package com.hfg.bio.seq.format.genbank;

import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import com.hfg.math.Range;
import com.hfg.util.CompareUtil;
import com.hfg.util.StringUtil;

//------------------------------------------------------------------------------
/**
 * Literature citation container.
 *
 * @author J. Alex Taylor, hairyfatguy.com
 */
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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 GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// jataylor@hairyfatguy.com
//------------------------------------------------------------------------------

public class GenBankReference implements Comparable<GenBankReference>
{
   private List<String> mAuthors;
   private String mTitle;
   private String mJournal;
   private String mSubmissionRecordInfo;
   private Integer mVolume;
   private Integer mIssue;
   private Integer mYear;
   private Range<Integer> mPages;
   private Integer mPubmedId;

   private static final Pattern sJournalPattern = Pattern.compile("^(.+?)\\s+(\\d+)\\s+\\((\\d+)\\),\\s+(\\d+)-(\\d+)\\s+\\((\\d{4})\\)$");

   //##########################################################################
   // PUBLIC METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      boolean result = false;

      if (inObj2 != null
            && inObj2 instanceof GenBankReference)
      {
         result = (0 == compareTo((GenBankReference)inObj2));
      }

      return result;
   }

   //--------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      int hashCode = getAuthorString().hashCode();
      hashCode += 31 * (getTitle() != null ? getTitle().hashCode() : 0);
      hashCode += 31 * (getJournal() != null ? getJournal().hashCode() : 0);
      hashCode += 31 * (getVolume() != null ? getVolume().hashCode() : 0);
      hashCode += 31 * (getIssue() != null ? getIssue().hashCode() : 0);
      hashCode += 31 * (getYear() != null ? getYear().hashCode() : 0);
      hashCode += 31 * (getPages() != null ? getPages().hashCode() : 0);

      return hashCode;
   }

   //--------------------------------------------------------------------------
   @Override
   public int compareTo(GenBankReference inObj2)
   {
      int result = 0;

      if (null == inObj2)
      {
         result = 1;
      }
      else
      {
         result = CompareUtil.compare(getTitle(), inObj2.getTitle());
         if (0 == result)
         {
            if (getPages() != null)
            {
               if (inObj2.getPages() != null)
               {
                  result = getPages().compareTo(inObj2.getPages());
               }
               else
               {
                  result = 1;
               }
            }
            else if (inObj2.getPages() != null)
            {
               result = -1;
            }

            if (0 == result)
            {
               result = CompareUtil.compare(getAuthorString(), inObj2.getAuthorString());

               if (0 == result)
               {
                  result = CompareUtil.compare(getYear(), inObj2.getYear());

                  if (0 == result)
                  {
                     result = CompareUtil.compare(getVolume(), inObj2.getVolume());

                     if (0 == result)
                     {
                        result = CompareUtil.compare(getIssue(), inObj2.getIssue());

                        if (0 == result)
                        {
                           result = CompareUtil.compare(getJournal(), inObj2.getJournal());
                        }
                     }
                  }
               }
            }
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   public GenBankReference setAuthors(String inAuthorList)
   {
      String[] authors = inAuthorList.split("[;,]");
      for (String author : authors)
      {
         addAuthor(author);
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public GenBankReference addAuthor(String inAuthor)
   {
      if (null == mAuthors)
      {
         mAuthors = new ArrayList<String>(25);
      }

      mAuthors.add(inAuthor);

      return this;
   }

   //--------------------------------------------------------------------------
   public List<String> getAuthors()
   {
      return mAuthors;
   }

   //--------------------------------------------------------------------------
   public String getAuthorString()
   {
      return (mAuthors != null ? StringUtil.join(mAuthors, ", ") : "");
   }


   //--------------------------------------------------------------------------
   public GenBankReference setTitle(String inValue)
   {
      mTitle = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String getTitle()
   {
      return mTitle;
   }


   //--------------------------------------------------------------------------
   // Simple example:
   //     J. Exp. Med. 181 (3), 1245-1250 (1995)
   //
   // Submission record example:
   //     Submitted (07-NOV-1994) Giachino C., Basel Institute for
   //     Immunology, Grenzacherstrasse 487, Basel, Switzerland, 4005
   //
   public void parseJournalString(String inValue)
   {
      if (inValue.startsWith("Submitted"))
      {
         mSubmissionRecordInfo = inValue;
      }
      else
      {
         Matcher m = sJournalPattern.matcher(inValue);
         if (m.matches())
         {
            mJournal = m.group(1);
            mVolume  = Integer.parseInt(m.group(2));
            mIssue   = Integer.parseInt(m.group(3));
            mPages   = new Range<>(Integer.parseInt(m.group(4)), Integer.parseInt(m.group(5)));
            mYear    = Integer.parseInt(m.group(6));
         }
         else
         {
            mJournal = inValue;
         }
      }
   }

   //--------------------------------------------------------------------------
   public GenBankReference setJournal(String inValue)
   {
      mJournal = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String getJournal()
   {
      return mJournal;
   }

   //--------------------------------------------------------------------------
   public String getSubmissionRecordInfo()
   {
      return mSubmissionRecordInfo;
   }


   //--------------------------------------------------------------------------
   public GenBankReference setVolume(Integer inValue)
   {
      mVolume = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Integer getVolume()
   {
      return mVolume;
   }


   //--------------------------------------------------------------------------
   public GenBankReference setIssue(Integer inValue)
   {
      mIssue = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Integer getIssue()
   {
      return mIssue;
   }


   //--------------------------------------------------------------------------
   public GenBankReference setYear(Integer inValue)
   {
      mYear = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Integer getYear()
   {
      return mYear;
   }


   //--------------------------------------------------------------------------
   public GenBankReference setPubmedId(Integer inValue)
   {
      mPubmedId = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Integer getPubmedId()
   {
      return mPubmedId;
   }


   //--------------------------------------------------------------------------
   public GenBankReference setPages(Range<Integer> inValue)
   {
      mPages = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Range<Integer> getPages()
   {
      return mPages;
   }

}