/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3 of the License, or (at your option) any later version.
 *  
 * Jalview 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.io;

import java.io.File;
import java.io.InputStream;

import jalview.datamodel.*;

/**
 * A low level class for alignment and feature IO with alignment formatting
 * methods used by both applet and application for generating flat alignment
 * files. It also holds the lists of magic format names that the applet and
 * application will allow the user to read or write files with.
 * 
 * @author $author$
 * @version $Revision$
 */
public class AppletFormatAdapter
{
  /**
   * List of valid format strings used in the isValidFormat method
   */
  public static final String[] READABLE_FORMATS = new String[]
  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
      "PDB", "JnetFile" }; // , "SimpleBLAST" };

  /**
   * List of valid format strings for use by callers of the formatSequences
   * method
   */
  public static final String[] WRITEABLE_FORMATS = new String[]
  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "AMSA" };

  /**
   * List of extensions corresponding to file format types in WRITABLE_FNAMES
   * that are writable by the application.
   */
  public static final String[] WRITABLE_EXTENSIONS = new String[]
  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", "sto,stk" };

  /**
   * List of writable formats by the application. Order must correspond with the
   * WRITABLE_EXTENSIONS list of formats.
   */
  public static final String[] WRITABLE_FNAMES = new String[]
  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", "STH"};

  /**
   * List of readable format file extensions by application in order
   * corresponding to READABLE_FNAMES
   */
  public static final String[] READABLE_EXTENSIONS = new String[]
  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
      "sto,stk" }; // ,

  // ".blast"
  // };

  /**
   * List of readable formats by application in order corresponding to
   * READABLE_EXTENSIONS
   */
  public static final String[] READABLE_FNAMES = new String[]
  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
      "Stockholm" };// ,

  // "SimpleBLAST"
  // };

  public static String INVALID_CHARACTERS = "Contains invalid characters";

  // TODO: make these messages dynamic
  public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
          + prettyPrint(READABLE_FORMATS);

  /**
   * 
   * @param els
   * @return grammatically correct(ish) list consisting of els elements.
   */
  public static String prettyPrint(String[] els)
  {
    StringBuffer list = new StringBuffer();
    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
    {
      list.append(els[i]);
      list.append(",");
    }
    list.append(" and " + els[els.length - 1] + ".");
    return list.toString();
  }

  public static String FILE = "File";

  public static String URL = "URL";

  public static String PASTE = "Paste";

  public static String CLASSLOADER = "ClassLoader";

  AlignFile afile = null;

  String inFile;

  /**
   * character used to write newlines
   */
  protected String newline = System.getProperty("line.separator");

  public void setNewlineString(String nl)
  {
    newline = nl;
  }

  public String getNewlineString()
  {
    return newline;
  }

  /**
   * check that this format is valid for reading
   * 
   * @param format
   *          a format string to be compared with READABLE_FORMATS
   * @return true if format is readable
   */
  public static final boolean isValidFormat(String format)
  {
    return isValidFormat(format, false);
  }

  /**
   * validate format is valid for IO
   * 
   * @param format
   *          a format string to be compared with either READABLE_FORMATS or
   *          WRITEABLE_FORMATS
   * @param forwriting
   *          when true, format is checked for containment in WRITEABLE_FORMATS
   * @return true if format is valid
   */
  public static final boolean isValidFormat(String format,
          boolean forwriting)
  {
    boolean valid = false;
    String[] format_list = (forwriting) ? WRITEABLE_FORMATS
            : READABLE_FORMATS;
    for (int i = 0; i < format_list.length; i++)
    {
      if (format_list[i].equalsIgnoreCase(format))
      {
        return true;
      }
    }

    return valid;
  }

  /**
   * Constructs the correct filetype parser for a characterised datasource
   * 
   * @param inFile
   *          data/data location
   * @param type
   *          type of datasource
   * @param format
   *          File format of data provided by datasource
   * 
   * @return DOCUMENT ME!
   */
  public Alignment readFile(String inFile, String type, String format)
          throws java.io.IOException
  {
    // TODO: generalise mapping between format string and io. class instances
    // using Constructor.invoke reflection
    this.inFile = inFile;
    try
    {
      if (format.equals("FASTA"))
      {
        afile = new FastaFile(inFile, type);
      }
      else if (format.equals("MSF"))
      {
        afile = new MSFfile(inFile, type);
      }
      else if (format.equals("PileUp"))
      {
        afile = new PileUpfile(inFile, type);
      }
      else if (format.equals("CLUSTAL"))
      {
        afile = new ClustalFile(inFile, type);
      }
      else if (format.equals("BLC"))
      {
        afile = new BLCFile(inFile, type);
      }
      else if (format.equals("PIR"))
      {
        afile = new PIRFile(inFile, type);
      }
      else if (format.equals("PFAM"))
      {
        afile = new PfamFile(inFile, type);
      }
      else if (format.equals("JnetFile"))
      {
        afile = new JPredFile(inFile, type);
        ((JPredFile) afile).removeNonSequences();
      }
      else if (format.equals("PDB"))
      {
        afile = new MCview.PDBfile(inFile, type);
      }
      else if (format.equals("STH"))
      {
        afile = new StockholmFile(inFile, type);
      }
      else if (format.equals("SimpleBLAST"))
      {
        afile = new SimpleBlastFile(inFile, type);
      }

