X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FPAEContactMatrixTest.java;fp=test%2Fjalview%2Fdatamodel%2FPAEContactMatrixTest.java;h=67edb37da53fef7cf3511f07fe8d5fe488b36752;hb=5652c334235561d2b533a292969e2fb8566d8dac;hp=0000000000000000000000000000000000000000;hpb=65ed1da9a1710a9ce132c7edfce54955dc1ddf99;p=jalview.git

diff --git a/test/jalview/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
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+++ b/test/jalview/datamodel/PAEContactMatrixTest.java
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+package jalview.datamodel;
+
+import static org.testng.Assert.*;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.SeqsetUtils;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+import jalview.ws.datamodel.MappableContactMatrixI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+
+public class PAEContactMatrixTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  static float[][] PAEdata = { { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f },
+      { 2.0f, 1.0f, 2.0f, 3.0f, 4.0f },
+      { 3.0f, 2.0f, 1.0f, 2.0f, 3.0f },
+      { 4.0f, 3.0f, 2.0f, 1.0f, 2.0f },
+      { 5.0f, 4.0f, 3.0f, 2.0f, 1.0f } };
+
+  /**
+   * test associations for a PAE matrix
+   */
+  @Test(groups = { "Functional" })
+  public void testSeqAssociatedPAEMatrix()
+  {
+    Sequence seq = new Sequence("Seq", "ASDQE");
+    AlignmentAnnotation aa = seq
+            .addContactList(new PAEContactMatrix(seq, PAEdata));
+    assertNotNull(seq.getContactListFor(aa, 0));
+    assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
+    assertNotNull(seq.getContactListFor(aa, 1));
+    assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
+    assertNotNull(seq.getContactListFor(aa, 2));
+    assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
+    assertNotNull(seq.getContactListFor(aa, 3));
+    assertEquals(seq.getContactListFor(aa, 3).getContactAt(3), 1.0);
+    assertNotNull(seq.getContactListFor(aa, 4));
+    assertEquals(seq.getContactListFor(aa, 4).getContactAt(4), 1.0);
+
+    assertNotNull(seq.getContactListFor(aa, seq.getEnd() - 1));
+    assertNull(seq.getContactListFor(aa, seq.getEnd()));
+
+    ContactListI cm = seq.getContactListFor(aa, seq.getStart());
+    assertEquals(cm.getContactAt(seq.getStart()), 1d);
+    verifyPAEmatrix(seq, aa, 0, 0, 4);
+
+    // Now associated with sequence not starting at 1
+    seq = new Sequence("Seq/5-9", "ASDQE");
+    ContactMatrixI paematrix = new PAEContactMatrix(seq, PAEdata);
+    aa = seq.addContactList(paematrix);
+    assertNotNull(aa);
+    // individual annotation elements need to be distinct for Matrix associated
+    // rows
+    Annotation ae5 = aa.getAnnotationForPosition(5);
+    Annotation ae6 = aa.getAnnotationForPosition(6);
+    assertNotNull(ae5);
+    assertNotNull(ae6);
+    assertTrue(ae5 != ae6);
+
+    cm = seq.getContactListFor(aa, 0);
+    assertEquals(cm.getContactAt(0), 1d);
+    verifyPAEmatrix(seq, aa, 0, 0, 4);
+
+    // test clustering
+    paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
+
+    // remap - test the MappableContactMatrix.liftOver method
+    SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    Mapping sqmap = new Mapping(seq,
+            new MapList(new int[]
+            { 5, 8, 10, 10 }, new int[] { 5, 9 }, 1, 1));
+    assertTrue(paematrix instanceof MappableContactMatrixI);
+
+    MappableContactMatrixI remapped = ((MappableContactMatrixI) paematrix)
+            .liftOver(newseq, sqmap);
+    assertTrue(remapped instanceof PAEContactMatrix);
+
+    AlignmentAnnotation newaa = newseq.addContactList(remapped);
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
+    // no mapping for position 9
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
+    // last column
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
+
+    // verify MappedPositions includes discontinuity
+    int[] mappedCl = newseq.getContactListFor(newaa, 5)
+            .getMappedPositionsFor(0, 4);
+    assertEquals(4, mappedCl.length,
+            "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+    // make it harder.
