else {
     169         $CalculatedValue = '';
     170       }
     171       push @CalculatedValues, $CalculatedValue;
     172     }
     173
     174     ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
     175   }
     176   close NEWTEXTFILE;
     177   close TEXTFILE;
     178
     179 }
     180
     181 # Write out new line using old and new calculated data...
     182 sub ComposeAndWriteNewLine {
     183   my($NewTextFileRef, $OldLineWordsRef, $ColNumsBeforeNewRef, $ColNumsAfterNewRef, $CalculatedValuesRef) = @_;
     184   my($NewLine, $ColNum, $Value, @NewLineWords);
     185
     186   @NewLineWords = ();
     187   for $ColNum (@{$ColNumsBeforeNewRef}) {
     188     push @NewLineWords, $OldLineWordsRef->[$ColNum];
     189   }
     190   for $Value (@{$CalculatedValuesRef}) {
     191     push @NewLineWords, $Value;
     192   }
     193   for $ColNum (@{$ColNumsAfterNewRef}) {
     194     push @NewLineWords, $OldLineWordsRef->[$ColNum];
     195   }
     196   $NewLine = JoinWords(\@NewLineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
     197   print $NewTextFileRef "$NewLine\n";
     198 }
     199
     200 # Print out error message...
     201 sub PrintErrorMsg {
     202   my($Line, $ErrorMsg) = @_;
     203
     204   if ($OptionsInfo{DetailLevel} >= 2 ) {
     205     print "$ErrorMsg: $Line\n";
     206   }
     207   elsif ($OptionsInfo{DetailLevel} >= 1) {
     208     print "$ErrorMsg\n";
     209   }
     210 }
     211
     212 # Process formula columns and other information...
     213 sub RetrieveColumnsAndLabelsInfo {
     214   RetrieveFormulaColumnsInfo();
     215   RetrieveStartColumnsAndValueLabelsInfo();
     216 }
     217
     218 # Make sure specified formula column are okay...
     219 sub RetrieveFormulaColumnsInfo {
     220   my($Index, $TextFile);
     221
     222   @{$TextFilesInfo{FormulaColNum}} = ();
     223
     224  FILELIST: for $Index (0 .. $#TextFilesList) {
     225     $TextFile = $TextFilesList[$Index];
     226
     227     $TextFilesInfo{FormulaColNum}[$Index] = 0;
     228
     229     if ($TextFilesInfo{FileOkay}[$Index]) {
     230       my($FormulaColNum, $FormulaColValid);
     231
     232       $FormulaColNum = 0;
     233       $FormulaColValid = 0;
     234       if ($OptionsInfo{SpecifiedFormulaCol}) {
     235         if ($OptionsInfo{ColMode} =~ /^colnum$/i) {
     236           if ($OptionsInfo{SpecifiedFormulaCol} <= $TextFilesInfo{ColCount}[$Index]) {
     237             $FormulaColNum = $OptionsInfo{SpecifiedFormulaCol} - 1;
     238             $FormulaColValid = 1;
     239           }
     240         }
     241         else {
     242           if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$OptionsInfo{SpecifiedFormulaCol}})) {
     243             $FormulaColNum =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$OptionsInfo{SpecifiedFormulaCol}};
     244             $FormulaColValid = 1;
     245           }
     246         }
     247       }
     248       else {
     249         # Grab the first column with the word Formula in its label...
     250         my($ColLabel);
     251         LABEL: for $ColLabel (@{$TextFilesInfo{ColLabels}[$Index]}) {
     252           if ($ColLabel =~ /Formula/i) {
     253             $FormulaColNum =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
     254             $FormulaColValid = 1;
     255             last LABEL;
     256           }
     257         }
     258       }
     259       if ($FormulaColValid) {
     260         $TextFilesInfo{FormulaColNum}[$Index] = $FormulaColNum;
     261       }
     262       else {
     263         if ($OptionsInfo{SpecifiedFormulaCol}) {
     264           warn "Warning: Ignoring file $TextFile: Formula column specified, $OptionsInfo{SpecifiedFormulaCol}, using \"f --formulacol\" option doesn't exist\n";
     265         }
     266         else {
     267           warn "Warning: Ignoring file $TextFile: Column label containing the word Formula doesn't exist\n";
     268         }
     269         $TextFilesInfo{FileOkay}[$Index] = 0;
     270       }
     271     }
     272   }
     273 }
     274
     275 # Setup starting column number for adding calculated values and
     276 # column lables to use for these values...
