/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * 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
 * GNU 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.gui;

import jalview.schemes.*;

import java.io.*;

import java.net.*;

import java.util.*;

import java.util.jar.*;

import javax.swing.*;

import org.exolab.castor.xml.*;

import jalview.binding.*;




/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class Jalview2XML_V1
{
   jalview.schemes.UserColourScheme GetUserColourScheme(
        JalviewModelSequence jms, String id)
    {
        UserColours[] uc = jms.getUserColours();
        UserColours colours = null;

        for (int i = 0; i < uc.length; i++)
        {
            if (uc[i].getId().equals(id))
            {
                colours = uc[i];

                break;
            }
        }

        int csize = colours.getUserColourScheme().getColourCount();
        java.awt.Color[] newColours = new java.awt.Color[csize];

        for (int i = 0; i < csize; i++)
        {
            newColours[i] = new java.awt.Color(Integer.parseInt(
                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
        }

        return new jalview.schemes.UserColourScheme(newColours);
    }

    /**
     * DOCUMENT ME!
     *
     * @param file DOCUMENT ME!
     */
    public AlignFrame LoadJalviewAlign(final String file)
    {

        jalview.gui.AlignFrame af = null;

        try
        {
            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
            URL url = null;

            if (file.startsWith("http://"))
            {
                url = new URL(file);
            }

            JarInputStream jin = null;
            JarEntry jarentry = null;
            int entryCount = 1;

            do
            {
                if (url != null)
                {
                    jin = new JarInputStream(url.openStream());
                }
                else
                {
                    jin = new JarInputStream(new FileInputStream(file));
                }

                for (int i = 0; i < entryCount; i++)
                {
                    jarentry = jin.getNextJarEntry();
                  }

                  class NoDescIDResolver implements IDResolver
                  {
                    public Object resolve(String idref)
                    {
                      System.out.println(idref+" used");
                      return null;
                    }
                  }


                if (jarentry != null)
                {
                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
                    JalviewModel object = new JalviewModel();

                    object = (JalviewModel) object.unmarshal(in);

                    af = LoadFromObject(object, file);
                    entryCount++;
                }
            }
            while (jarentry != null);
        }
        catch (final java.net.UnknownHostException ex)
        {
          ex.printStackTrace();
          javax.swing.SwingUtilities.invokeLater(new Runnable()
          {
            public void run()
            {

              System.err.println("Couldn't locate Jalview XML file : " +
                                 ex + "\n");
              JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                                    "Couldn't locate " + file,
                                                    "URL not found",
                                                    JOptionPane.WARNING_MESSAGE);
            }
          });
        }
        catch (Exception ex)
        {
          ex.printStackTrace();
          System.err.println("Exception whilst loading jalview XML file : " +
                             ex + "\n");
          javax.swing.SwingUtilities.invokeLater(new Runnable()
          {
            public void run()
            {

              JOptionPane.showInternalMessageDialog(Desktop.desktop,
                  "Error loading  " + file,
                  "Error loading Jalview file",
                  JOptionPane.WARNING_MESSAGE);
            }
          });
        }

        return af;
    }

    AlignFrame LoadFromObject(JalviewModel object, String file)
    {
        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());
            seqids.add(jseqs[i]);
        }

        ///SequenceFeatures are added to the DatasetSequence,
        // so we must create the dataset before loading features
        /////////////////////////////////
        jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
        al.setDataset(null);
        /////////////////////////////////

        for (int i = 0; i < vamsasSeq.length; i++)
        {
          if (JSEQ[i].getFeaturesCount() > 0)
          {
            Features[] features = JSEQ[i].getFeatures();
            for (int f = 0; f < features.length; f++)
            {
              jalview.datamodel.SequenceFeature sf
                  = new jalview.datamodel.SequenceFeature(features[f].getType(),
                  features[f].getDescription(), features[f].getStatus(),
                  features[f].getBegin(), features[f].getEnd(),
                  null);

              al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
            }
          }
          if (JSEQ[i].getPdbidsCount() > 0)
          {
            Pdbids[] ids = JSEQ[i].getPdbids();
            for (int p = 0; p < ids.length; p++)
            {
              jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
              entry.setId(ids[p].getId());
              entry.setType(ids[p].getType());
              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
            }

          }
        }

         /////////////////////////////////
        //////////////////////////////////
        //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,
                            jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
                }
                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, view.getWidth(), view.getHeight());

        af.setFileName(file, "Jalview");

        for (int i = 0; i < JSEQ.length; i++)
        {
          af.viewport.setSequenceColour(
              af.viewport.alignment.getSequenceAt(i),
              new java.awt.Color(
                  JSEQ[i].getColour()));
        }



        //  af.changeColour() );
        /////////////////////////
        //LOAD GROUPS
        if (jms.getJGroupCount() > 0)
        {
            JGroup[] groups = jms.getJGroup();

            for (int i = 0; i < groups.length; i++)
            {
                ColourSchemeI cs = null;

                if (groups[i].getColour() != null)
                {
                    if (groups[i].getColour().startsWith("ucs"))
                    {
                        cs = GetUserColourScheme(jms, groups[i].getColour());
                    }
                    else
                    {
                        cs = ColourSchemeProperty.getColour(al,
                                groups[i].getColour());
                    }

                    if(cs!=null)
                      cs.setThreshold(groups[i].getPidThreshold(), true);

                }

                Vector seqs = new Vector();
                int[] ids = groups[i].getSeq();

                for (int s = 0; s < ids.length; s++)
                {
                    seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
                            ids[s]));
                }

                jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
                        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()));

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

                al.addGroup(sg);
            }
        }



        af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
            view.getHeight());
        af.viewport.setStartRes(view.getStartRes());
        af.viewport.setStartSeq(view.getStartSeq());
        af.viewport.setShowAnnotation(view.getShowAnnotation());
        af.viewport.setAbovePIDThreshold(view.getPidSelected());
        af.viewport.setColourText(view.getShowColourText());
        af.viewport.setConservationSelected(view.getConservationSelected());
        af.viewport.setShowJVSuffix(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());
        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
        af.viewport.setShowAnnotation(view.getShowAnnotation());
        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
        af.viewport.setShowBoxes(view.getShowBoxes());
        af.viewport.setShowText(view.getShowText());

        ColourSchemeI cs = null;

        if (view.getBgColour() != null)
        {
            if (view.getBgColour().startsWith("ucs"))
            {
                cs = GetUserColourScheme(jms, view.getBgColour());
            }
            else
            {
                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
            }

            if(cs!=null)
            {
              cs.setThreshold(view.getPidThreshold(), true);
              cs.setConsensus(af.viewport.hconsensus);
            }
        }

        af.viewport.setGlobalColourScheme(cs);
        af.viewport.setColourAppliesToAllGroups(false);
        af.changeColour(cs);
        if (view.getConservationSelected() && cs!=null)
        {
          cs.setConservationInc(view.getConsThreshold());
        }

        af.viewport.setColourAppliesToAllGroups(true);
        af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();


        if(jms.getFeatureSettings()!=null)
        {
          af.viewport.featuresDisplayed = new Hashtable();
          String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
         for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
         {
           Setting setting = jms.getFeatureSettings().getSetting(fs);

           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
               new java.awt.Color(setting.getColour()));

           renderOrder[fs] = setting.getType();

           if(setting.getDisplay())
             af.viewport.featuresDisplayed.put(
                 setting.getType(), new Integer(setting.getColour()));
         }
         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
        }

        af.setMenusFromViewport(af.viewport);

        Desktop.addInternalFrame(af, view.getTitle(),
             view.getWidth(), view.getHeight());

        //LOAD TREES
        ///////////////////////////////////////
        if (jms.getTreeCount() > 0)
        {
            try
            {
                for (int t = 0; t < jms.getTreeCount(); t++)
                {

                    Tree tree = jms.getTree(t);

                    TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
                                tree.getNewick()), tree.getTitle(),
                                tree.getWidth(), tree.getHeight(),
                                tree.getXpos(), tree.getYpos());

                    tp.fitToWindow.setState(tree.getFitToWindow());
                    tp.fitToWindow_actionPerformed(null);

                    if(tree.getFontName()!=null)
                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),
                                          tree.getFontStyle(),
                                          tree.getFontSize()));
                    else
                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
                                            view.getFontStyle(),
                                            tree.getFontSize()));

                    tp.showPlaceholders(tree.getMarkUnlinked());
                    tp.showBootstrap(tree.getShowBootstrap());
                    tp.showDistances(tree.getShowDistances());

                    tp.treeCanvas.threshold = tree.getThreshold();

                    if (tree.getCurrentTree())
                      af.viewport.setCurrentTree(tp.getTree());
                }

            }
            catch (Exception ex)
            {
                ex.printStackTrace();
            }

        }

        return af;
    }
}