package jalview.io;

import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.json.binding.v1.AlignmentPojo;
import jalview.json.binding.v1.SequenceFeaturesPojo;
import jalview.json.binding.v1.SequencePojo;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;

import java.awt.Color;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;

import com.json.JSONException;

public class BioJsHTMLOutput
{
  private AlignmentViewport av;

  private jalview.api.FeatureRenderer fr;

  private String globalColorScheme;

  private FeaturesDisplayedI displayedFeatures;

  private String jalviewVersion;

  private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";

  public BioJsHTMLOutput(AlignmentPanel ap,
          FeatureRenderer fr1)
  {

    jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
    webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
            "www.jalview.org", "http://www.jalview.org")
            + "/services/launchApp";
    if (ap != null)
    {
      this.av = ap.av;
      this.globalColorScheme = ColourSchemeProperty.getColourName(av
              .getGlobalColourScheme());
      this.fr = ap.cloneFeatureRenderer();
      displayedFeatures = av.getFeaturesDisplayed();
    }
  }

  private void exportJalviewAlignmentAsBioJsHtmlFile()
  {
    try
    {
      String outputFile = getOutputFile();
      String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
              .getAlignment());
      String bioJSTemplateString = getBioJsTemplateAsString(this);
      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
              .replaceAll(
"#sequenceData#", jalviewAlignmentJson)
              .toString();

      PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
              outputFile));
      out.print(generatedBioJsWithJalviewAlignmentAsJson);
      out.flush();
      out.close();
      jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
    } catch (NoFileSelectedException ex)
    {
      // do noting if no file was selected
    } catch (Exception e)
    {
      e.printStackTrace();
    }
  }

  public String getOutputFile() throws NoFileSelectedException
  {
    String selectedFile = null;
    JalviewFileChooser jvFileChooser = new JalviewFileChooser(
            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
            { "html" }, new String[]
            { "HTML files" }, "HTML files");
    jvFileChooser.setFileView(new JalviewFileView());

    // TODO uncomment when supported by MassageManager
    jvFileChooser.setDialogTitle(MessageManager
            .getString("label.save_as_biojs_html"));
    jvFileChooser.setDialogTitle("save as BioJs HTML");
    jvFileChooser.setToolTipText(MessageManager.getString("action.save"));

    int fileChooserOpt = jvFileChooser.showSaveDialog(null);
    if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
    {
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
              .getSelectedFile().getParent());
      selectedFile = jvFileChooser.getSelectedFile().getPath();
    }
    else
    {
      throw new NoFileSelectedException("No file was selected.");
    }

    return selectedFile;
  }

  public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
          throws IOException, JSONException
  {
    AlignmentPojo bjsAlignment = new AlignmentPojo();

    // bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
    // bjsAlignment.setJalviewVersion(jalviewVersion);
    // bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);

    int count = 0;
    for (SequenceI seq : alignment.getSequences())
    {
      StringBuilder name = new StringBuilder();
      name.append(seq.getName()).append("/").append(seq.getStart())
              .append("-").append(seq.getEnd());

      SequencePojo seqPojo = new SequencePojo();
      seqPojo.setId(String.valueOf(++count));
      seqPojo.setEnd(seq.getEnd());
      seqPojo.setStart(seq.getStart());
      seqPojo.setName(name.toString());
      seqPojo.setSeq(seq.getSequenceAsString());

      SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
      if (seqFeatures != null)
      {
        ArrayList<SequenceFeaturesPojo> bjsSeqFeatures = new ArrayList<SequenceFeaturesPojo>();
        for (SequenceFeature sf : seqFeatures)
        {
          if (displayedFeatures != null
                  && displayedFeatures.isVisible(sf.getType()))
          {

            // TODO: translate graduated/complex colourschemes to biojs model
            String featureColour = jalview.util.Format.getHexString(fr
                    .findFeatureColour(Color.white, seq,
                            seq.findIndex(sf.getBegin())));
            // SequenceFeaturesPojo bjsFeature = new SequenceFeaturesPojo();
            // bjsFeature.setFillColor(featureColour);
            // bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
            // bjsFeature.setXend(seq.findIndex(sf.getEnd()));
            // bjsFeature.setType(sf.getType());
            // bjsSeqFeatures.add(bjsFeature);
          }
        }
        // seqPojo.setFeatures(bjsSeqFeatures);
      }
      bjsAlignment.getSeqs().add(seqPojo);
    }

    return new com.json.JSONObject(bjsAlignment).toString()
            .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
  }

  public static String getBioJsTemplateAsString(Object currentObj)
          throws IOException
  {
    InputStreamReader isReader = null;
    BufferedReader buffReader = null;
    StringBuilder sb = new StringBuilder();
    URL url = currentObj.getClass().getResource(
            "/templates/BioJSTemplate.txt");
    if (url != null)
    {
      try
      {
        isReader = new InputStreamReader(url.openStream());
        buffReader = new BufferedReader(isReader);
        String line;
        String lineSeparator = System.getProperty("line.separator");
        while ((line = buffReader.readLine()) != null)
        {
          sb.append(line).append(lineSeparator);
        }

      } catch (Exception ex)
      {
        ex.printStackTrace();
      } finally
      {
        if (isReader != null)
        {
          isReader.close();
        }

        if (buffReader != null)
        {
          buffReader.close();
        }
      }
    }
    return sb.toString();
  }

  public String getGlobalColorScheme()
  {
    return globalColorScheme;
  }

  public void setGlobalColorScheme(String globalColorScheme)
  {
    this.globalColorScheme = globalColorScheme;
  }

}