     277 sub RetrieveStartColumnsAndValueLabelsInfo {
     278   my($Index, $TextFile, $SpecifiedStartColNum, $StartColNum, $Label, $Value, $NewLabel, $Count, $BeforeStartColNum, $AfterStartColNum, $FirstColNum, $LastColNum, $ColNum, $Part1StartColNum, $Part1EndColNum, $Part2StartColNum, $Part2EndColNum, @Part1ColNums, @Part2ColNums);
     279
     280   # Start column number for inserting new values...
     281   $SpecifiedStartColNum = "last";
     282   if (defined($OptionsInfo{StartCol})) {
     283     if (length($OptionsInfo{StartCol})) {
     284       $SpecifiedStartColNum = $OptionsInfo{StartCol}
     285     }
     286   }
     287
     288   # Column labels for for new calculated values...
     289   my(%NewValueLabels) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass');
     290   if (@{$OptionsInfo{SpecifiedValueLabels}}) {
     291     for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) {
     292       $Value = $OptionsInfo{SpecifiedValueLabels}[$Index];
     293       $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1];
     294       if (exists $NewValueLabels{$Value}) {
     295         $NewValueLabels{$Value} = $Label;
     296       }
     297     }
     298   }
     299
     300   @{$TextFilesInfo{ColNumsBeforeNew}} = ();
     301   @{$TextFilesInfo{ColNumsAfterNew}} = ();
     302   @{$TextFilesInfo{ValueLabelsMap}} = ();
     303
     304   FILELIST: for $Index (0 .. $#TextFilesList) {
     305     $TextFile = $TextFilesList[$Index];
     306
     307     @{$TextFilesInfo{ColNumsBeforeNew}[$Index]} = ();
     308     @{$TextFilesInfo{ColNumsAfterNew}[$Index]} = ();
     309     %{$TextFilesInfo{ValueLabelsMap}[$Index]} = ();
     310
     311     if (!$TextFilesInfo{FileOkay}[$Index]) {
     312       next FILELIST;
     313     }
     314
     315     if ($SpecifiedStartColNum !~ /^last$/i) {
     316       if ($OptionsInfo{ColMode} =~ /^collabel$/i) {
     317         if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedStartColNum})) {
     318           $StartColNum = $TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedStartColNum};
     319         }
     320         else {
     321           die "Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column name doesn't exist in  $TextFile  \n";
     322         }
     323       }
     324       else {
     325         if ($SpecifiedStartColNum > 0 && $SpecifiedStartColNum <= $TextFilesInfo{ColCount}[$Index]) {
     326           $StartColNum -= 1;
     327         }
     328         else {
     329           die "Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column number doesn't exist in  $TextFile  \n";
     330         }
     331       }
     332     }
     333     else {
     334       $StartColNum = $TextFilesInfo{ColCount}[$Index] - 1;
     335     }
     336     # Set up columns lists for before and after the addition of calculated column values
     337     # for each text file...
     338     my($BeforeStartColNum, $AfterStartColNum, $FirstColNum, $LastColNum, $ColNum, $Part1StartColNum, $Part1EndColNum, $Part2StartColNum, $Part2EndColNum, @Part1ColNums, @Part2ColNums);
     339
     340     $FirstColNum = 0; $LastColNum = $TextFilesInfo{ColCount}[$Index] - 1;
     341
     342     $BeforeStartColNum = $StartColNum - 1;
     343     $AfterStartColNum = $StartColNum + 1;
     344
     345     if ($OptionsInfo{StartColMode} =~ /^after$/i) {
     346       $Part1StartColNum = $FirstColNum; $Part1EndColNum = $StartColNum;
     347       $Part2StartColNum = $AfterStartColNum; $Part2EndColNum = $LastColNum;
     348     }
     349     else {
     350       $Part1StartColNum = $FirstColNum; $Part1EndColNum = $BeforeStartColNum;
     351       $Part2StartColNum = $StartColNum; $Part2EndColNum = $LastColNum;
     352     }
     353     @Part1ColNums = (); @Part2ColNums = ();
     354     for $ColNum (0 .. $TextFilesInfo{ColCount}[$Index]) {
     355       if ($ColNum >= $Part1StartColNum && $ColNum <= $Part1EndColNum) {
     356         push @Part1ColNums, $ColNum;
     357       }
     358     }
     359     for $ColNum (0 .. $TextFilesInfo{ColCount}[$Index]) {
     360       if ($ColNum >= $Part2StartColNum && $ColNum <= $Part2EndColNum) {
     361         push @Part2ColNums, $ColNum;
     362       }
     363     }
     364     push @{$TextFilesInfo{ColNumsBeforeNew}[$Index]}, @Part1ColNums;
     365     push @{$TextFilesInfo{ColNumsAfterNew}[$Index]}, @Part2ColNums;
     366
     367     # Setup column labels for calculated values...
