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+<html>
+<head>
+<title>MayaChemTools:Code:ModifyNewLineChar.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
+</head>
+<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
+</center>
+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: ModifyNewLineChar.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+   5 <span class="c"># $Revision: 1.26 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
+  37 
+  38 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
+  39 
+  40 <span class="c"># Autoflush STDOUT</span>
+  41 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  42 
+  43 <span class="c"># Starting message...</span>
+  44 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
+  45 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Starting...\n\n&quot;</span><span class="sc">;</span>
+  46 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  47 
+  48 <span class="c"># Get the options and setup script...</span>
+  49 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  50 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  51   <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+  52 <span class="s">}</span>
+  53 
+  54 <span class="k">my</span><span class="s">(</span> <span class="i">@FilesList</span><span class="s">)</span><span class="sc">;</span>
+  55 <span class="i">@FilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;&quot;</span><span class="s">)</span><span class="sc">;</span>
+  56 
+  57 <span class="c"># Process options...</span>
+  58 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  60 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  61 
+  62 <span class="k">print</span> <span class="q">&quot;Checking input file(s)...\n&quot;</span><span class="sc">;</span>
+  63 <span class="k">my</span><span class="s">(</span><span class="i">%FilesInfo</span><span class="s">)</span><span class="sc">;</span>
+  64 <span class="i">RetrieveFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  65 
+  66 <span class="c"># Generate output files...</span>
+  67 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  68 <span class="k">if</span> <span class="s">(</span><span class="i">@FilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  69   <span class="k">print</span> <span class="q">&quot;\nProcessing files...\n&quot;</span><span class="sc">;</span>
+  70 <span class="s">}</span>
+  71 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#FilesList</span><span class="s">)</span> <span class="s">{</span>
+  72   <span class="k">if</span> <span class="s">(</span><span class="i">$FilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  73     <span class="k">print</span> <span class="q">&quot;\nProcessing file $FilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+  74     <span class="i">ModifyNewLineChar</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  75   <span class="s">}</span>
+  76 <span class="s">}</span>
+  77 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  78 
+  79 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  80 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
+  81 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  82 
+  83 <span class="c">###############################################################################</span>
+  84 
+  85 <span class="c"># Modify new line characters...</span>
+<a name="ModifyNewLineChar-"></a>  86 <span class="k">sub </span><span class="m">ModifyNewLineChar</span> <span class="s">{</span>
+  87   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  88   <span class="k">my</span><span class="s">(</span><span class="i">$File</span><span class="cm">,</span> <span class="i">$NewFile</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$Nothing</span><span class="s">)</span><span class="sc">;</span>
+  89 
+  90   <span class="i">$File</span> = <span class="i">$FilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+  91   <span class="i">$NewFile</span> = <span class="i">$FilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+  92 
+  93   <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span>
+  94 
+  95   <span class="k">print</span> <span class="q">&quot;Generating new $NewFile file...\n&quot;</span><span class="sc">;</span>
+  96 
+  97   <span class="k">open</span> <span class="w">NEWFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $NewFile: !$ \n&quot;</span><span class="sc">;</span>
+  98   <span class="k">open</span> <span class="w">FILE</span><span class="cm">,</span> <span class="q">&quot;$File&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $File: $! \n&quot;</span><span class="sc">;</span>
+  99 
+ 100   <span class="k">while</span> <span class="s">(</span><span class="q">&lt;FILE&gt;</span><span class="s">)</span> <span class="s">{</span>
+ 101     <span class="j">LINE:</span> <span class="s">{</span>
+ 102       <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Unix$/i</span><span class="s">)</span> <span class="s">{</span> <span class="q">s/(\r\n)|(\r)|(\n)/\n/g</span><span class="sc">;</span> <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> <span class="s">}</span>
+ 103       <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Windows$/i</span><span class="s">)</span> <span class="s">{</span> <span class="q">s/(\r\n)|(\r)|(\n)/\r\n/g</span><span class="sc">;</span> <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> <span class="s">}</span>
+ 104       <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Mac$/i</span><span class="s">)</span> <span class="s">{</span> <span class="q">s/(\r\n)|(\r)|(\n)/\r/g</span><span class="sc">;</span> <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> <span class="s">}</span>
+ 105       <span class="i">$Nothing</span> = <span class="n">1</span><span class="sc">;</span>
+ 106     <span class="s">}</span>
+ 107     <span class="k">print</span> <span class="i">NEWFILE</span><span class="sc">;</span>
+ 108   <span class="s">}</span>
+ 109 
+ 110   <span class="k">close</span> <span class="w">NEWFILE</span><span class="sc">;</span>
