Import version 1.2 from https://sourceforge.net/projects/abi2xml/

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Instead of using

https://sourceforge.net/projects/abi2xml/

the development of abi2xml will continue at

https://github.com/eriksjolund/abi2xml

The file abi2xml-1.2.tar.gz was downloaded from
https://sourceforge.net/projects/abi2xml/files/abi2xml/1.2/
and its contents were added to this git commit.

According to the Sourceforge page the file
was modified 3 April 2006.

Signed-off-by: Erik Sjölund <erik.sjolund@gmail.com>

AUTHORS

@@ -0,0 +1,17 @@
+Design and implementation: Erik Sjolund  
+( Erik Sjönd )
+email: erik.sjolund@gmail.com
+
+in assignment from:
+Martti Tammi and Erik Arner
+Karolinska Insitutet, Stockholm, Sweden ( http://www.ki.se ) 
+
+Many thanks to Martti Tammi and Erik Arner who gave me expert advice concerning
+the Abi format.
+
+Many thanks to Clark Tibbetts for describing the ABI format in his publication 
+( see README file )
+
+Erik Arner also provided valuable feedback and ideas about "polishing" the end
+product. Some new command line flags arose that way.
+

ChangeLog

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+2005-11-26  Erik Sjolund  <erik.sjolund@gmail.com>
+
+	* Release 1.1 
+
+	* AUTHORS: typo fix
+
+	* src/main.cpp: Add functionality to convert a whole directory of abi files
+	* src/gengetopt/abi2xml.ggo: Add command line flags for directory processing
+
+2006-03-30  Erik Sjolund  <erik.sjolund@gmail.com>
+
+	* Release 1.2 
+
+	* : ported the code to Qt 4.1
+
+

INSTALL

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+Prerequisites: You must have the qt library ( version >= 4.1 ) installed ( see http://www.trolltech.com )
+
+For instance Fedora Core 4 is a Linux distribution where abi2xml is known to build. But first you need to download, build 
+and install Qt-4.1 first, as it is not included in Fedora Core 4.
+
+abi2xml is also known to build on Windows with Qt-4.1. The qt library is also available on MacOS, so abi2xml should probably work there too although
+this has not yet been tested.
+
+To install this program on a Unix platform ( e.g. Linux ), follow these steps:
+
+1. qmake
+2. make
+3. make install
+
+You should then find the executable in the bin subdirectory.
+
+
+

README

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+This program parses the binary file format coming from a
+ABI PRISM TM 377 DNA Sequencer and writes the information in
+plain text to an xml file.
+
+The ABI file binary format is described in this publication:
+http://www.cs.cmu.edu/afs/cs/project/genome/WWW/Papers/clark.html
+
+     -------------------------------------------
+
+     Raw Data File Formats,
+     and the Digital and Analog Raw Data Streams
+     of the ABI PRISM TM 377 DNA Sequencer
+
+     A preliminary technical examination
+
+     by
+
+     Clark Tibbetts, Ph. D.
+     Professor of Microbiology
+
+     A5217 Medical Center North
+     Vanderbilt University
+     Nashville, TN 37232-2363
+
+     August 1995
+
+     ----------------------------------------------
+
+
+Usage: 
+   abi2xml -i binaryfile -o xmlfile
+
+Other option flags are also available. To list them type "abi2xml --help".
+
+An xslt script can be useful when you want to retrieve information from the xml file. 
+Take a look in the xslt_examples sub directory. There you find some example scripts.
+
+You run a xslt script like this:
+xsltproc xsltscript abi2xml-generated-xmlfile
+
+( xsltproc is a command line utility from the package libxslt )
+
+
+

TODO

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+Todo list:
+
+* implement datarecord "KUKU"
+* implement datarecord "THUM"
+* implement datarecord "GELT"
+
+* implement a command line flag to list available codecs.
+
+  Qt 4.0 has a new function to list available codecs.
+  http://doc.trolltech.com/4.0/qtextcodec.html
+  "QList<QByteArray> availableCodecs ()"
+
+
+
+

abi2xml.pro

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+# File generated by kdevelop's qmake manager. 
+# ------------------------------------------- 
+# Subdir relative project main directory: .
+# Target is a subdirs project 
+
+TEMPLATE=subdirs
+SUBDIRS += src 
+