      Alignment al = new Alignment(afile.getSeqsAsArray());

      afile.addAnnotations(al);

      return al;
    } catch (Exception e)
    {
      e.printStackTrace();
      System.err.println("Failed to read alignment using the '" + format
              + "' reader.\n" + e);

      if (e.getMessage() != null
              && e.getMessage().startsWith(INVALID_CHARACTERS))
      {
        throw new java.io.IOException(e.getMessage());
      }

      // Finally test if the user has pasted just the sequence, no id
      if (type.equalsIgnoreCase("Paste"))
      {
        try
        {
          // Possible sequence is just residues with no label
          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
          Alignment al = new Alignment(afile.getSeqsAsArray());
          afile.addAnnotations(al);
          return al;

        } catch (Exception ex)
        {
          if (ex.toString().startsWith(INVALID_CHARACTERS))
          {
            throw new java.io.IOException(e.getMessage());
          }

          ex.printStackTrace();
        }
      }

      // If we get to this stage, the format was not supported
      throw new java.io.IOException(SUPPORTED_FORMATS);
    }
  }

  /**
   * Constructs the correct filetype parser for an already open datasource
   * 
   * @param source
   *          an existing datasource
   * @param format
   *          File format of data that will be provided by datasource
   * 
   * @return DOCUMENT ME!
   */
  public Alignment readFromFile(FileParse source, String format)
          throws java.io.IOException
  {
    // TODO: generalise mapping between format string and io. class instances
    // using Constructor.invoke reflection
    // This is exactly the same as the readFile method except we substitute
    // 'inFile, type' with 'source'
    this.inFile = source.getInFile();
    String type = source.type;
    try
    {
      if (format.equals("FASTA"))
      {
        afile = new FastaFile(source);
      }
      else if (format.equals("MSF"))
      {
        afile = new MSFfile(source);
      }
      else if (format.equals("PileUp"))
      {
        afile = new PileUpfile(source);
      }
      else if (format.equals("CLUSTAL"))
      {
        afile = new ClustalFile(source);
      }
      else if (format.equals("BLC"))
      {
        afile = new BLCFile(source);
      }
      else if (format.equals("PIR"))
      {
        afile = new PIRFile(source);
      }
      else if (format.equals("PFAM"))
      {
        afile = new PfamFile(source);
      }
      else if (format.equals("JnetFile"))
      {
        afile = new JPredFile(source);
        ((JPredFile) afile).removeNonSequences();
      }
      else if (format.equals("PDB"))
      {
        afile = new MCview.PDBfile(source);
      }
      else if (format.equals("STH"))
      {
        afile = new StockholmFile(source);
      }
      else if (format.equals("SimpleBLAST"))
      {
        afile = new SimpleBlastFile(source);
      }

      Alignment al = new Alignment(afile.getSeqsAsArray());

      afile.addAnnotations(al);

      return al;
    } catch (Exception e)
    {
      e.printStackTrace();
      System.err.println("Failed to read alignment using the '" + format
              + "' reader.\n" + e);

      if (e.getMessage() != null
              && e.getMessage().startsWith(INVALID_CHARACTERS))
      {
        throw new java.io.IOException(e.getMessage());
      }

      // Finally test if the user has pasted just the sequence, no id
      if (type.equalsIgnoreCase("Paste"))
      {
        try
        {
          // Possible sequence is just residues with no label
          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
          Alignment al = new Alignment(afile.getSeqsAsArray());
          afile.addAnnotations(al);
          return al;

        } catch (Exception ex)
        {
          if (ex.toString().startsWith(INVALID_CHARACTERS))
          {
            throw new java.io.IOException(e.getMessage());
          }

          ex.printStackTrace();
        }
      }

      // If we get to this stage, the format was not supported
      throw new java.io.IOException(SUPPORTED_FORMATS);
    }
  }

