X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;fp=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=c5d09c16eeccff48b0a518c82376cc957a7bcc61;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=7958e9bea5be0c232f8f28b162bf2f3ee351ef5f;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 7958e9b..c5d09c1 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,8 +27,12 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentGenerator;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
@@ -39,6 +43,7 @@ import java.util.Iterator;
 import java.util.List;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -50,6 +55,14 @@ import org.testng.annotations.Test;
  */
 public class AlignmentTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // @formatter:off
   private static final String TEST_DATA = 
           "# STOCKHOLM 1.0\n" +
@@ -94,11 +107,11 @@ public class AlignmentTest
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format)
+  protected AlignmentI loadAlignment(final String data, FileFormatI format)
           throws IOException
   {
-    AlignmentI a = new FormatAdapter().readFile(data,
-            AppletFormatAdapter.PASTE, format);
+    AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+            format);
     a.setDataset(null);
     return a;
   }
@@ -577,7 +590,7 @@ public class AlignmentTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
-    al = loadAlignment(TEST_DATA, "STH");
+    al = loadAlignment(TEST_DATA, FileFormat.Stockholm);
     int i = 0;
     for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
     {
@@ -599,6 +612,12 @@ public class AlignmentTest
     AlignmentAnnotation ann = iter.next();
     assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
     assertFalse(iter.hasNext());
+
+    // invalid id
+    anns = al.findAnnotation("CalcIdForD.melanogaster.?");
+    assertFalse(iter.hasNext());
+    anns = al.findAnnotation(null);
+    assertFalse(iter.hasNext());
   }
 
   @Test(groups = { "Functional" })
@@ -643,9 +662,9 @@ public class AlignmentTest
   public void testAlignAs_dnaAsDna() throws IOException
   {
     // aligned cDNA:
-    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
     // unaligned cDNA:
-    AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");
+    AlignmentI al2 = loadAlignment(CDNA_SEQS_2, FileFormat.Fasta);
 
     /*
      * Make mappings between sequences. The 'aligned cDNA' is playing the role
@@ -669,8 +688,8 @@ public class AlignmentTest
   public void testAlignAs_proteinAsCdna() throws IOException
   {
     // see also AlignmentUtilsTests
-    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
-    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
     makeMappings(al1, al2);
 
     // Fudge - alignProteinAsCdna expects mappings to be on protein
@@ -693,8 +712,8 @@ public class AlignmentTest
     /*
      * Load alignments and add mappings for cDNA to protein
      */
-    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
-    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
     makeMappings(al1, al2);
 
     /*
@@ -750,8 +769,8 @@ public class AlignmentTest
      * Load alignments and add mappings from nucleotide to protein (or from
      * first to second if both the same type)
      */
-    AlignmentI al1 = loadAlignment(fromSeqs, "FASTA");
-    AlignmentI al2 = loadAlignment(toSeqs, "FASTA");
+    AlignmentI al1 = loadAlignment(fromSeqs, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(toSeqs, FileFormat.Fasta);
     makeMappings(al1, al2);
 
     /*
@@ -808,9 +827,9 @@ public class AlignmentTest
     String dna1 = "A-Aa-gG-GCC-cT-TT";
     String dna2 = "c--CCGgg-TT--T-AA-A";
     AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1
-            + "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA");
+            + "\n>Dna2/20-31\n" + dna2 + "\n", FileFormat.Fasta);
     AlignmentI al2 = loadAlignment(
-            ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", "FASTA");
+            ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", FileFormat.Fasta);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
     // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
@@ -850,7 +869,7 @@ public class AlignmentTest
   @Test(groups = "Functional")
   public void testCopyConstructor() throws IOException
   {
-    AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE);
+    AlignmentI protein = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
     // create sequence and alignment datasets
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
@@ -887,7 +906,7 @@ public class AlignmentTest
   public void testCreateDatasetAlignment() throws IOException
   {
     AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
-            AppletFormatAdapter.PASTE, "FASTA");
+            DataSourceType.PASTE, FileFormat.Fasta);
     /*
      * create a dataset sequence on first sequence
      * leave the second without one
@@ -1119,4 +1138,135 @@ public class AlignmentTest
     assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
   }
 
+  @Test(groups = { "Functional" })
+  public void testFindGroup()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+    SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+
+    assertNull(a.findGroup(null, 0));
+    assertNull(a.findGroup(seq1, 1));
+    assertNull(a.findGroup(seq1, -1));
+
+    /*
+     * add a group consisting of just "DEF"
+     */
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(3);
+    sg1.setEndRes(5);
+    a.addGroup(sg1);
+
+    assertNull(a.findGroup(seq1, 2)); // position not in group
+    assertNull(a.findGroup(seq1, 6)); // position not in group
+    assertNull(a.findGroup(seq2, 5)); // sequence not in group
+    assertSame(a.findGroup(seq1, 3), sg1); // yes
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * add a group consisting of 
+     * EF--
+     * KLMN
+     */
+    SequenceGroup sg2 = new SequenceGroup();
+    sg2.addSequence(seq1, false);
+    sg2.addSequence(seq2, false);
+    sg2.setStartRes(4);
+    sg2.setEndRes(7);
+    a.addGroup(sg2);
+
+    assertNull(a.findGroup(seq1, 2)); // unchanged
+    assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+    /*
+     * if a residue is in more than one group, method returns
+     * the first found (in order groups were added)
+     */
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * seq2 only belongs to the second group
+     */
+    assertSame(a.findGroup(seq2, 4), sg2);
+    assertSame(a.findGroup(seq2, 5), sg2);
+    assertSame(a.findGroup(seq2, 6), sg2);
+    assertSame(a.findGroup(seq2, 7), sg2);
+    assertNull(a.findGroup(seq2, 3));
+    assertNull(a.findGroup(seq2, 8));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceByIndex()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete -ve index, nothing happens
+    a.deleteSequence(-1);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete beyond end of alignment, nothing happens
+    a.deleteSequence(14);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceBySeq()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(10);
+    a.deleteSequence(seq);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete non-existent sequence, nothing happens
+    seq = new Sequence("cds", "GCCTCGGAT");
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteHiddenSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete a sequence which is hidden, check it is NOT removed from hidden
+    // sequences
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(2);
+    a.getHiddenSequences().hideSequence(seq);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+    a.deleteSequence(2);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+
+    // delete a sequence which is not hidden, check hiddenSequences are not
+    // affected
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 2);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+  }
+
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testSetDataset_selfReference()
+  {
+    SequenceI seq = new Sequence("a", "a");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+    alignment.setDataset(alignment);
+  }
 }