src/abi2xml.cpp

@@ -0,0 +1,146 @@
+
+
+/*******************************************************************************
+ *                                                                             *
+ *   Copyright (C) 2003  Erik Sjolund,  (<html>Erik Sj&ouml;lund</html>)       *
+ *                       Center for Genomics and Bioinformatics,               *
+ *                       Karolinska Institutet,                                *
+ *                       Stockholm,                                            *
+ *                       Sweden                                                *
+ *                                                                             *
+ *  Author: Erik Sjolund                                                       *
+ *  Email: erik.sjolund@adivo.se                                               *
+ *                                                                             *
+ *  This program is free software; you can redistribute it and/or modify       *
+ *  it under the terms of the GNU General Public License as published by       *
+ *  the Free Software Foundation; either version 2 of the License, or          *
+ *  (at your option) any later version.                                        *
+ *                                                                             *
+ *  This program is distributed in the hope that it will be useful,            *
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              * 
+ *  General Public License for more details.                                   *
+ *                                                                             *
+ *  You should have received a copy of the GNU General Public License          *
+ *  along with this program; if not, write to the Free Software                *
+ *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  *
+ *                                                                             *
+ *******************************************************************************
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <iostream>
+#include <qdatastream.h>
+#include <qiodevice.h>
+
+#include <qregexp.h>
+#include <algorithm>
+
+#include "abi2xml.h"
+#include "datarecordmaker.h"
+#include "datarecord.h"
+#include <QByteArray>
+
+Abi2xml::Abi2xml( QDataStream & stream_, QDomElement parseRoot,  Params *params_ ) 
+  : stream ( stream_ ), params( params_ )
+{
+  device = stream.device();
+  domDoc = parseRoot.ownerDocument();
+  domDataStructs = domDoc.createElement( "dataStructures" );
+  parseRoot.appendChild( domDataStructs );
+  parseInfo = domDoc.createElement( "parseInfo" );
+  parseRoot.appendChild( parseInfo );
+}
+ Abi2xml::~Abi2xml()
+{
+}
+
+void Abi2xml::parse()
+{
+  m_offset_to_ABIF = offset_to_ABIF();
+  qint32 num_rec =  num_records();
+  qint32 offset_to_first = offset_to_first_record();
+  quint16 blk_size = block_size();
+  if ( blk_size != 28 )
+  {
+     std::cerr << "Warning: Blocksize is not 28. Maybe you passed a non-valid indata file." << std::endl;
+     exit(1);
+  }
+  parseInfo.setAttribute("block_size" , blk_size);
+  parseInfo.setAttribute("offset_to_first_record",offset_to_first);
+  parseInfo.setAttribute("read_num_tagged_file_records",num_rec);  
+  for ( int i=0 ; i< num_rec; ++i )
+  {
+    qlonglong offset =  offset_to_first + i * blk_size;
+    device->seek( offset );
+    DataRecord * record = DataRecordMaker::newDataRecord( stream, m_offset_to_ABIF, params );
+    Q_ASSERT( record );
+    if ( record )
+    {
+      QDomElement elem = domDoc.createElement( record->xmlElementName() );
+      domDataStructs.appendChild( elem );
+      record->produceDom( elem );
+    } else
+    {
+      exit( 1 );
+    }
+  }
+}
+
+quint16 Abi2xml::block_size()
+{
+  device->seek( 16 + m_offset_to_ABIF );
+  quint16 number;
+  stream >> number; 
+  return number;
+}
+
+qint32 Abi2xml::num_records()
+{
+  qint32 number = read_int32_at( 18 + m_offset_to_ABIF );
+  return number;
+}
+
+qint32 Abi2xml::offset_to_first_record()
+{
+  qint32 number = read_int32_at( 26 + m_offset_to_ABIF );
+  return number + m_offset_to_ABIF;
+}
+
+qint32 Abi2xml::read_int32_at( qlonglong offset )
+{
+  device->seek( offset );
+  qint32 number;
+  stream >> number;
+  return number;
+}
+
+qint32 Abi2xml::offset_to_ABIF()
+{
+  qint32 index = 0;
+  qint32 size = device->size();
+  int len = 5;
+  bool found = false;
+  while ( ( ! found && ( index <= size - len )) )
+  {
+    device->seek( index );
+    char array[ len ];
+    stream.readRawData(&array[0], len );
+    array[ len -1 ] = '\0';
+    QString str = QString(&array[0]);
+    if  ( str == "ABIF" ) {
+      found = true;
+      break;
+    }
+    ++index;
+  }
+  if ( ! found )
+  {
+    std::cerr << "could not find a qualitive guess of the start position" << std::endl;
+    exit(1);  
+  }
+   return index;
+}

src/abi2xml.h

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+/*******************************************************************************
+ *                                                                             *
+ *   Copyright (C) 2003  Erik Sjolund,  (<html>Erik Sj&ouml;lund</html>)       *
+ *                       Center for Genomics and Bioinformatics,               *
+ *                       Karolinska Institutet,                                *
+ *                       Stockholm,                                            *
+ *                       Sweden                                                *
+ *                                                                             *
+ *  Author: Erik Sjolund                                                       *
+ *  Email: erik.sjolund@adivo.se                                               *
+ *                                                                             *
+ *  This program is free software; you can redistribute it and/or modify       *
+ *  it under the terms of the GNU General Public License as published by       *
+ *  the Free Software Foundation; either version 2 of the License, or          *
+ *  (at your option) any later version.                                        *
+ *                                                                             *
+ *  This program is distributed in the hope that it will be useful,            *
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              * 
+ *  General Public License for more details.                                   *
+ *                                                                             *
+ *  You should have received a copy of the GNU General Public License          *
+ *  along with this program; if not, write to the Free Software                *
+ *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  *
+ *                                                                             *
+ *******************************************************************************
+ */
+
+#ifndef ABI2XML_H
+#define ABI2XML_H
+
+// include files for QT
+
+#include <QIODevice>
+#include <QList>
+#include <QDomElement>
+
+class QDataStream;
+class DataRecord;
+struct Params;
+
+class Abi2xml
+{
+public:
+  Abi2xml( QDataStream & stream, QDomElement, Params *params );
+ ~Abi2xml();
+ void parse();
+ quint16 block_size();
+ qint32 num_records(  );
+ qint32 offset_to_first_record();
+ qint32 offset_to_ABIF();
+protected:
+  qint32 read_int32_at( qlonglong offset );
+  QIODevice * device;
+  QDataStream & stream;
+  DataRecord * dataRecord;
+  QDomElement  domDataStructs;
+  QDomElement parseInfo;
+  qint32 m_offset_to_ABIF;
+  QDomDocument domDoc;
+  Params *params;
+};
+
+#endif 
+