/*
 * 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.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;

import jalview.api.FeatureColourI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
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
{

  private static String simpleGffFile = "examples/testdata/simpleGff3.gff";

  @Test(groups = { "Functional" })
  public void testParse() throws Exception
  {
    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 " + "Features file test"
            + "\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(8, sfs.length);
    SequenceFeature sf = sfs[0];
    assertEquals("Pfam family%LINK%", sf.description);
    assertEquals(0, sf.begin);
    assertEquals(0, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("Pfam", sf.type);
    assertEquals(1, sf.links.size());
    assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
            sf.links.get(0));

    sf = sfs[1];
    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[2];
    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[3];
    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[4];
    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[5];
    assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
            sf.description);
    assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
            sf.links.get(0));
    assertEquals(8, sf.begin);
    assertEquals(83, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("Pfam", sf.type);
    sf = sfs[6];
    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[7];
    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));
    assertEquals(89, sf.begin);
    assertEquals(89, sf.end);
    assertEquals("netphos", sf.featureGroup);
    assertEquals("PHOSPHORYLATION (T)", sf.type);
  }

  /**
   * Test parsing a features file with a mix of Jalview and GFF formatted
   * content
   * 
   * @throws Exception
   */
  @Test(groups = { "Functional" })
  public void testParse_mixedJalviewGff() throws Exception
  {
    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();
    // GFF2 uses space as name/value separator in column 9
    String gffData = "METAL\tcc9900\n" + "GFF\n"
            + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
            + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
    FeaturesFile featuresFile = new FeaturesFile(gffData,
            FormatAdapter.PASTE);
    assertTrue("Failed to parse features file",
            featuresFile.parse(al.getDataset(), colours, true));

    // verify colours read or synthesized
    colours = af.getFeatureRenderer().getFeatureColours();
    assertEquals("1 feature group colours not found", 1, colours.size());
    assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));

    // verify feature on FER_CAPAA
    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
            .getSequenceFeatures();
    assertEquals(1, sfs.length);
    SequenceFeature sf = sfs[0];
    assertEquals("Iron-sulfur,2Fe-2S", sf.description);
    assertEquals(44, sf.begin);
    assertEquals(45, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("METAL", sf.type);
    assertEquals(4f, sf.getScore(), 0.001f);

    // verify feature on FER1_SOLLC
    sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
    assertEquals(1, sfs.length);
    sf = sfs[0];
    assertEquals("uniprot", sf.description);
    assertEquals(55, sf.begin);
    assertEquals(130, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("Pfam", sf.type);
    assertEquals(2f, sf.getScore(), 0.001f);
  }

  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, FormatAdapter.FILE,
            new IdentifyFile().identify(ff, FormatAdapter.FILE));

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

  /**
   * Test parsing a features file with GFF formatted content only
   * 
   * @throws Exception
   */
  @Test(groups = { "Functional" })
  public void testParse_pureGff3() throws Exception
  {
    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();
    // GFF3 uses '=' separator for name/value pairs in colum 9
    String gffData = "##gff-version 3\n"
            + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
            + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
            + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
    FeaturesFile featuresFile = new FeaturesFile(gffData,
            FormatAdapter.PASTE);
    assertTrue("Failed to parse features file",
            featuresFile.parse(al.getDataset(), colours, true));

    // verify feature on FER_CAPAA
    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
            .getSequenceFeatures();
    assertEquals(1, sfs.length);
    SequenceFeature sf = sfs[0];
    // description parsed from Note attribute
    assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
    assertEquals(39, sf.begin);
    assertEquals(39, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("METAL", sf.type);
    assertEquals(
            "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
            sf.getValue("ATTRIBUTES"));

    // verify feature on FER1_SOLLC1
    sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
    assertEquals(1, sfs.length);
    sf = sfs[0];
    // ID used for description if available
    assertEquals("$23", sf.description);
    assertEquals(55, sf.begin);
    assertEquals(130, sf.end);
    assertEquals("uniprot", sf.featureGroup);
    assertEquals("Pfam", sf.type);
    assertEquals(3f, sf.getScore(), 0.001f);
  }

  /**
   * Test parsing a features file with Jalview format features (but no colour
   * descriptors or startgroup to give the hint not to parse as GFF)
   * 
   * @throws Exception
   */
  @Test(groups = { "Functional" })
  public void testParse_jalviewFeaturesOnly() throws Exception
  {
    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();

    /*
     * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
     */
    String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
            + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
    FeaturesFile featuresFile = new FeaturesFile(featureData,
            FormatAdapter.PASTE);
    assertTrue("Failed to parse features file",
            featuresFile.parse(al.getDataset(), colours, true));

    // verify FER_CAPAA feature
    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
            .getSequenceFeatures();
    assertEquals(1, sfs.length);
    SequenceFeature sf = sfs[0];
    assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
    assertEquals(39, sf.begin);
    assertEquals(39, sf.end);
    assertEquals("METAL", sf.type);