  /**
   * Construct an output class for an alignment in a particular filetype TODO:
   * allow caller to detect errors and warnings encountered when generating
   * output
   * 
   * @param format
   *          string name of alignment format
   * @param alignment
   *          the alignment to be written out
   * @param jvsuffix
   *          passed to AlnFile class controls whether /START-END is added to
   *          sequence names
   * 
   * @return alignment flat file contents
   */
  public String formatSequences(String format, AlignmentI alignment,
          boolean jvsuffix)
  {
    try
    {
      AlignFile afile = null;

      if (format.equalsIgnoreCase("FASTA"))
      {
        afile = new FastaFile();
      }
      else if (format.equalsIgnoreCase("MSF"))
      {
        afile = new MSFfile();
      }
      else if (format.equalsIgnoreCase("PileUp"))
      {
        afile = new PileUpfile();
      }
      else if (format.equalsIgnoreCase("CLUSTAL"))
      {
        afile = new ClustalFile();
      }
      else if (format.equalsIgnoreCase("BLC"))
      {
        afile = new BLCFile();
      }
      else if (format.equalsIgnoreCase("PIR"))
      {
        afile = new PIRFile();
      }
      else if (format.equalsIgnoreCase("PFAM"))
      {
        afile = new PfamFile();
      }
      else if (format.equalsIgnoreCase("STH"))
      {
        afile = new StockholmFile(alignment);
      }
      else if (format.equalsIgnoreCase("AMSA"))
      {
        afile = new AMSAFile(alignment);
      }
      else
      {
        throw new Exception(
                "Implementation error: Unknown file format string");
      }
      afile.setNewlineString(newline);
      afile.addJVSuffix(jvsuffix);

      afile.setSeqs(alignment.getSequencesArray());

      String afileresp = afile.print();
      if (afile.hasWarningMessage())
      {
        System.err.println("Warning raised when writing as " + format
                + " : " + afile.getWarningMessage());
      }
      return afileresp;
    } catch (Exception e)
    {
      System.err.println("Failed to write alignment as a '" + format
              + "' file\n");
      e.printStackTrace();
    }

    return null;
  }

  public static String checkProtocol(String file)
  {
    String protocol = FILE;
    String ft = file.toLowerCase().trim();
    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
            || ft.indexOf("file:") == 0)
    {
      protocol = URL;
    }
    return protocol;
  }

  public static void main(String[] args)
  {
    int i = 0;
    while (i < args.length)
    {
      File f = new File(args[i]);
      if (f.exists())
      {
        try
        {
          System.out.println("Reading file: " + f);
          AppletFormatAdapter afa = new AppletFormatAdapter();
          String fName = f.getName();
          String extension = fName.substring(fName.lastIndexOf(".") + 1, fName.length());
          if (extension.equals("stk") || extension.equals("sto"))
          {  
        	  afa.test(f);
          }
          else
          {
          Runtime r = Runtime.getRuntime();
          System.gc();
          long memf = -r.totalMemory() + r.freeMemory();
          long t1 = -System.currentTimeMillis();
          Alignment al = afa.readFile(args[i], FILE,
                  new IdentifyFile().Identify(args[i], FILE));
          t1 += System.currentTimeMillis();
          System.gc();
          memf += r.totalMemory() - r.freeMemory();
          if (al != null)
          {
            System.out.println("Alignment contains " + al.getHeight()
                    + " sequences and " + al.getWidth() + " columns.");
            try
            {
              System.out.println(new AppletFormatAdapter().formatSequences(
                      "FASTA", al, true));
            } catch (Exception e)
            {
              System.err
                      .println("Couln't format the alignment for output as a FASTA file.");
              e.printStackTrace(System.err);
            }
          }
          else
          {
            System.out.println("Couldn't read alignment");
          }
          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
          System.out
                  .println("Difference between free memory now and before is "
                          + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
          }
        } catch (Exception e)
        {
          System.err.println("Exception when dealing with " + i
                  + "'th argument: " + args[i] + "\n" + e);
        }
     
      }
      else
      {
        System.err.println("Ignoring argument '" + args[i] + "' (" + i
                + "'th)- not a readable file.");
      }
      i++;
    }
  }

  private void test(File f) {
		System.out.println("Reading file: " + f);
	    String ff = f.getPath();
		try 
		{
		  Alignment al = readFile(ff, FILE, new IdentifyFile().Identify(ff, FILE));
	      for (int i = 0; i < al.getSequencesArray().length; ++i) {
	    	  al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
	      }
		  AlignFile stFile = new StockholmFile(al);
	      stFile.setSeqs(al.getSequencesArray());

