+/*
+ * 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.datamodel;
import static 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;
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}};
-
+ 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));
+ 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);
+ assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
assertNotNull(seq.getContactListFor(aa, 1));
- assertEquals(seq.getContactListFor(aa, 1).getContactAt(1),1.0);
+ assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
assertNotNull(seq.getContactListFor(aa, 2));
- assertEquals(seq.getContactListFor(aa, 2).getContactAt(2),1.0);
+ assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
assertNotNull(seq.getContactListFor(aa, 3));
- assertEquals(seq.getContactListFor(aa, 3).getContactAt(3),1.0);
+ 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));
+ 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);
-
+ 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");
+ 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);
+ assertEquals(cm.getContactAt(0), 1d);
verifyPAEmatrix(seq, aa, 0, 0, 4);
-
+
+ // test clustering
+ paematrix.setGroupSet(
+ GroupSet.makeGroups(paematrix, false, 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));
+ 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);
+
+ 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)));
+ 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)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
// last column
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
+ 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);
+ // check for null on out of bounds
+ ContactListI alcl = alForSeq.getContactListFor(newaa,
+ newaa.annotations.length);
+ assertNull(alcl, "Should've gotten null!");
+ // now check for mapping
+ 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");
+
+ 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);
+
+ 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");
+
+ 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);
+
+ 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.
+ * 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)));
+ 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);
-
+ 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)
+ private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,
+ int topl, int rowl, int rowr)
{
- for (int f=rowl;f<=rowr;f++) {
+ 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);
- assertEquals(clist.getContactAt(f-topl),1d, "for column and row "+f+" relative to "+topl);
- }
+ 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());
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff