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Merged
josemduarte merged 41 commits into from
Oct 29, 2021
Merged

Support extended pdbid #950

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6c22796
Support for extended PDBID PDB_nnnnNXXX
aalhossary Jul 27, 2021
dc12461
Some deprecated functions removal
aalhossary Jul 31, 2021
7b08387
Fix typo
aalhossary Aug 3, 2021
c39632c
Targeted most of Spencer's comments
aalhossary Aug 4, 2021
7dd8528
Fixed a bug in PDBId.equals() method
aalhossary Aug 4, 2021
e8466b9
Changing PDBID in SCOP record to lower case
aalhossary Aug 4, 2021
12efad9
public static PDBId field XXXX
aalhossary Sep 22, 2021
d4dfc95
Behavior is now an enum
aalhossary Oct 1, 2021
22e9158
Expose Pattern objects instead of Strings
aalhossary Oct 1, 2021
5c6bcdc
ID stored internally in a reduced format (without initial "PDB_" prefix)
aalhossary Oct 1, 2021
76112f0
Enhancements and bug fix
aalhossary Oct 2, 2021
d95e561
Added BDBId Unit test
aalhossary Oct 2, 2021
f54dd7d
Merge branch 'master' into Support_Extended_PDBID
aalhossary Oct 2, 2021
727aff6
Added @Deprecated codeTag
aalhossary Oct 2, 2021
960a1e6
Adding more TODOs
aalhossary Oct 2, 2021
605c6f8
more replacement of deprecated methods
aalhossary Oct 2, 2021
ec53cee
Removed PDBIdException
aalhossary Oct 9, 2021
fd48eba
review and untouch regular expressions
aalhossary Oct 9, 2021
84d9654
Un-deprecate, copy javadoc, and remove @author on methods
aalhossary Oct 10, 2021
e900fe5
Remove NullPointerException
aalhossary Oct 10, 2021
711fb8a
Bug fix
aalhossary Oct 10, 2021
f92db27
clean commented out code
aalhossary Oct 10, 2021
d9e15e0
Update CHANGELOG
aalhossary Oct 10, 2021
b410f16
Fix unit test
aalhossary Oct 13, 2021
6c8d267
PdbPair does not accept null
aalhossary Oct 12, 2021
a03a657
Addressing reviewer's comments
aalhossary Oct 13, 2021
a55aa95
Change capitalization state
aalhossary Oct 14, 2021
732a2c2
Fix probable NPE + keep consistent PdbId method naming convention
aalhossary Oct 14, 2021
34cb49e
Addressed some of the reviewer's comments.
aalhossary Oct 14, 2021
40a55d2
Use JUnit 5
aalhossary Oct 14, 2021
141d667
PdbId class Documentation
aalhossary Oct 15, 2021
c91a4dc
JavaDoc style update
aalhossary Oct 15, 2021
9ce50fe
Minor updates
aalhossary Oct 15, 2021
0fb6742
Reverting a wrong optimization
aalhossary Oct 15, 2021
02bfee4
Merge branch 'biojavaorigin/master' into Support_Extended_PDBID
aalhossary Oct 16, 2021
0d96963
Adding BioJava development code
aalhossary Oct 16, 2021
87fbc10
Javadoc
aalhossary Oct 21, 2021
17f366e
XXXX PdbId objects are not equal unless they are the same object
aalhossary Oct 22, 2021
ef9cf3f
No more XXXX. ANY malformed PdbId gracefully set to null
aalhossary Oct 23, 2021
02974cd
Addressing Reviewer's comments
aalhossary Oct 26, 2021
108fe97
Removing TODOs
aalhossary Oct 27, 2021
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Added BDBId Unit test
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@aalhossary
aalhossary committed Oct 2, 2021
commit d95e5616d61e42bcefbf7dee2fc0a4d1f7ccc86b
272 changes: 272 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/TestPDBId.java
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package org.biojava.nbio.structure;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.util.Arrays;

import org.biojava.nbio.structure.PDBId.PDBIdException;
import org.junit.Test;

public class TestPDBId {
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@Test
public void testGetIdInDefaultFormat() {
try {
PDBId pdbId = new PDBId("1abc");
String id = pdbId.getId();
assertEquals(id, "1ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
try {
PDBId pdbId = new PDBId("PDB_55551abc");
String id = pdbId.getId();
assertEquals(id, "PDB_55551ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
}

@Test
public void testGetIdPrefereShortFormat() {
try {
PDBId pdbId = new PDBId("1abc");
String id = pdbId.getId(PDBId.Behavior.PREFER_SHORT);
assertEquals(id, "1ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
try {
PDBId pdbId = new PDBId("PDB_55551abc");
String id = pdbId.getId(PDBId.Behavior.PREFER_SHORT);
assertEquals(id, "PDB_55551ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
}

@Test
public void testGetIdPrefereExtendedFormat() {
try {
PDBId pdbId = new PDBId("1abc");
String id = pdbId.getId(PDBId.Behavior.PREFER_EXTENDED);
assertEquals(id, "PDB_00001ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
try {
PDBId pdbId = new PDBId("PDB_55551abc");
String id = pdbId.getId(PDBId.Behavior.PREFER_EXTENDED);
assertEquals(id, "PDB_55551ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
}

@Test
public void testGetIdInShortFormat() {
try {
PDBId pdbId = new PDBId("1abc");
String id = pdbId.getShortId();
assertEquals(id, "1ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Unexpected Exception thrown");
}
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try {
PDBId pdbId = new PDBId("PDB_55551abc");
pdbId.getShortId();
fail("wrongly shortened a non-shortable ID");
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} catch (PDBIdException e) {}
}


