/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * 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/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.gui;

import jalview.analysis.Conservation;
import jalview.binding.Annotation;
import jalview.binding.AnnotationElement;
import jalview.binding.Features;
import jalview.binding.JGroup;
import jalview.binding.JSeq;
import jalview.binding.JalviewModel;
import jalview.binding.JalviewModelSequence;
import jalview.binding.Pdbids;
import jalview.binding.Sequence;
import jalview.binding.SequenceSet;
import jalview.binding.Setting;
import jalview.binding.Tree;
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;

import java.io.InputStreamReader;
import java.io.Reader;
import java.net.UnknownHostException;
import java.util.Hashtable;
import java.util.Vector;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class Jalview2XML_V1
{
  boolean raiseGUI = true;

  public Jalview2XML_V1()
  {

  };

  public Jalview2XML_V1(boolean raiseGUI)
  {
    this.raiseGUI = raiseGUI;
  };

  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 jarInputStreamProvider jprovider)
  {
    final String file = jprovider.getFilename();
    jalview.gui.AlignFrame af = null;

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

      do
      {
        jin = jprovider.getJarInputStream();

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

        if (jarentry != null)
        {
          entryCount++;
          if (jarentry.getName().endsWith(".xml"))
          {
            Reader in = new InputStreamReader(jin, "UTF-8");
            JalviewModel object = new JalviewModel();

            object = object.unmarshal(in);

            af = LoadFromObject(object, file);
          }
        }
        jin.close();
      } while (jarentry != null);
    } catch (final UnknownHostException ex)
    {
      ex.printStackTrace();
      if (raiseGUI)
      {
        javax.swing.SwingUtilities.invokeLater(new Runnable()
        {
          @Override
          public void run()
          {

            System.err.println(
                    "Couldn't locate Jalview XML file : " + ex + "\n");
            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                    MessageManager.formatMessage("label.couldnt_locate",
                            new String[]
                            { file }),
                    MessageManager.getString("label.url_not_found"),
                    JvOptionPane.WARNING_MESSAGE);
          }
        });
      }
      ;
    } catch (Exception ex)
    {
      System.err.println("Exception whilst loading jalview XML file : ");
      ex.printStackTrace();
      if (raiseGUI)
      {
        javax.swing.SwingUtilities.invokeLater(new Runnable()
        {
          @Override
          public void run()
          {

            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                    MessageManager.formatMessage(
                            "label.error_loading_file_params", new String[]
                            { file }),
                    MessageManager
                            .getString("label.error_loading_jalview_file"),
                    JvOptionPane.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++)
        {
          SequenceFeature sf = new SequenceFeature(features[f].getType(),
                  features[f].getDescription(), features[f].getBegin(),
                  features[f].getEnd(), null);
          sf.setStatus(features[f].getStatus());
          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());
          if (ids[p].getType() != null)
          {
            if (ids[p].getType().equalsIgnoreCase("PDB"))
            {
              entry.setType(PDBEntry.Type.PDB);
            }
            else
            {
              entry.setType(PDBEntry.Type.FILE);
            }
          }
          al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
          StructureSelectionManager
                  .getStructureSelectionManager(Desktop.instance)
                  .registerPDBEntry(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, FileFormat.Jalview);

    for (int i = 0; i < JSEQ.length; i++)
    {
      af.viewport.setSequenceColour(
              af.viewport.getAlignment().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.getColourScheme(al,
                    groups[i].getColour());
          }
        }
        int pidThreshold = groups[i].getPidThreshold();

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

        for (int s = 0; s < ids.length; s++)
        {
          seqs.addElement(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.getGroupColourScheme().setThreshold(pidThreshold, true);

        sg.setOutlineColour(
                new java.awt.Color(groups[i].getOutlineColour()));

        if (groups[i].getConsThreshold() != 0)
        {
          Conservation c = new Conservation("All", sg.getSequences(null), 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.getRanges().setStartRes(view.getStartRes());
    // startSeq set in af.alignPanel.updateLayout below
    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()), true);

    af.viewport.setRenderGaps(view.getRenderGaps());
    af.viewport.setWrapAlignment(view.getWrapAlignment());

    af.viewport.setShowAnnotation(view.isShowAnnotation());
    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.getColourScheme(al, view.getBgColour());
      }

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

    af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
            true);
    af.viewport.getResidueShading()
            .setConsensus(af.viewport.getSequenceConsensusHash());
    af.viewport.setColourAppliesToAllGroups(false);
    af.alignPanel.updateLayout();
    af.changeColour(cs);
    if (view.getConservationSelected() && cs != null)
    {
      af.viewport.getResidueShading()
              .setConservationInc(view.getConsThreshold());
    }

    af.viewport.setColourAppliesToAllGroups(true);
    af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());

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

        featureColours.put(setting.getType(),
                new java.awt.Color(setting.getColour()));

        renderOrder[fs] = setting.getType();

        if (setting.getDisplay())
        {
          featuresDisplayed.put(setting.getType(),
                  new Integer(setting.getColour()));
        }
      }
      FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
              new Hashtable(), featureColours, 1.0f, null);
      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
              .transferSettings(frs);
    }

    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.getTreeCanvas().setThreshold(tree.getThreshold());

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

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

    }

    return af;
  }
}