+
+    SequenceI alseq = newseq.getSubSequence(6, 10);
+    alseq.insertCharAt(2, 2, '-');
+    AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
+    newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
+            null);
+    ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+    assertNotNull(alcl);
+    mappedCl = alcl.getMappedPositionsFor(0, 4);
+    assertNotNull(mappedCl);
+    assertEquals(4, mappedCl.length,
+            "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+    // remap2 - test with original matrix map from 1-5 remapped to 5-9
+
+    seq = new Sequence("Seq/1-5", "ASDQE");
+    paematrix = new PAEContactMatrix(seq, PAEdata);
+    assertTrue(paematrix instanceof MappableContactMatrixI);
+    aa = seq.addContactList(paematrix);
+
+    newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    sqmap = new Mapping(seq,
+            new MapList(new int[]
+            { 5, 9 }, new int[] { 1, 5 }, 1, 1));
+
+    remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
+    assertTrue(remapped instanceof PAEContactMatrix);
+
+    newaa = newseq.addContactList(remapped);
+    verify_mapping(newseq, newaa);
+
+    // remap3 - remap2 but mapping sense in liftover is reversed
+
+    seq = new Sequence("Seq/1-5", "ASDQE");
+    paematrix = new PAEContactMatrix(seq, PAEdata);
+    assertTrue(paematrix instanceof MappableContactMatrixI);
+    aa = seq.addContactList(paematrix);
+
+    newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    sqmap = new Mapping(newseq,
+            new MapList(new int[]
+            { 1, 5 }, new int[] { 5, 9 }, 1, 1));
+
+    remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
+    assertTrue(remapped instanceof PAEContactMatrix);
+
+    newaa = newseq.addContactList(remapped);
+    verify_mapping(newseq, newaa);
+  }
+
+  /**
+   * checks that the PAE matrix is located at positions 1-9 in newseq, and
+   * columns are not truncated.
+   * 
+   * @param newseq
+   * @param newaa
+   */
+  private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)
+  {
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
+    // last column should be null this time
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
+
+    verifyPAEmatrix(newseq, newaa, 4, 4, 8);
+  }
+
+  private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,
+          int topl, int rowl, int rowr)
+  {
+    int[] mappedCl;
+    for (int f = rowl; f <= rowr; f++)
+    {
+      ContactListI clist = seq.getContactListFor(aa, f);
+      assertNotNull(clist, "No ContactListI for position " + (f));
+      assertEquals(clist.getContactAt(0), (double) f - topl + 1,
+              "for column " + f + " relative to " + topl);
+      mappedCl = clist.getMappedPositionsFor(0, 0);
+      assertNotNull(mappedCl);
+      assertEquals(mappedCl[0], mappedCl[1]);
+      assertEquals(mappedCl[0], seq.findIndex(seq.getStart() + topl));
+      assertEquals(clist.getContactAt(f - topl), 1d,
+              "for column and row " + f + " relative to " + topl);
+    }
+  }
+
+  /**
+   * check mapping and resolution methods work
+   */
+  @Test(groups= {"Functional"})
+  public void testMappableContactMatrix() {
+    SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    MapList map = new MapList(new int[]
+            { 5, 9 }, new int[] { 1, 5 }, 1, 1);
+    AlignmentAnnotation aa = newseq
+            .addContactList(new PAEContactMatrix(newseq,map, PAEdata,null));
+    ContactListI clist = newseq.getContactListFor(aa, 4);
+    assertNotNull(clist);
+    clist = newseq.getContactListFor(aa, 3);
+    assertNull(clist);
+    
+    ContactMatrixI cm = newseq.getContactMatrixFor(aa);
+    MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+    int[] pos = mcm.getMappedPositionsFor(newseq, 0);
+    assertNull(pos);
+
+    pos = mcm.getMappedPositionsFor(newseq, 1);
+    assertNotNull(pos);
+    assertEquals(pos[0],4+newseq.getStart());
+    
+    pos = mcm.getMappedPositionsFor(newseq, 6); // after end of matrix
+    assertNull(pos);
+    pos = mcm.getMappedPositionsFor(newseq, 5); // at end of matrix
+    assertNotNull(pos);
+    assertEquals(pos[0],8+newseq.getStart());
+    SequenceI alseq = newseq.deriveSequence();
+    alseq.insertCharAt(5,'-');
+    pos = mcm.getMappedPositionsFor(alseq, 5); // at end of matrix
+    assertNotNull(pos);
+    assertEquals(pos[0],8+newseq.getStart());
+    
+    
+  }
+}