X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;fp=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=cf3c7e5ed4027d0fb977666aea2453536139cfc7;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
deleted file mode 100644
index cf3c7e5..0000000
--- a/test/jalview/io/SequenceAnnotationReportTest.java
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@@ -1,382 +0,0 @@
-/*
- * 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.assertTrue;
-
-import jalview.api.FeatureColourI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.io.gff.GffConstants;
-import jalview.renderer.seqfeatures.FeatureRenderer;
-import jalview.schemes.FeatureColour;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
-import java.awt.Color;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import junit.extensions.PA;
-
-public class SequenceAnnotationReportTest
-{
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  @Test(groups = "Functional")
-  public void testAppendFeature_disulfideBond()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-    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);
-    StringBuilder sb = new StringBuilder();
-    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);
-    StringBuilder sb = new StringBuilder();
-    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
-            "group");
-
-    FeatureRendererModel fr = new FeatureRenderer(null);
-    Map<String, float[][]> minmax = fr.getMinMax();
-    sar.appendFeature(sb, 1, fr, 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, fr, 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, fr, sf);
-    assertEquals("METAL 1 3; Fe2-S", sb.toString());
-  }
-
-  @Test(groups = "Functional")
-  public void testAppendFeature_noScore()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-    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());
-  }
-
-  /**
-   * A specific attribute value is included if it is used to colour the feature
-   */
-  @Test(groups = "Functional")
-  public void testAppendFeature_colouredByAttribute()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
-            Float.NaN, "group");
-    sf.setValue("clinical_significance", "Benign");
-
-    /*
-     * first with no colour by attribute
-     */
-    FeatureRendererModel fr = new FeatureRenderer(null);
-    sar.appendFeature(sb, 1, fr, sf);
-    assertEquals("METAL 1 3; Fe2-S", sb.toString());
-
-    /*
-     * then with colour by an attribute the feature lacks
-     */
-    FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
-            null, 5, 10);
-    fc.setAttributeName("Pfam");
-    fr.setColour("METAL", fc);
-    sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
-    assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
-
-    /*
-     * then with colour by an attribute the feature has
-     */
-    fc.setAttributeName("clinical_significance");
-    sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
-    assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
-            sb.toString());
-  }
-
-  @Test(groups = "Functional")
-  public void testAppendFeature_withScoreStatusAttribute()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-    SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
-            "group");
-    sf.setStatus("Confirmed");
-    sf.setValue("clinical_significance", "Benign");
-
-    FeatureRendererModel fr = new FeatureRenderer(null);
-    Map<String, float[][]> minmax = fr.getMinMax();
-    FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
-            null, 12, 22);
-    fc.setAttributeName("clinical_significance");
-    fr.setColour("METAL", fc);
-    minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf);
-
-    assertEquals(
-            "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
-            sb.toString());
-  }
-
-  @Test(groups = "Functional")
-  public void testAppendFeature_DescEqualsType()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-    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);
-    StringBuilder sb = new StringBuilder();
-    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());
-  }
-
-  @Test(groups = "Functional")
-  public void testCreateSequenceAnnotationReport()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-
-    SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
-    seq.setDescription("SeqDesc");
-
-    sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-
-    /*
-     * positional features are ignored
-     */
-    seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5,
-            10, 1f, null));
-    assertEquals("<i><br>SeqDesc</i>", sb.toString());
-
-    /*
-     * non-positional feature
-     */
-    seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f,
-            null));
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-    String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos Score=1.0</i>";
-    assertEquals(expected, sb.toString());
-
-    /*
-     * non-positional features not wanted
-     */
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, false, null);
-    assertEquals("<i><br>SeqDesc</i>", sb.toString());
-
-    /*
-     * add non-pos feature with score inside min-max range for feature type
-     * minmax holds { [positionalMin, positionalMax], [nonPosMin, nonPosMax] }
-     * score is only appended for positional features so ignored here!
-     * minMax are not recorded for non-positional features
-     */
-    seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f,
-            null));
-
-    FeatureRendererModel fr = new FeatureRenderer(null);
-    Map<String, float[][]> minmax = fr.getMinMax();
-    minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
-
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos</i>";
-    assertEquals(expected, sb.toString());
-    
-    /*
-     * 'linkonly' features are ignored; this is obsolete, as linkonly
-     * is only set by DasSequenceFetcher, and DAS is history
-     */
-    SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f,
-            null);
-    sf.setValue("linkonly", Boolean.TRUE);
-    seq.addSequenceFeature(sf);
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    assertEquals(expected, sb.toString()); // unchanged!
-
-    /*
-     * 'clinical_significance' attribute only included when
-     * used for feature colouring
-     */
-    SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
-            5f, null);
-    sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign");
-    seq.addSequenceFeature(sf2);
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana</i>";
-    assertEquals(expected, sb.toString());
-
-    /*
-     * add dbrefs
-     */
-    seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1"));
-    seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419"));
-
-    // with showDbRefs = false
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
-    assertEquals(expected, sb.toString()); // unchanged
-
-    // with showDbRefs = true, colour Variant features by clinical_significance
-    sb.setLength(0);
-    FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
-            null, 2, 3);
-    fc.setAttributeName("clinical_significance");
-    fr.setColour("Variant", fc);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1<br>Metal ; Desc<br>"
-            + "Type1 ; Nonpos<br>Variant ; Havana; clinical_significance=benign</i>";
-    assertEquals(expected, sb.toString());
-    // with showNonPositionalFeatures = false
-    sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
-    expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</i>";
-    assertEquals(expected, sb.toString());
-
-    // see other tests for treatment of status and html
-  }
-
-  /**
-   * Test that exercises an abbreviated sequence details report, with ellipsis
-   * where there are more than 40 different sources, or more than 4 dbrefs for a
-   * single source
-   */
-  @Test(groups = "Functional")
-  public void testCreateSequenceAnnotationReport_withEllipsis()
-  {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuilder sb = new StringBuilder();
-  
-    SequenceI seq = new Sequence("s1", "ABC");
-
-    int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
-    for (int i = 0; i <= maxSources; i++)
-    {
-      seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1"));
-    }
-    
-    int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE");
-    for (int i = 0; i <= maxRefs; i++)
-    {
-      seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i));
-    }
-  
-    sar.createSequenceAnnotationReport(sb, seq, true, true, null, true);
-    String report = sb.toString();
-    assertTrue(report
-            .startsWith("<i><br>UNIPROT P30410, P30411, P30412, P30413,...<br>PDB0 3iu1"));
-    assertTrue(report
-            .endsWith("<br>PDB7 3iu1<br>PDB8,...<br>(Output Sequence Details to list all database references)</i>"));
-  }
-}