package jalview.gui;

import java.io.*;
import java.util.*;
import java.util.jar.*;

import jalview.binding.*;
import jalview.schemes.*;
import javax.swing.JInternalFrame;


public class Jalview2XML
{

  // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
  public static void SaveState(File statefile)
  {
      long creation = System.currentTimeMillis();
      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
      try{
        FileOutputStream fos = new FileOutputStream(statefile);
        JarOutputStream jout = new JarOutputStream(fos);
        //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
        ////////////////////////////////////////////////////
        PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));

        Vector shortNames = new Vector();
        for (int i = 0; i < frames.length; i++)
        {
          if (frames[i] instanceof AlignFrame)
          {
            AlignFrame af = (AlignFrame) frames[i];

            String shortName = af.getTitle();

            shortName = shortName.replace('/', '_');
            shortName = shortName.replace('\\', '_');

            int count=1;
            while( shortNames.contains(shortName) )
            {
              if(shortName.endsWith("_"+(count-1)))
                shortName = shortName.substring(0, shortName.lastIndexOf("_"));

              shortName = shortName.concat("_"+count);
              count++;
            }
            shortNames.addElement(shortName);

            if(!shortName.endsWith(".xml"))
              shortName = shortName+".xml";

            SaveState( af, creation, shortName, jout, out);
           }
        }
        out.close();
        jout.close();
      }
      catch(Exception ex){ex.printStackTrace();}
  }

  // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
  public static void SaveState( AlignFrame af, String jarFile, String fileName)
  {
    try{
      FileOutputStream fos = new FileOutputStream(jarFile);
      JarOutputStream jout = new JarOutputStream(fos);
      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
      ////////////////////////////////////////////////////
      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));

      SaveState(af, System.currentTimeMillis(), fileName, jout, out);
      out.close();
      jout.close();
    }catch(Exception ex){}
  }

  public static void SaveState( AlignFrame af, long timeStamp,
      String fileName, JarOutputStream jout, PrintWriter out)
  {

    Vector seqids = new Vector();

    AlignViewport av = af.viewport;

    JalviewModel object = new JalviewModel();
    object.setVamsasModel( new VamsasModel() );

    object.setCreationDate( new java.util.Date(timeStamp) );

    jalview.datamodel.AlignmentI jal = af.viewport.alignment;

    SequenceSet vamsasSet = new SequenceSet();
    Sequence vamsasSeq;
    JalviewModelSequence jms = new JalviewModelSequence();

    vamsasSet.setGapChar(jal.getGapCharacter()+"");

    JSeq jseq;


    //SAVE SEQUENCES
    int id = 0;
    for(int i=0; i<jal.getHeight(); i++)
    {
      seqids.add(jal.getSequenceAt(i));

      vamsasSeq = new Sequence( );
      vamsasSeq.setId(id+"");
      vamsasSeq.setName(jal.getSequenceAt(i).getName());
      vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());

      jseq = new JSeq();
      jseq.setStart(jal.getSequenceAt(i).getStart());
      jseq.setEnd(jal.getSequenceAt(i).getEnd());

      jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());

      jseq.setId( id );

      jms.addJSeq(jseq);
      vamsasSet.addSequence(vamsasSeq);
      id++;
    }

    //SAVE TREES
    if(af.viewport.currentTree!=null)
    {
      object.getVamsasModel().addTree(af.viewport.currentTree.toString());
    }

    //SAVE ANNOTATIONS
    if(jal.getAlignmentAnnotation()!=null)
    {

      jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();
      for(int i=0; i<aa.length; i++)
      {
        if(aa[i].label.equals("Quality")
        || aa[i].label.equals("Conservation")
        || aa[i].label.equals("Consensus"))
       {    continue;}

        Annotation an = new Annotation();
        an.setDescription(aa[i].description);
        an.setGraph(aa[i].isGraph);
        an.setLabel(aa[i].label);

        AnnotationElement ae;

        for(int a=0; a<aa[i].annotations.length; a++)
        {
          if(aa[i]==null || aa[i].annotations[a]==null)
            continue;

          ae = new AnnotationElement();
          ae.setDescription(aa[i].annotations[a].description);
          ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
          ae.setValue(aa[i].annotations[a].value);
          ae.setPosition(a);
          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure+"");
          an.addAnnotationElement(ae);
        }

        vamsasSet.addAnnotation(an);
      }

    }

    //SAVE GROUPS
    if(jal.getGroups()!=null)
    {
      JGroup [] groups = new JGroup[jal.getGroups().size()];
      for(int i=0; i<groups.length; i++)
      {
        groups[i] = new JGroup();
        jalview.datamodel.SequenceGroup sg
            = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);
        groups[i].setStart( sg.getStartRes() );
        groups[i].setEnd( sg.getEndRes() );
        groups[i].setName( sg.getName());

