+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.util;
import static org.testng.AssertJUnit.assertEquals;
public class MapListTest
{
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSomething()
{
- MapList ml = new MapList(new int[]
- { 1, 5, 10, 15, 25, 20 }, new int[]
- { 51, 1 }, 1, 3);
- MapList ml1 = new MapList(new int[]
- { 1, 3, 17, 4 }, new int[]
- { 51, 1 }, 1, 3);
- MapList ml2 = new MapList(new int[]
- { 1, 60 }, new int[]
- { 1, 20 }, 3, 1);
+ MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
+ 51, 1 }, 1, 3);
+ MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 },
+ new int[] { 51, 1 }, 1, 3);
+ MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3,
+ 1);
// test internal consistency
int to[] = new int[51];
testMap(ml, 1, 60);
- MapList mldna = new MapList(new int[]
- { 2, 2, 6, 8, 12, 16 }, new int[]
+ MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 }, new int[]
{ 1, 3 }, 3, 1);
int[] frm = mldna.locateInFrom(1, 1);
- testLocateFrom(mldna, 1, 1, new int[]
- { 2, 2, 6, 7 });
+ testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
testMap(mldna, 1, 3);
/*
* for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
if (mmap[1][i - 1] == -1)
{
System.out.print(i + "=XXX");
-
+
}
else
{
if (mmap[1][i - 1] == -1)
{
System.out.print(i + "=XXX");
-
+
}
else
{
* Tests for method that locates ranges in the 'from' map for given range in
* the 'to' map.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testLocateInFrom_noIntrons()
{
/*
* Simple mapping with no introns
*/
- int[] codons = new int[]
- { 1, 12 };
- int[] protein = new int[]
- { 1, 4 };
+ int[] codons = new int[] { 1, 12 };
+ int[] protein = new int[] { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
* Tests for method that locates ranges in the 'from' map for given range in
* the 'to' map.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testLocateInFrom_withIntrons()
{
/*
* Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
* 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
*/
- int[] codons =
- { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
- int[] protein =
- { 1, 4 };
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
* Tests for method that locates ranges in the 'to' map for given range in the
* 'from' map.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testLocateInTo_noIntrons()
{
/*
* Simple mapping with no introns
*/
- int[] codons = new int[]
- { 1, 12 };
- int[] protein = new int[]
- { 1, 4 };
+ int[] codons = new int[] { 1, 12 };
+ int[] protein = new int[] { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
* Tests for method that locates ranges in the 'to' map for given range in the
* 'from' map.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testLocateInTo_withIntrons()
{
/*
* Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
* 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
*/
- int[] codons =
- { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
/*
* Mapped proteins at positions 1, 3, 4, 6 in the sequence
*/
- int[] protein =
- { 1, 1, 3, 4, 6, 6 };
+ int[] protein = { 1, 1, 3, 4, 6, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
/*
/**
* Test equals method.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testEquals()
{
- int[] codons = new int[]
- { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
- int[] protein = new int[]
- { 1, 4 };
+ int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = new int[] { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
MapList ml1 = new MapList(codons, protein, 3, 1); // same values
MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
/**
* Test for the method that flattens a list of ranges into a single array.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetRanges()
{
List<int[]> ranges = new ArrayList<int[]>();
- ranges.add(new int[]
- { 2, 3 });
- ranges.add(new int[]
- { 5, 6 });
+ ranges.add(new int[] { 2, 3 });
+ ranges.add(new int[] { 5, 6 });
assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
}
/**
* Check state after construction
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConstructor()
{
- int[] codons =
- { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
- int[] protein =
- { 1, 1, 3, 4, 6, 6 };
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = { 1, 1, 3, 4, 6, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals(3, ml.getFromRatio());
assertEquals(2, ml.getFromLowest());
/**
* Test the method that creates an inverse mapping
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetInverse()
{
- int[] codons =
- { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
- int[] protein =
- { 1, 1, 3, 4, 6, 6 };
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = { 1, 1, 3, 4, 6, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
MapList ml2 = ml.getInverse();
prettyPrint(ml2.getFromRanges()));
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testToString()
{
- MapList ml = new MapList(new int[]
- { 1, 5, 10, 15, 25, 20 }, new int[]
- { 51, 1 }, 1, 3);
+ MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
+ 51, 1 }, 1, 3);
String s = ml.toString();
assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
s);
git://source.jalview.org / jalview.git / blobdiff