	      String stockholmoutput = stFile.print();
	      Alignment al_input = readFile(stockholmoutput, AppletFormatAdapter.PASTE, "STH");
	      if (al != null && al_input!= null) 
	      {
	        System.out.println("Alignment contains: " + al.getHeight() + " and " + al_input.getHeight()
	               + " sequences; " + al.getWidth() +  " and " + al_input.getWidth() + " columns.");
	        AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
	        AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
	        
	        // check Alignment annotation
	        if (aa_new != null && aa_original != null) 
	        {
	          System.out.println("Alignment contains: " + aa_new.length
	        	+ "  and " + aa_original.length  + " alignment annotation(s)");
	          for (int i = 0; i < aa_original.length; i++)
	          {
	            if (!equalss(aa_original[i], aa_new[i]))
	            	System.out.println("Different alignment annotation");
	          }
	        }
	        
	        // check sequences, annotation and features
	        SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
	        seq_original = al.getSequencesArray();
	        SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
	        seq_new = al_input.getSequencesArray();
	        SequenceFeature[] sequenceFeatures_original,sequenceFeatures_new;
	        AlignmentAnnotation annot_original, annot_new;
	        //
	        for (int i = 0; i < al.getSequencesArray().length; i++) 
	        {
	          String name = seq_original[i].getName();
	          int start = seq_original[i].getStart();	
	          int end = seq_original[i].getEnd();
	          System.out.println("Check sequence: " + name + "/" + start + "-" + end);   
	          
	              // search equal sequence
	          for (int in = 0; in < al_input.getSequencesArray().length; in++) {
	            if (name.equals(seq_new[in].getName()) && 
	               		start == seq_new[in].getStart() && 
	               		end ==seq_new[in].getEnd())
	            {
	              String ss_original = seq_original[i].getSequenceAsString();
	              String ss_new = seq_new[in].getSequenceAsString();
	              if (!ss_original.equals(ss_new))
	              {
	                System.out.println("The sequences " + name + "/" + start + "-" + end + " are not equal");
	              } 
	     
	                  // compare sequence features
	              if (seq_original[i].getSequenceFeatures() != null && seq_new[in].getSequenceFeatures() != null) 
	              {
	            	  System.out.println("There are feature!!!");
	                sequenceFeatures_original = new SequenceFeature[seq_original[i].getSequenceFeatures().length];
	           	    sequenceFeatures_original = seq_original[i].getSequenceFeatures(); 
	                sequenceFeatures_new = new SequenceFeature[seq_new[in].getSequenceFeatures().length];
	           	    sequenceFeatures_new = seq_new[in].getSequenceFeatures();
	           	    
	           	    if (seq_original[i].getSequenceFeatures().length == seq_new[in].getSequenceFeatures().length) 
	           	    {
	           	       for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++) {
	                     if (!sequenceFeatures_original[feat].equals(sequenceFeatures_new[feat])) {
	                       System.out.println("Different features");
	                       break;
	                     }
	                   }
	                } else
	                {
	                	System.out.println("different number of features");
	                }
	              } else if (seq_original[i].getSequenceFeatures() == null && seq_new[in].getSequenceFeatures() == null)
	              {
	            	  System.out.println("No sequence features");
	              } else if (seq_original[i].getSequenceFeatures() != null && seq_new[in].getSequenceFeatures() == null) 
	              {
	            	System.out.println("Coudn't compare sequence features new one");
	              }
	           	    // compare alignment annotation    
	              if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() != null) 
	              {
	                for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++) 
	                {
	                  if (al.getSequenceAt(i).getAnnotation()[j] != null &&
	                     al_input.getSequenceAt(in).getAnnotation()[j] != null) 
	                  {
	                    annot_original = al.getSequenceAt(i).getAnnotation()[j];
	                    annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
	                    if (!equalss(annot_original, annot_new))
	                      System.out.println("Different annotation");  
	                  } 
	                }
	              } else if (al.getSequenceAt(i).getAnnotation() == null && al_input.getSequenceAt(in).getAnnotation() == null) 
	              {
	            	  System.out.println("No annotations");
	              } else if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() == null)
	              {
	            	  System.out.println("Coudn't compare annotations new one"); 
	              }
	              break;
	            }
	          }  	
	        }
	      } else 
	      {
	        System.out.println("Couldn't read alignment");
	      }
	    } catch (Exception e)
	    {
	      System.err.println("Couln't format the alignment for output file.");
	      e.printStackTrace(System.err);
	    }
	  }