    // verify FER1_SOLLC feature
    sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
    assertEquals(1, sfs.length);
    sf = sfs[0];
    assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
    assertEquals(86, sf.begin);
    assertEquals(87, sf.end);
    assertEquals("METALLIC", sf.type);
  }

  private void checkDatasetfromSimpleGff3(AlignmentI dataset)
  {
    assertEquals("no sequences extracted from GFF3 file", 2,
            dataset.getHeight());
  
    SequenceI seq1 = dataset.findName("seq1");
    SequenceI seq2 = dataset.findName("seq2");
    assertNotNull(seq1);
    assertNotNull(seq2);
    assertFalse(
            "Failed to replace dummy seq1 with real sequence",
            seq1 instanceof SequenceDummy
                    && ((SequenceDummy) seq1).isDummy());
    assertFalse(
            "Failed to replace dummy seq2 with real sequence",
            seq2 instanceof SequenceDummy
                    && ((SequenceDummy) seq2).isDummy());
    String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
    assertFalse("dummy replacement buggy for seq1",
            placeholderseq.equals(seq1.getSequenceAsString()));
    assertFalse("dummy replacement buggy for seq2",
            placeholderseq.equals(seq2.getSequenceAsString()));
    assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
    assertEquals("Wrong number of features", 3,
            seq1.getSequenceFeatures().length);
    assertNull(seq2.getSequenceFeatures());
    assertEquals(
            "Wrong number of features",
            0,
            seq2.getSequenceFeatures() == null ? 0 : seq2
                    .getSequenceFeatures().length);
    assertTrue(
            "Expected at least one CDNA/Protein mapping for seq1",
            dataset.getCodonFrame(seq1) != null
                    && dataset.getCodonFrame(seq1).size() > 0);
  
  }

  @Test(groups = { "Functional" })
  public void readGff3File() throws IOException
  {
    FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
            FormatAdapter.FILE);
    Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
    gffreader.addProperties(dataset);
    checkDatasetfromSimpleGff3(dataset);
  }

  @Test(groups = { "Functional" })
  public void simpleGff3FileClass() throws IOException
  {
    AlignmentI dataset = new Alignment(new SequenceI[] {});
    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
            FormatAdapter.FILE);
  
    boolean parseResult = ffile.parse(dataset, null, false, false);
    assertTrue("return result should be true", parseResult);
    checkDatasetfromSimpleGff3(dataset);
  }

  @Test(groups = { "Functional" })
  public void simpleGff3FileLoader() throws IOException
  {
    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
            simpleGffFile, FormatAdapter.FILE);
    assertTrue(
            "Didn't read the alignment into an alignframe from Gff3 File",
            af != null);
    checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
  }

  @Test(groups = { "Functional" })
  public void simpleGff3RelaxedIdMatching() throws IOException
  {
    AlignmentI dataset = new Alignment(new SequenceI[] {});
    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
            FormatAdapter.FILE);
  
    boolean parseResult = ffile.parse(dataset, null, false, true);
    assertTrue("return result (relaxedID matching) should be true",
            parseResult);
    checkDatasetfromSimpleGff3(dataset);
  }

  @Test(groups = { "Functional" })
  public void testPrintJalviewFormat() throws Exception
  {
    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();
    String features = "METAL\tcc9900\n"
            + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
            + "Pfam\tred\n"
            + "STARTGROUP\tuniprot\n"
            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
            + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
            + "ENDGROUP\tuniprot\n";
    FeaturesFile featuresFile = new FeaturesFile(features,
            FormatAdapter.PASTE);
    featuresFile.parse(al.getDataset(), colours, false);

    /*
     * first with no features displayed
     */
    FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
    Map<String, FeatureColourI> visible = fr
            .getDisplayedFeatureCols();
    String exported = featuresFile.printJalviewFormat(
            al.getSequencesArray(), visible);
    String expected = "No Features Visible";
    assertEquals(expected, exported);

    /*
     * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
     */
    fr.setVisible("METAL");
    fr.setVisible("GAMMA-TURN");
    visible = fr.getDisplayedFeatureCols();
    exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
            visible);
    expected = "METAL\tcc9900\n"
            + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
            + "\nSTARTGROUP\tuniprot\n"
            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
            + "ENDGROUP\tuniprot\n";
    assertEquals(expected, exported);

    /*
     * now set Pfam visible
     */
    fr.setVisible("Pfam");
    visible = fr.getDisplayedFeatureCols();
    exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
            visible);
    /*
     * note the order of feature types is uncontrolled - derives from
     * FeaturesDisplayed.featuresDisplayed which is a HashSet
     */
    expected = "METAL\tcc9900\n"
            + "Pfam\tff0000\n"
            + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
            + "\nSTARTGROUP\tuniprot\n"
            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
            + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
            + "ENDGROUP\tuniprot\n";
    assertEquals(expected, exported);
  }
}