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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
[jalview.git]
/
test
/
jalview
/
util
/
DBRefUtilsTest.java
diff --git
a/test/jalview/util/DBRefUtilsTest.java
b/test/jalview/util/DBRefUtilsTest.java
index
96935ce
..
963ca7c
100644
(file)
--- a/
test/jalview/util/DBRefUtilsTest.java
+++ b/
test/jalview/util/DBRefUtilsTest.java
@@
-32,14
+32,24
@@
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import java.util.Arrays;
import java.util.List;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DBRefUtilsTest
{
import org.testng.annotations.Test;
public class DBRefUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the method that selects DBRefEntry items whose source is in a supplied
* list
/**
* Test the method that selects DBRefEntry items whose source is in a supplied
* list
@@
-54,29
+64,36
@@
public class DBRefUtilsTest
DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
// Source is converted to upper-case by this constructor!
DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
// Source is converted to upper-case by this constructor!
DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
- DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 };
+ List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 });
String[] sources = new String[] { "EMBL", "UNIPROT" };
String[] sources = new String[] { "EMBL", "UNIPROT" };
- DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
- assertEquals(3, selected.length);
- assertSame(ref1, selected[0]);
- assertSame(ref2, selected[1]);
- assertSame(ref3, selected[2]);
+ List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(3, selected.size());
+ assertSame(ref1, selected.get(0));
+ assertSame(ref2, selected.get(1));
+ assertSame(ref3, selected.get(2));
sources = new String[] { "EMBL" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
sources = new String[] { "EMBL" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
- assertEquals(1, selected.length);
- assertSame(ref1, selected[0]);
+ assertEquals(1, selected.size());
+ assertSame(ref1, selected.get(0));
sources = new String[] { "UNIPROT" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
sources = new String[] { "UNIPROT" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
- assertEquals(2, selected.length);
- assertSame(ref2, selected[0]);
- assertSame(ref3, selected[1]);
+ assertEquals(2, selected.size());
+ assertSame(ref2, selected.get(0));
+ assertSame(ref3, selected.get(1));
- sources = new String[] { "Uniprot", "EMBLCDS" };
+ sources = new String[] { "EMBLCDS" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
assertNull(selected);
selected = DBRefUtils.selectRefs(dbrefs, sources);
assertNull(selected);
+
+ sources = new String[] { "embl", "uniprot" };
+ selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(3, selected.size());
+ assertSame(ref1, selected.get(0));
+ assertSame(ref2, selected.get(1));
+ assertSame(ref3, selected.get(2));
}
/**
}
/**
@@
-99,6
+116,11
@@
public class DBRefUtilsTest
assertEquals("UNIPROTKB/SWISS-CHEESE",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
assertEquals("UNIPROTKB/SWISS-CHEESE",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
+
+ // these are not 'known' to Jalview
+ assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+ assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
+
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-140,9
+162,9
@@
public class DBRefUtilsTest
{
SequenceI seq = new Sequence("Seq1", "ABCD");
DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
{
SequenceI seq = new Sequence("Seq1", "ABCD");
DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
- DBRefEntry[] refs = seq.getDBRefs();
- assertEquals(1, refs.length);
- assertSame(ref, refs[0]);
+ List<DBRefEntry> refs = seq.getDBRefs();
+ assertEquals(1, refs.size());
+ assertSame(ref, refs.get(0));
assertEquals("EMBL", ref.getSource());
assertEquals("1.2", ref.getVersion());
assertEquals("a7890", ref.getAccessionId());
assertEquals("EMBL", ref.getSource());
assertEquals("1.2", ref.getVersion());
assertEquals("a7890", ref.getAccessionId());
@@
-158,9
+180,12
@@
public class DBRefUtilsTest
SequenceI seq = new Sequence("Seq1", "ABCD");
DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
"1WRI A; 7-80;");
SequenceI seq = new Sequence("Seq1", "ABCD");
DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
"1WRI A; 7-80;");
- DBRefEntry[] refs = seq.getDBRefs();
- assertEquals(1, refs.length);
- assertSame(ref, refs[0]);
+ // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
+ // PDB ref in Stockholm
+
+ List<DBRefEntry> refs = seq.getDBRefs();
+ assertEquals(1, refs.size());
+ assertSame(ref, refs.get(0));
assertEquals("PDB", ref.getSource());
assertEquals("1.2", ref.getVersion());
// DBRef id is pdbId + chain code
assertEquals("PDB", ref.getSource());
assertEquals("1.2", ref.getVersion());
// DBRef id is pdbId + chain code
@@
-193,9
+218,9
@@
public class DBRefUtilsTest
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
- List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3, ref4, ref5 }, target);
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(
+ Arrays.asList(new DBRefEntry[] {
+ ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
@@
-227,9
+252,9
@@
public class DBRefUtilsTest
new int[] { 1, 1 }, 2, 2));
ref3.setMap(map3);
new int[] { 1, 1 }, 2, 2));
ref3.setMap(map3);
- List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3 }, target);
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(
+ Arrays.asList(new DBRefEntry[] {
+ ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
assertEquals(2, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
assertEquals(2, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
@@
-242,7
+267,7
@@
public class DBRefUtilsTest
@Test(groups = { "Functional" })
public void testSearchRefs_accessionid()
{
@Test(groups = { "Functional" })
public void testSearchRefs_accessionid()
{
-
+
DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
// constructor does not upper-case accession id
DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
// constructor does not upper-case accession id
@@
-252,9
+277,9
@@
public class DBRefUtilsTest
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
- DBRefEntry[] dbrefs = new DBRefEntry[] { ref1,
- ref2, ref3, ref4, ref5 };
+
+ List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] {
+ ref1, ref2, ref3, ref4, ref5 });
List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
@@
-270,7
+295,7
@@
public class DBRefUtilsTest
public void testSearchRefs_wildcardAccessionid()
{
DBRefEntry target = new DBRefEntry("EMBL", "2", null);
public void testSearchRefs_wildcardAccessionid()
{
DBRefEntry target = new DBRefEntry("EMBL", "2", null);
-
+
DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
// constructor changes embl to EMBL
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
// constructor changes embl to EMBL
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
@@
-281,10
+306,10
@@
public class DBRefUtilsTest
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
- List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3, ref4, ref5 }, target);
+
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(
+ Arrays.asList(new DBRefEntry[] {
+ ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
assertEquals(4, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
assertEquals(4, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));