	  /*
	   * compare annotations
	   */
	   private boolean equalss(AlignmentAnnotation annot_or, AlignmentAnnotation annot_new)
	   {
		   if (annot_or.annotations.length != annot_new.annotations.length) 
		   {
		     return false; 
		   }
		   for (int i = 0; i < annot_or.annotations.length; i++)
		   {
		     if (annot_or.annotations[i] != null && annot_new.annotations[i] != null)
		     {
	           if (!annot_or.annotations[i].displayCharacter.equals(annot_new.annotations[i].displayCharacter) && 
	        		   annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure &&
	        	   !annot_or.annotations[i].description.equals(annot_new.annotations[i].description)) 
	           {
	             return false;
	           }      
		     } else if (annot_or.annotations[i] == null && annot_new.annotations[i] == null) 
		     {
		       continue; 
		     } else 
		     {
		       return false;  
		     }
		   }
		   return true;
	   }
  /**
   * try to discover how to access the given file as a valid datasource that
   * will be identified as the given type.
   * 
   * @param file
   * @param format
   * @return protocol that yields the data parsable as the given type
   */
  public static String resolveProtocol(String file, String format)
  {
    return resolveProtocol(file, format, false);
  }

  public static String resolveProtocol(String file, String format,
          boolean debug)
  {
    // TODO: test thoroughly!
    String protocol = null;
    if (debug)
    {
      System.out.println("resolving datasource started with:\n>>file\n"
              + file + ">>endfile");
    }

    // This might throw a security exception in certain browsers
    // Netscape Communicator for instance.
    try
    {
      boolean rtn = false;
      InputStream is = System.getSecurityManager().getClass()
              .getResourceAsStream("/" + file);
      if (is != null)
      {
        rtn = true;
        is.close();
      }
      if (debug)
      {
        System.err.println("Resource '" + file + "' was "
                + (rtn ? "" : "not") + " located by classloader.");
      }
      ;
      if (rtn)
      {
        protocol = AppletFormatAdapter.CLASSLOADER;
      }

    } catch (Exception ex)
    {
      System.err
              .println("Exception checking resources: " + file + " " + ex);
    }

    if (file.indexOf("://") > -1)
    {
      protocol = AppletFormatAdapter.URL;
    }
    else
    {
      // skipping codebase prepend check.
      protocol = AppletFormatAdapter.FILE;
    }
    FileParse fp = null;
    try
    {
      if (debug)
      {
        System.out.println("Trying to get contents of resource as "
                + protocol + ":");
      }
      fp = new FileParse(file, protocol);
      if (!fp.isValid())
      {
        fp = null;
      }
      else
      {
        if (debug)
        {
          System.out.println("Successful.");
        }
      }
    } catch (Exception e)
    {
      if (debug)
      {
        System.err.println("Exception when accessing content: " + e);
      }
      fp = null;
    }
    if (fp == null)
    {
      if (debug)
      {
        System.out.println("Accessing as paste.");
      }
      protocol = AppletFormatAdapter.PASTE;
      fp = null;
      try
      {
        fp = new FileParse(file, protocol);
        if (!fp.isValid())
        {
          fp = null;
        }
      } catch (Exception e)
      {
        System.err.println("Failed to access content as paste!");
        e.printStackTrace();
        fp = null;
      }
    }
    if (fp == null)
    {
      return null;
    }
    if (format == null || format.length() == 0)
    {
      return protocol;
    }
    else
    {
      try
      {
        String idformat = new jalview.io.IdentifyFile().Identify(file,
                protocol);
        if (idformat == null)
        {
          if (debug)
          {
            System.out.println("Format not identified. Inaccessible file.");
          }
          return null;
        }
        if (debug)
        {
          System.out.println("Format identified as " + idformat
                  + "and expected as " + format);
        }
        if (idformat.equals(format))
        {
          if (debug)
          {
            System.out.println("Protocol identified as " + protocol);
          }
          return protocol;
        }
        else
        {
          if (debug)
          {
            System.out
                    .println("File deemed not accessible via " + protocol);
          }
          fp.close();
          return null;
        }
      } catch (Exception e)
      {
        if (debug)
        {
          System.err.println("File deemed not accessible via " + protocol);
          e.printStackTrace();
        }
        ;

      }
    }
    return null;
  }
}