+ 111   <span class="k">close</span> <span class="w">FILE</span><span class="sc">;</span>
+ 112 <span class="s">}</span>
+ 113 
+ 114 <span class="c"># Retrieve input files info...</span>
+<a name="RetrieveFilesInfo-"></a> 115 <span class="k">sub </span><span class="m">RetrieveFilesInfo</span> <span class="s">{</span>
+ 116   <span class="k">my</span><span class="s">(</span><span class="i">$File</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$NewFileName</span><span class="s">)</span><span class="sc">;</span>
+ 117 
+ 118   <span class="i">%FilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 119 
+ 120   <span class="i">@</span>{<span class="i">$FilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 121   <span class="i">@</span>{<span class="i">$FilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 122 
+ 123   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#FilesList</span><span class="s">)</span> <span class="s">{</span>
+ 124     <span class="i">$File</span> = <span class="i">$FilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 125 
+ 126     <span class="i">$FilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 127     <span class="i">$FilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 128 
+ 129     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$File</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 130       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $File: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+ 131       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 132     <span class="s">}</span>
+ 133 
+ 134     <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">FILE</span><span class="cm">,</span> <span class="q">&quot;$File&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 135       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $File: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 136       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 137     <span class="s">}</span>
+ 138     <span class="k">close</span> <span class="w">FILE</span><span class="sc">;</span>
+ 139 
+ 140     <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 141     <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$File</span><span class="s">)</span><span class="sc">;</span>
+ 142     <span class="i">$NewFileName</span> = <span class="i">$FileName</span><span class="sc">;</span>
+ 143     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@FilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 144       <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+ 145       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 146         <span class="i">$NewFileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 147       <span class="s">}</span>
+ 148       <span class="k">else</span> <span class="s">{</span>
+ 149         <span class="i">$NewFileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+ 150       <span class="s">}</span>
+ 151     <span class="s">}</span>
+ 152     <span class="k">else</span> <span class="s">{</span>
+ 153       <span class="i">$NewFileName</span> .= <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span>
+ 154     <span class="s">}</span>
+ 155 
+ 156     <span class="k">if</span> <span class="s">(</span><span class="i">$FileExt</span><span class="s">)</span> <span class="s">{</span>
+ 157       <span class="i">$NewFileName</span> .= <span class="q">&quot;.$FileExt&quot;</span><span class="sc">;</span>
+ 158     <span class="s">}</span>
+ 159 
+ 160     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>}<span class="s">)</span> <span class="s">{</span>
+ 161       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFileName</span><span class="s">)</span> <span class="s">{</span>
+ 162         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $File: New Text file, $NewFileName, already exists\n&quot;</span><span class="sc">;</span>
+ 163         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 164       <span class="s">}</span>
+ 165     <span class="s">}</span>
+ 166     <span class="i">$FilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 167     <span class="i">$FilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="i">$NewFileName</span><span class="sc">;</span>
+ 168   <span class="s">}</span>
+ 169 <span class="s">}</span>
+ 170 
+ 171 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 172 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 173   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 174 
+ 175   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 176 
+ 177   <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 178   <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 179 
+ 180 <span class="s">}</span>
+ 181 
+ 182 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 183 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 184 
+ 185   <span class="c"># Retrieve all the options...</span>
+ 186   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 187   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&quot;Unix&quot;</span><span class="sc">;</span>
+ 188 
+ 189   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 190     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 191   <span class="s">}</span>
+ 192   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 193     <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 194       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir},  for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 195     <span class="s">}</span>
+ 196     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+ 197   <span class="s">}</span>
+ 198   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(Unix|Windows|Mac)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 199     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m --mode\&quot; is not valid. Allowed values: Unix, Windows, or Mac\n&quot;</span><span class="sc">;</span>
+ 200   <span class="s">}</span>
+ 201 <span class="s">}</span>
+ 202 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>