@Test
public void testIsShortPDBID() {
assertTrue("Didn't accept lower case", PDBId.isShortPDBID("1abc"));
assertTrue("Didn't accept upper case", PDBId.isShortPDBID("4HHB"));
assertFalse("Accepted wrong format", PDBId.isShortPDBID("HHHB"));
assertFalse("Accepted extended format", PDBId.isShortPDBID("PDB_00001ABC"));
}

@Test
public void testIsExtendedPDBID() {
assertTrue("Didn't accept lower case", PDBId.isExtendedPDBID("PDB_00001abc"));
assertTrue("Didn't accept upper case", PDBId.isExtendedPDBID("PDB_00004HHB"));
assertTrue("Didn't accept upper case", PDBId.isExtendedPDBID("PDB_22224HHB"));
assertFalse("Accepted wrong format", PDBId.isExtendedPDBID("PDB_AAAA4HHB"));
assertFalse("Accepted short format", PDBId.isExtendedPDBID("1ABC"));
}

@Test
public void testIsShortCompatible() {
assertTrue("Didn't accept lower case", PDBId.isShortCompatible("PDB_00001abc"));
assertTrue("Didn't accept upper case", PDBId.isShortCompatible("PDB_00004HHB"));
assertFalse("Accepted short format", PDBId.isShortCompatible("1ABC"));
assertFalse("Accepted wrong format", PDBId.isShortCompatible("PDB_AAAA4HHB"));

//Although this is wrong, returning true is the expected behavior of
// this method; because it does NOT validate the passed in string.
assertTrue("Accepted wrong format", PDBId.isShortCompatible("PDB_0000XXXXXXXXXXXXX"));
}

@Test
public void testToExtendedFormat() {
try {
assertEquals(PDBId.toExtendedId("1abc"), "PDB_00001ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Couldn't extend Id");
}

try {
assertEquals(PDBId.toExtendedId("PDB_00001abc"), "PDB_00001ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Didn't recognize extended format");
}

try {
PDBId.toExtendedId("PDB_aaaa1abc");
fail("Accepted wrong format");
} catch (PDBIdException e) {}
}

@Test
public void testToShortFormat() {
try {
assertEquals(PDBId.toShortId("PDB_00001ABC"), "1ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Couldn't shorten Id");
}

try {
assertEquals(PDBId.toShortId("1abc"), "1ABC");
} catch (PDBIdException e) {
e.printStackTrace();
fail("Didn't recognize short format");
}

try {
PDBId.toShortId("PDB_aaaa1abc");
fail("Accepted wrong format");
} catch (PDBIdException e) {}

try {
PDBId.toShortId("aabc");
fail("Accepted wrong format");
} catch (PDBIdException e) {}
}

@Test
public void testHashCodeAndEquals() {
PDBId id1, id2, id3/* , id4 */;
PDBId other;
try {
id1 = new PDBId("1abc");
id2 = new PDBId("PDB_00001ABC");
id3 = new PDBId("1ABC");
// id4 = new PDBId("pdb_00001abc");
other = new PDBId("2ABC");

assertEquals(id1.hashCode(), id2.hashCode());
assertEquals(id1.hashCode(), id3.hashCode());
// assertEquals(id1.hashCode(), id4.hashCode());
assertNotEquals(id1.hashCode(), other.hashCode());

assertTrue(id1.equals(id2));
assertTrue(id1.equals(id3));
// assertTrue(id1.equals(id4));
assertFalse(id1.equals(other));

} catch (PDBIdException e) {
e.printStackTrace();
fail("unexpected exception thrown");
}
}

@Test
public void testClone() {
PDBId id1, clone;
try {
id1 = new PDBId("1abc");
clone = (PDBId) id1.clone();

assertFalse(id1 == clone);
assertTrue(id1.equals(clone));
assertEquals(id1.hashCode(), clone.hashCode());
} catch (PDBIdException e) {
e.printStackTrace();
fail("unexpected exception thrown");
} catch (CloneNotSupportedException e) {
e.printStackTrace();
fail("unexpected exception thrown while cloning");
}
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}


@Test
public void testCompareTo() {
PDBId id1, id2, id3, id4, id5 ;
PDBId[] array, expected;
try {
id1 = new PDBId("1abc");
id2 = new PDBId("PDB_00011ABC");
id3 = new PDBId("2ABC");
id4 = new PDBId("PDB_00001ABA");
id5 = new PDBId("1100");

array = new PDBId[] {id1, id2, id3, id4, id5};
System.out.println(Arrays.deepToString(array));
Arrays.sort(array);
System.out.println(Arrays.deepToString(array));
expected = new PDBId[] {id5, id4, id1, id3, id2};
System.out.println(Arrays.deepToString(expected));
assertArrayEquals(expected, array);


//let's try to have some "distinct but equal" objects.
id1 = new PDBId("1abc");
id2 = new PDBId("PDB_00011ABC");
id3 = new PDBId("2ABC");
id4 = new PDBId("PDB_00001ABA");
id5 = new PDBId("1ABA");

array = new PDBId[] {id1, id2, id3, id4, id5};
// System.out.println(Arrays.deepToString(array));
Arrays.sort(array);
// System.out.println(Arrays.deepToString(array));
expected = new PDBId[] {id5, id4, id1, id3, id2};
// System.out.println(Arrays.deepToString(expected));
assertArrayEquals(expected, array); // They should be.
//Now let the real test begins
boolean foundEqualButNotTheSame = false;
for (int i = 0; i < expected.length; i++) {
if(expected[i] == array[i]) {
foundEqualButNotTheSame = true;
break;
}
}
assertTrue("Couldn't detect 2 objects that are equal but not the same", foundEqualButNotTheSame);
} catch (PDBIdException e) {
e.printStackTrace();
fail("unexpected exception thrown");
}
}


}