package jalview.io;

import static org.testng.AssertJUnit.assertEquals;

import jalview.datamodel.SequenceFeature;

import java.util.Hashtable;
import java.util.Map;

import org.testng.annotations.Test;

public class SequenceAnnotationReportTest
{
  @Test(groups = "Functional")
  public void testAppendFeature_disulfideBond()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    sb.append("123456");
    SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
            3, 1.2f, "group");

    // residuePos == 2 does not match start or end of feature, nothing done:
    sar.appendFeature(sb, 2, null, sf);
    assertEquals("123456", sb.toString());

    // residuePos == 1 matches start of feature, text appended (but no <br>)
    // feature score is not included
    sar.appendFeature(sb, 1, null, sf);
    assertEquals("123456disulfide bond 1:3", sb.toString());

    // residuePos == 3 matches end of feature, text appended
    // <br> is prefixed once sb.length() > 6
    sar.appendFeature(sb, 3, null, sf);
    assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
            sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_status()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
            Float.NaN, "group");
    sf.setStatus("Confirmed");

    sar.appendFeature(sb, 1, null, sf);
    assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_withScore()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
            "group");

    Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
    sar.appendFeature(sb, 1, minmax, sf);
    /*
     * map has no entry for this feature type - score is not shown:
     */
    assertEquals("METAL 1 3; Fe2-S", sb.toString());

    /*
     * map has entry for this feature type - score is shown:
     */
    minmax.put("METAL", new float[][] { { 0f, 1f }, null });
    sar.appendFeature(sb, 1, minmax, sf);
    // <br> is appended to a buffer > 6 in length
    assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
            sb.toString());

    /*
     * map has min == max for this feature type - score is not shown:
     */
    minmax.put("METAL", new float[][] { { 2f, 2f }, null });
    sb.setLength(0);
    sar.appendFeature(sb, 1, minmax, sf);
    assertEquals("METAL 1 3; Fe2-S", sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_noScore()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
            Float.NaN, "group");

    sar.appendFeature(sb, 1, null, sf);
    assertEquals("METAL 1 3; Fe2-S", sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_clinicalSignificance()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
            Float.NaN, "group");
    sf.setValue("clinical_significance", "Benign");

    sar.appendFeature(sb, 1, null, sf);
    assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_withScoreStatusClinicalSignificance()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
            "group");
    sf.setStatus("Confirmed");
    sf.setValue("clinical_significance", "Benign");
    Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
    minmax.put("METAL", new float[][] { { 0f, 1f }, null });
    sar.appendFeature(sb, 1, minmax, sf);

    assertEquals("METAL 1 3; Fe2-S Score=1.3; (Confirmed); Benign",
            sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_DescEqualsType()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
            Float.NaN, "group");

    // description is not included if it duplicates type:
    sar.appendFeature(sb, 1, null, sf);
    assertEquals("METAL 1 3", sb.toString());

    sb.setLength(0);
    sf.setDescription("Metal");
    // test is case-sensitive:
    sar.appendFeature(sb, 1, null, sf);
    assertEquals("METAL 1 3; Metal", sb.toString());
  }

  @Test(groups = "Functional")
  public void testAppendFeature_stripHtml()
  {
    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
    StringBuffer sb = new StringBuffer();
    SequenceFeature sf = new SequenceFeature("METAL",
            "<html><body>hello<em>world</em></body></html>", 1, 3,
            Float.NaN, "group");

    sar.appendFeature(sb, 1, null, sf);
    // !! strips off </body> but not <body> ??
    assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());

    sb.setLength(0);
    sf.setDescription("<br>&kHD>6");
    sar.appendFeature(sb, 1, null, sf);
    // if no <html> tag, html-encodes > and < (only):
    assertEquals("METAL 1 3; &lt;br&gt;&kHD&gt;6", sb.toString());
  }
}