        if(sg.cs instanceof ConservationColourScheme)
          groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);

        if (sg.cs instanceof ResidueColourScheme)
          groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());
       else if (sg.cs instanceof ScoreColourScheme)
         groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());


        groups[i].setColour( ColourSchemeProperty.getColourName(sg.cs) );
        groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
        groups[i].setDisplayBoxes(sg.getDisplayBoxes());
        groups[i].setDisplayText(sg.getDisplayText());
        groups[i].setColourText(sg.getColourText());

        for(int s=0; s<sg.getSize(); s++)
        {
          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);
          int index = seqids.indexOf(seq);
          groups[i].addSeq(index);
        }

      }

      jms.setJGroup(groups);

    }

    ///////////SAVE VIEWPORT
    Viewport view = new Viewport();
   view.setTitle(af.getTitle());
   view.setXpos(af.getX());
   view.setYpos(af.getY());
   view.setWidth(af.getWidth());
   view.setHeight(af.getHeight());
   view.setStartRes(av.startRes);
   view.setStartSeq(av.startSeq);
   view.setBgColour( ColourSchemeProperty.getColourName
                     ( av.getGlobalColourScheme()));

   ColourSchemeI cs = av.getGlobalColourScheme();
   if(cs instanceof ConservationColourScheme)
     view.setConsThreshold( ((ConservationColourScheme)cs).inc);

   if (cs instanceof ResidueColourScheme)
     view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
  else if (cs instanceof ScoreColourScheme)
     view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());


   view.setConservationSelected(av.getConservationSelected());
   view.setPidSelected(av.getAbovePIDThreshold());
   view.setFontName(av.font.getFontName());
   view.setFontSize(av.font.getSize());
   view.setFontStyle(av.font.getStyle());
   view.setRenderGaps(av.renderGaps);
   view.setShowAnnotation(av.getShowAnnotation());
   view.setShowBoxes(av.getShowBoxes());
   view.setShowColourText(av.getColourText());
   view.setShowConservation(av.showConservation);
   view.setShowFullId(av.getShowFullId());
   view.setShowIdentity(av.showIdentity);
   view.setShowQuality(av.showQuality);
   view.setShowSequenceFeatures(av.showSequenceFeatures);
   view.setShowText(av.getShowText());
   view.setWrapAlignment(av.getWrapAlignment());

   jms.addViewport( view );

    object.setJalviewModelSequence(jms);
    object.getVamsasModel().addSequenceSet(vamsasSet);


    try
    {
     if(!fileName.endsWith(".xml"))
              fileName = fileName+".xml";

     JarEntry entry = new JarEntry(fileName);
     jout.putNextEntry(entry);

      object.marshal(out);
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }


  public static void LoadJalviewAlign(String file)
  {
    JalviewModel object = new JalviewModel();
    try{
      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
      JarInputStream jin = new JarInputStream(new FileInputStream(file));
      JarEntry jarentry=null;
      int entryCount = 1;
      do{
        jin = new JarInputStream(new FileInputStream(file));
        for(int i=0; i<entryCount; i++)
          jarentry = jin.getNextJarEntry();

        if(jarentry!=null)
        {
          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
          object = (JalviewModel) object.unmarshal(in);
          LoadFromObject(object);
          entryCount++;
        }
      }while(jarentry!=null);

    }
    catch(Exception ex)
    {   System.out.println("HERE"+ex); return; }

  }

  static void LoadFromObject(JalviewModel object)
  {
     Vector seqids = new Vector();
     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
     Sequence [] vamsasSeq = vamsasSet.getSequence();

     JalviewModelSequence jms = object.getJalviewModelSequence();
     //////////////////////////////////
     //LOAD SEQUENCES
     jalview.datamodel.Sequence [] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
     JSeq [] JSEQ = object.getJalviewModelSequence().getJSeq();
     for(int i=0; i<vamsasSeq.length; i++)
     {
       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
                                                 vamsasSeq[i].getSequence());

       jseqs[i].setStart( JSEQ[i].getStart());
       jseqs[i].setEnd( JSEQ[i].getEnd());
       jseqs[i].setColor( new java.awt.Color(JSEQ[i].getColour()) );
       seqids.add(jseqs[i]);
     }

     /////////////////////////////////
     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
     /////////////////////////////////