     368     for $Value (keys %NewValueLabels) {
     369       $Label = $NewValueLabels{$Value};
     370
     371       # Make sure it doesn't already exists...
     372       $Count = 1;
     373       $NewLabel = $Label;
     374       while (exists $TextFilesInfo{ColLabelToNumMap}[$Index]{$NewLabel}) {
     375         $Count++;
     376         $NewLabel = $Label . $Count;
     377       }
     378       $TextFilesInfo{ValueLabelsMap}[$Index]{$Value} = $NewLabel;
     379     }
     380   }
     381 }
     382
     383 # Retrieve information about input text files...
     384 sub RetrieveTextFilesInfo {
     385   my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, @ColLabels, $OutFileRoot,  $OutFile, $ColNum, $ColLabel);
     386
     387   %TextFilesInfo = ();
     388
     389   @{$TextFilesInfo{FileOkay}} = ();
     390   @{$TextFilesInfo{ColCount}} = ();
     391   @{$TextFilesInfo{ColLabels}} = ();
     392   @{$TextFilesInfo{ColLabelToNumMap}} = ();
     393   @{$TextFilesInfo{InDelim}} = ();
     394   @{$TextFilesInfo{OutFile}} = ();
     395
     396   FILELIST: for $Index (0 .. $#TextFilesList) {
     397     $TextFile = $TextFilesList[$Index];
     398
     399     $TextFilesInfo{FileOkay}[$Index] = 0;
     400     $TextFilesInfo{ColCount}[$Index] = 0;
     401     $TextFilesInfo{InDelim}[$Index] = "";
     402     $TextFilesInfo{OutFile}[$Index] = "";
     403
     404     @{$TextFilesInfo{ColLabels}[$Index]} = ();
     405     %{$TextFilesInfo{ColLabelToNumMap}[$Index]} = ();
     406
     407     if (!(-e $TextFile)) {
     408       warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
     409       next FILELIST;
     410     }
     411     if (!CheckFileType($TextFile, "csv tsv")) {
     412       warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
     413       next FILELIST;
     414     }
     415     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
     416     if ($FileExt =~ /^tsv$/i) {
     417       $InDelim = "\t";
     418     }
     419     else {
     420       $InDelim = "\,";
     421       if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
     422         warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n";
     423         next FILELIST;
     424       }
     425       if ($Options{indelim} =~ /^semicolon$/i) {
     426         $InDelim = "\;";
     427       }
     428     }
     429
     430     if (!open TEXTFILE, "$TextFile") {
     431       warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
     432       next FILELIST;
     433     }
     434
     435     $Line = GetTextLine(\*TEXTFILE);
     436     @ColLabels = quotewords($InDelim, 0, $Line);
     437     close TEXTFILE;
     438
     439     $FileDir = ""; $FileName = ""; $FileExt = "";
     440     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
     441     $FileExt = "csv";
     442     if ($Options{outdelim} =~ /^tab$/i) {
     443       $FileExt = "tsv";
     444     }
     445     if ($Options{root} && (@TextFilesList == 1)) {
     446       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
     447       if ($RootFileName && $RootFileExt) {
     448         $FileName = $RootFileName;
     449       }
     450       else {
     451         $FileName = $Options{root};
     452       }
     453       $OutFileRoot = $FileName;
     454     }
     455     else {
     456       $OutFileRoot = $FileName . "ElementalAnalysis";
     457     }
     458
     459     $OutFile = $OutFileRoot . ".$FileExt";
     460     if (lc($OutFile) eq lc($TextFile)) {
     461       warn "Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n";
     462       next FILELIST;
     463     }
     464     if (!$Options{overwrite}) {
     465       if (-e $OutFile) {
     466         warn "Warning: Ignoring file $TextFile: The file $OutFile already exists\n";
     467         next FILELIST;
     468       }
     469     }
     470
     471     $TextFilesInfo{FileOkay}[$Index] = 1;
     472     $TextFilesInfo{InDelim}[$Index] = $InDelim;
     473     $TextFilesInfo{OutFile}[$Index] = "$OutFile";
     474
     475     $TextFilesInfo{ColCount}[$Index] = @ColLabels;
     476     push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
     477     for $ColNum (0 .. $#ColLabels) {
     478       $ColLabel = $ColLabels[$ColNum];
     479       $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel} = $ColNum;
     480     }
     481   }
     482
     483 }
     484
     485 # Process option values...
