X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=bb5d1c4f1a47716ac71ec292a466cdc721917aac;hb=5d003f492184b893aa4c2f437c6021626b573c45;hp=f5515718539f9c7b2455d4e0a474a87187f9c069;hpb=5aa038bdff10329d3b895dceb8d6f5161820a55c;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index f551571..bb5d1c4 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -1,64 +1,146 @@
+/*
+ * 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.datamodel.SequenceFeature;
-
-import java.util.Hashtable;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.api.FeatureColourI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.Mapping;
+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.util.MapList;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+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);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    StringBuilder sb = new StringBuilder();
     sb.append("123456");
-    SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
-            3, 1.2f, "group");
+    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);
+    sar.appendFeature(sb, 2, null, sf, null, 0);
     assertEquals("123456", sb.toString());
 
-    // residuePos == 1 matches start of feature, text appended (but no <br>)
+    // residuePos == 1 matches start of feature, text appended (but no <br/>)
     // feature score is not included
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     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",
+    // <br/> is prefixed once sb.length() > 6
+    sar.appendFeature(sb, 3, null, sf, null, 0);
+    assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3",
             sb.toString());
   }
 
   @Test(groups = "Functional")
+  public void testAppendFeatures_longText()
+  {
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    StringBuilder sb = new StringBuilder();
+    String longString = "Abcd".repeat(50);
+    SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3,
+            "group");
+
+    sar.appendFeature(sb, 1, null, sf, null, 0);
+    assertTrue(sb.length() < 100);
+
+    List<SequenceFeature> sfl = new ArrayList<>();
+    sb.setLength(0);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    sfl.add(sf);
+    int n = sar.appendFeatures(sb, 1, sfl, new FeatureRenderer(null), 200); // text
+                                                                            // should
+                                                                            // terminate
+                                                                            // before
+                                                                            // 200
+                                                                            // characters
+    String s = sb.toString();
+    assertTrue(s.length() < 200);
+    assertEquals(n, 7); // should be 7 features left over
+
+  }
+
+  @Test(groups = "Functional")
   public void testAppendFeature_status()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    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);
+
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     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();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    StringBuilder sb = new StringBuilder();
     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);
+    FeatureRendererModel fr = new FeatureRenderer(null);
+    Map<String, float[][]> minmax = fr.getMinMax();
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     /*
      * map has no entry for this feature type - score is not shown:
      */
@@ -68,9 +150,9 @@ public class SequenceAnnotationReportTest
      * 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",
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
+    // <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());
 
     /*
@@ -78,89 +160,340 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 2f, 2f }, null });
     sb.setLength(0);
-    sar.appendFeature(sb, 1, minmax, sf);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_noScore()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
-  
-    sar.appendFeature(sb, 1, null, sf);
+
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     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_clinicalSignificance()
+  public void testAppendFeature_colouredByAttribute()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    StringBuilder sb = new StringBuilder();
     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());
+
+    /*
+     * first with no colour by attribute
+     */
+    FeatureRendererModel fr = new FeatureRenderer(null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
+    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, null, 0);
+    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, null, 0);
+    assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
+            sb.toString());
   }
 
   @Test(groups = "Functional")
-  public void testAppendFeature_withScoreStatusClinicalSignificance()
+  public void testAppendFeature_withScoreStatusAttribute()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    StringBuilder sb = new StringBuilder();
     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[][]>();
+
+    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, minmax, sf);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
 
-    assertEquals("METAL 1 3; Fe2-S Score=1.3; (Confirmed); Benign",
+    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);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    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);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("Metal");
     // test is case-sensitive:
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Metal", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_stripHtml()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    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);
+
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     // !! strips off </body> but not <body> ??
-    assertEquals("METAL 1 3; <body>hello<em>world</em>",
-            sb.toString());
+    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);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     // 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(false);
+    StringBuilder sb = new StringBuilder();
+
+    SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
+    seq.setDescription("SeqDesc");
+
+    /*
+     * positional features are ignored
+     */
+    seq.addSequenceFeature(
+            new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null));
+    sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+    assertEquals("<i>SeqDesc\n" + "\n" + "</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>SeqDesc\n" + "\n"
+            + "<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>SeqDesc\n\n</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>SeqDesc\n" + "\n"
+            + "<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 is only included in description 
+     * 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>SeqDesc\n" + "\n"
+            + "<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>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
+            + "PDB 3iu1\n"
+            + "<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>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
+            + "PDB 3iu1\n" + "</i>";
+    assertEquals(expected, sb.toString());
+
+    /*
+     * long feature description is truncated with ellipsis
+     */
+    sb.setLength(0);
+    sf2.setDescription(
+            "This is a very long description which should be truncated");
+    sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
+    expected = "<i>SeqDesc\n" + "\n"
+            + "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; This is a very long description which sh...; clinical_significance=benign</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(false);
+    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>\n" + "<br/>\n" + "UNIPROT P30410,\n"
+            + " P30411,\n" + " P30412,\n" + " P30413,...<br/>\n"
+            + "PDB0 3iu1<br/>\n" + "PDB1 3iu1<br/>"));
+    assertTrue(report.endsWith("PDB5 3iu1<br/>\n" + "PDB6 3iu1<br/>\n"
+            + "PDB7 3iu1<br/>\n" + "PDB8,...<br/>\n"
+            + "(Output Sequence Details to list all database references)\n"
+            + "</i>"));
+  }
+
+  /**
+   * Test adding a linked feature to the tooltip
+   */
+  @Test(groups = "Functional")
+  public void testAppendFeature_virtualFeature()
+  {
+    /*
+     * map CDS to peptide sequence
+     */
+    SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+    SequenceI peptide = new Sequence("Peptide/8-14", "PLRFQMD");
+    MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+            3, 1);
+    Mapping mapping = new Mapping(peptide, map);
+
+    /*
+     * assume variant feature found at CDS position 106 G>C
+     */
+    List<SequenceFeature> features = new ArrayList<>();
+    // vary ttg (Leu) to ttc (Phe)
+    SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+            Float.NaN, null);
+    features.add(sf);
+    MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+    StringBuilder sb = new StringBuilder();
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+    sar.appendFeature(sb, 1, null, sf, mf, 0);
+
+    /*
+     * linked feature shown in tooltip in protein coordinates
+     */
+    assertEquals("variant 9; G,C", sb.toString());
+
+    /*
+     * adding "alleles" attribute to variant allows peptide consequence
+     * to be calculated and added to the tooltip
+     */
+    sf.setValue("alleles", "G,C");
+    sb = new StringBuilder();
+    sar.appendFeature(sb, 1, null, sf, mf, 0);
+    assertEquals("variant 9; G,C p.Leu9Phe", sb.toString());
+
+    /*
+     * now a virtual peptide feature on CDS
+     * feature at 11-12 on peptide maps to 110-115 on CDS
+     * here we test for tooltip at 113 (t)
+     */
+    SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, 2.3f,
+            "Uniprot");
+    features.clear();
+    features.add(sf2);
+    mapping = new Mapping(peptide, map);
+    mf = new MappedFeatures(mapping, peptide, 113, 't', features);
+    sb = new StringBuilder();
+    sar.appendFeature(sb, 1, null, sf2, mf, 0);
+    assertEquals("metal 110 115; Fe Score=2.3", sb.toString());
+  }
 }