/*
 * 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.io;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;

import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.gui.AlignFrame;

import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.Map;

import org.testng.annotations.Test;

public class FeaturesFileTest
{

  static String TestFiles[][] = { { "Test example features import/export",
      "examples/uniref50.fa", "examples/exampleFeatures.txt" } };

  @Test(groups = { "Functional" })
  public void testParse() throws Exception
  {
    testFeaturesFileIO("Features file test");
  }

  public static AlignmentI readAlignmentFile(File f) throws IOException
  {
    System.out.println("Reading file: " + f);
    String ff = f.getPath();
    FormatAdapter rf = new FormatAdapter();

    AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
            new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));

    al.setDataset(null); // creates dataset sequences
    assertNotNull("Couldn't read supplied alignment data.", al);
    return al;
  }

  /**
   * Helper method for testing
   * 
   * @param testname
   * @param f
   *          alignment file
   * @param featFile
   *          features file to load on to the alignment
   * @throws IOException
   */
  public static void testFeaturesFileIO(String testname) throws IOException
  {
    File f = new File("examples/uniref50.fa");
    AlignmentI al = readAlignmentFile(f);
    AlignFrame af = new AlignFrame(al, 500, 500);
    Map<String, FeatureColourI> colours = af.getFeatureRenderer()
            .getFeatureColours();
    FeaturesFile featuresFile = new FeaturesFile(
            "examples/exampleFeatures.txt", FormatAdapter.FILE);
    assertTrue("Test " + testname + "\nFailed to parse features file.",
            featuresFile.parse(al.getDataset(), colours, true));

    /*
     * Refetch the colour map from the FeatureRenderer (to confirm it has been
     * updated - JAL-1904), and verify (some) feature group colours
     */
    colours = af.getFeatureRenderer().getFeatureColours();
    assertEquals("26 feature group colours not found", 26, colours.size());
    assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
    assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));

    /*
     * verify (some) features on sequences
     */
    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
            .getSequenceFeatures(); // FER_CAPAA
    assertEquals(7, sfs.length);
    SequenceFeature sf = sfs[0];
    assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
    assertEquals(39, sf.begin);
    assertEquals(39, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("METAL", sf.type);
    sf = sfs[1];
    assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
    assertEquals(44, sf.begin);
    assertEquals(44, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("METAL", sf.type);
    sf = sfs[2];
    assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
    assertEquals(47, sf.begin);
    assertEquals(47, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("METAL", sf.type);
    sf = sfs[3];
    assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
    assertEquals(77, sf.begin);
    assertEquals(77, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("METAL", sf.type);
    sf = sfs[4];
    assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
            sf.description);
    assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
            sf.links.get(0).toString());
    assertEquals(8, sf.begin);
    assertEquals(83, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("Pfam", sf.type);
    sf = sfs[5];
    assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
    assertEquals(3, sf.begin);
    assertEquals(93, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("Cath", sf.type);
    sf = sfs[6];
    assertEquals(
            "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
            sf.description);
    assertEquals(
            "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
            sf.links.get(0).toString());
    assertEquals(89, sf.begin);
    assertEquals(89, sf.end);
    assertEquals("netphos", sf.featureGroup);
    assertEquals("PHOSPHORYLATION (T)", sf.type);
  }
}