     486 sub ProcessOptions {
     487   %OptionsInfo = ();
     488
     489   $OptionsInfo{Mode} = $Options{mode};
     490
     491   $OptionsInfo{ColMode} = $Options{colmode};
     492   $OptionsInfo{StartColMode} = $Options{startcolmode};
     493
     494   $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
     495
     496   $OptionsInfo{DetailLevel} = $Options{detail};
     497   $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
     498   $OptionsInfo{Precision} = $Options{precision};
     499
     500   $OptionsInfo{InDelim} = $Options{indelim};
     501
     502   $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
     503   $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
     504
     505   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
     506   $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
     507
     508   $OptionsInfo{StartCol} = defined $Options{startcol} ? $Options{startcol} : undef;
     509
     510   $OptionsInfo{FormulaCol} = defined $Options{formulacol} ? $Options{formulacol} : undef;
     511   $OptionsInfo{SpecifiedFormulaCol} = "";
     512
     513   if (defined $Options{formulacol}) {
     514     $OptionsInfo{SpecifiedFormulaCol} = $Options{formulacol};
     515     if ($Options{colmode} =~ /^colnum$/i) {
     516       if (!IsPositiveInteger($OptionsInfo{SpecifiedFormulaCol})) {
     517         die "Error: Invalid value $Options{formulacol} specified using \"-f -formulacol\" option: Allowed values: > 0\n";
     518       }
     519     }
     520   }
     521
     522   # Setup what to calculate...
     523   @{$OptionsInfo{SpecifiedCalculations}} = ();
     524   if ($Options{mode} =~ /^All$/i) {
     525     @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
     526   }
     527   else {
     528     my($Mode, $ModeValue, @SpecifiedModeValues);
     529     $Mode = $Options{mode};
     530     $Mode =~ s/ //g;
     531     @SpecifiedModeValues = split /\,/, $Mode;
     532     for $ModeValue (@SpecifiedModeValues) {
     533       if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
     534         if ($ModeValue =~ /^All$/i) {
     535           die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
     536         }
     537         else {
     538           die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
     539         }
     540       }
     541       push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
     542     }
     543   }
     544
     545   $OptionsInfo{ValueColLabels} = defined $Options{valuecollabels} ? $Options{valuecollabels} : undef;
     546   @{$OptionsInfo{SpecifiedValueLabels}} = ();
     547
     548   if ($Options{valuecollabels}) {
     549     my($Value, $Label, @ValueLabels);
     550     @ValueLabels = split /\,/, $Options{valuecollabels};
     551     if (@ValueLabels % 2) {
     552       die "Error: The value specified, $Options{valuecollabels}, for option \"-v --valuecollabels\" is not valid: It must contain even number of comma delimited values\n";
     553     }
     554     my($Index);
     555     for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
     556       $Value = $ValueLabels[$Index];
     557       $Value =~ s/ //g;
     558       $Label = $ValueLabels[$Index + 1];
     559       if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
     560         die "Error: The value specified, $Value, using option \"-v --valuecollabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
     561       }
     562       push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label);
     563     }
     564   }
     565 }
     566
     567 # Setup script usage  and retrieve command line arguments specified using various options...
     568 sub SetupScriptUsage {
     569
     570   # Retrieve all the options...
     571   %Options = ();
     572   $Options{colmode} = "colnum";
     573   $Options{detail} = 1;
     574   $Options{mode} = "All";
     575   $Options{indelim} = "comma";
     576   $Options{outdelim} = "comma";
     577   $Options{precision} = 2;
     578   $Options{quote} = "yes";
     579   $Options{startcolmode} = "after";
     580
     581   if (!GetOptions(\%Options, "colmode|c=s", "detail|d=i", "fast", "formulacol|f=s", "help|h", "indelim=s", "mode|m=s", "outdelim=s", "overwrite|o", "precision|p=i", "quote|q=s", "root|r=s", "startcol|s=s", "startcolmode=s", "valuecollabels|v=s", "workingdir|w=s")) {
     582     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     583   }
     584   if ($Options{workingdir}) {
     585     if (! -d $Options{workingdir}) {
     586       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     587     }
     588     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     589   }
     590   if ($Options{colmode} !~ /^(colnum|collabel)$/i) {
     591     die "Error: The value specified, $Options{colmode}, for option \"-c --colmode\" is not valid. Allowed values: colnum or collabel\n";
     592   }
     593   if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
     594     die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
     595   }
     596   if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
     597     die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
     598   }
     599   if (!IsPositiveInteger($Options{precision})) {
     600     die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
     601   }
     602   if ($Options{quote} !~ /^(yes|no)$/i) {
     603     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
     604   }
     605   if ($Options{startcolmode} !~ /^(before|after)$/i) {
     606     die "Error: The value specified, $Options{quote}, for option \"--startcolmode\" is not valid. Allowed values: before or after\n";
     607   }
     608   if (!IsPositiveInteger($Options{detail})) {
     609     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
     610   }
     611 }
     612