     //////////////////////////////////
     //LOAD ANNOTATIONS
     if(vamsasSet.getAnnotation()!=null)
     {
       Annotation[] an = vamsasSet.getAnnotation();
       for (int i = 0; i < an.length; i++)
       {
         AnnotationElement[] ae = an[i].getAnnotationElement();
         jalview.datamodel.Annotation anot[]
             = new jalview.datamodel.Annotation[al.getWidth()];
         for (int aa = 0; aa < ae.length; aa++)
         {
           anot[ae[aa].getPosition()]
               = new jalview.datamodel.Annotation(
                   ae[aa].getDisplayCharacter(),
                   ae[aa].getDescription(),
                   ae[aa].getSecondaryStructure().charAt(0),
                   ae[aa].getValue()
               );
         }


          jalview.datamodel.AlignmentAnnotation jaa = null;
          if(an[i].getGraph())
            jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
                                        an[i].getDescription(), anot,
                                        0,0,1);
          else
            jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
                                        an[i].getDescription(), anot);
          al.addAnnotation(jaa);
       }
     }

      /////////////////////////////////
      // LOAD VIEWPORT
      Viewport[] views = jms.getViewport();
      Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER

      AlignFrame af = new AlignFrame(al);
    //  af.changeColour() );

    /////////////////////////
    //LOAD GROUPS
    if (jms.getJGroupCount()>0)
    {
      JGroup[] groups = jms.getJGroup();
      for (int i = 0; i < groups.length; i++)
      {
       ColourSchemeI cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );
       if (cs instanceof ResidueColourScheme)
         ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
       else if (cs instanceof ScoreColourScheme)
      ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());

        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup
                (groups[i].getName(),
                 cs,
                 groups[i].getDisplayBoxes(),
                 groups[i].getDisplayText(),
                 groups[i].getColourText(),
                 groups[i].getStart(),
                 groups[i].getEnd()) ;
        sg.setOutlineColour( new java.awt.Color(groups[i].getOutlineColour()));
        int [] ids = groups[i].getSeq();
        for(int s=0; s<ids.length; s++)
            sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));

        if(groups[i].getConsThreshold()!=0)
        {
          jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
              ResidueProperties.propHash, 3,
              sg.sequences, 0,
              sg.getWidth() - 1);
          c.calculate();
          c.verdict(false, 25);
          cs = new ConservationColourScheme(c, cs);
          sg.cs = cs;
        }


        al.addGroup(sg);
      }
    }


    Desktop.addInternalFrame(af, view.getTitle(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());
    af.viewport.setStartRes( view.getStartRes() );
    af.viewport.setStartSeq( view.getStartSeq() );
    af.viewport.showConservation = view.getShowConservation();
    af.viewport.showQuality = view.getShowQuality();
    af.viewport.showIdentity= view.getShowIdentity();
    af.viewport.setAbovePIDThreshold( view.getPidSelected() );
    af.viewport.setColourText( view.getShowColourText() );
    af.viewport.setConservationSelected( view.getConservationSelected());
    af.viewport.setShowFullId( view.getShowFullId());
    af.viewport.setFont( new java.awt.Font( view.getFontName(),
                                            view.getFontStyle(),
                                            view.getFontSize()));
    af.alignPanel.fontChanged();
    af.viewport.setRenderGaps( view.getRenderGaps() );

    af.viewport.setWrapAlignment( view.getWrapAlignment() );
    if(view.getWrapAlignment())
    {
      af.alignPanel.setWrapAlignment(view.getWrapAlignment());
    }
    else
    {
      af.viewport.setShowAnnotation(view.getShowAnnotation());
      af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
    }

    af.viewport.setShowBoxes( view.getShowBoxes() );
    af.viewport.setShowText( view.getShowText() );

    af.viewport.setGlobalColourScheme( ColourSchemeProperty.getColour(al, view.getBgColour()));
    af.viewport.setColourAppliesToAllGroups(false);
    af.changeColour( af.viewport.getGlobalColourScheme() );
    af.viewport.setColourAppliesToAllGroups(true);

    ColourSchemeI cs = af.viewport.getGlobalColourScheme();
    if(cs instanceof ConservationColourScheme)
      ( (ConservationColourScheme) cs).inc = view.getConsThreshold();

    if (cs instanceof ResidueColourScheme)
      ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
    else if (cs instanceof ScoreColourScheme)
      ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());

    //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
    if(object.getVamsasModel().getTreeCount()>0)
    {
      try{
        af.ShowNewickTree(new jalview.io.NewickFile(
            (String)object.getVamsasModel().getTree(0)), "Tree");
      }catch(Exception ex){ex.printStackTrace();}
    }

  }
}