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Patch/static analysis 2 #532

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merged 21 commits into from Jan 23, 2019
Merged

Patch/static analysis 2 #532

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0c5207b
Fix IntelliJ inspections, String init, unused monomer variable.
johnmay Jan 10, 2019
b3087c4
Fix redundant if, deprecated method call, and remove unused map field.
johnmay Jan 10, 2019
affc879
Tidy imports.
johnmay Jan 10, 2019
3e8bced
bondMap not needed, stereo in InChI is all atom based.
johnmay Jan 10, 2019
29f3f83
Cleanup HOST descriptors.
johnmay Jan 10, 2019
2f3eee2
Remove unsed sList array.
johnmay Jan 10, 2019
ed0759c
Params should be set on reaction type, clean up code.
johnmay Jan 10, 2019
050f7db
Initial cleanup, this class had a lot of warnings.
johnmay Jan 10, 2019
dfd6f28
Remove unused ZORders
johnmay Jan 10, 2019
b407027
Class cleanup
johnmay Jan 10, 2019
ee48add
Remove unused variable.
johnmay Jan 10, 2019
cd1a7d9
Capturing pseudo atom logic was previously wrong and removed, remove the
johnmay Jan 10, 2019
2fd5929
getDescriptorNames() replicates the redundant code.
johnmay Jan 10, 2019
8429a77
Cleanup
johnmay Jan 10, 2019
065380c
Add test and correct logic, trueBits needs to be set again.
johnmay Jan 10, 2019
fd45bb3
Remove unused atomArom and clean up warnings/style.
johnmay Jan 10, 2019
67c3c22
bondsToHydrogens should be updated here.
johnmay Jan 10, 2019
2cd06ab
Default to warn level.
johnmay Jan 10, 2019
0caedcd
Resolve assertion warnings.
johnmay Jan 10, 2019
07a3a96
Old classic, remove Integer vs int
johnmay Jan 10, 2019
4120c34
Okay maybe a warning rather than a fail, @egonw can decide.
johnmay Jan 10, 2019
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25 changes: 11 additions & 14 deletions base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPolymerTest.java
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Expand Up @@ -56,7 +56,7 @@ public void testAddAtom_IAtom() {
public void testAddAtom_IAtom_IMonomer() {
IPolymer oPolymer = (IPolymer) newChemObject();
IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = null;
IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
Expand Down Expand Up @@ -85,9 +85,9 @@ public void testGetMonomerCount() {
Assert.assertEquals(0, oPolymer.getMonomerCount());

IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
Expand All @@ -104,9 +104,9 @@ public void testGetMonomer_String() {
IPolymer oPolymer = (IPolymer) newChemObject();

IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
Expand All @@ -125,9 +125,9 @@ public void testGetMonomerNames() {
Assert.assertEquals(0, oPolymer.getMonomerNames().size());

IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
Expand All @@ -149,7 +149,7 @@ public void testGetMonomerNames() {
public void testRemoveMonomer_String() {
IPolymer oPolymer = (IPolymer) newChemObject();
IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C");
oPolymer.addAtom(oAtom1, oMono1);
Assert.assertTrue(oPolymer.getMonomerNames().contains(oMono1.getMonomerName()));
Expand All @@ -168,16 +168,13 @@ public void testRemoveMonomer_String() {
public void testToString() {
IPolymer polymer = (IPolymer) newChemObject();
IMonomer oMono1 = polymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = polymer.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom2 = polymer.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = polymer.getBuilder().newInstance(IAtom.class, "C");
polymer.addAtom(oAtom2, oMono1);
polymer.addAtom(oAtom3, oMono2);
Map<String, IMonomer> monomers = new Hashtable<String, IMonomer>();
monomers.put("TRP279", oMono1);
monomers.put("HOH", oMono2);
String description = polymer.toString();
for (int i = 0; i < description.length(); i++) {
Assert.assertTrue('\n' != description.charAt(i));
Expand All @@ -193,7 +190,7 @@ public void testToString() {
public void testClone() throws Exception {
IPolymer polymer = (IPolymer) newChemObject();
Object clone = polymer.clone();
Assert.assertTrue(clone instanceof IPolymer);
Assert.assertNotNull(clone);
}

}
30 changes: 13 additions & 17 deletions base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractStrandTest.java
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Expand Up @@ -89,7 +89,7 @@ public void testAddAtom_IAtom() {
public void testAddAtom_IAtom_IMonomer() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
Expand All @@ -105,9 +105,9 @@ public void testAddAtom_IAtom_IMonomer() {
public void testGetMonomerCount() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
oStrand.addAtom(oAtom2, oMono1);
Expand All @@ -120,9 +120,9 @@ public void testGetMonomerCount() {
public void testGetMonomer_String() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
oStrand.addAtom(oAtom2, oMono1);
Expand All @@ -137,9 +137,9 @@ public void testGetMonomer_String() {
public void testGetMonomerNames() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
oStrand.addAtom(oAtom2, oMono1);
Expand Down Expand Up @@ -167,7 +167,7 @@ public void testGetMonomerNames() {
public void testRemoveMonomer_String() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C");
oStrand.addAtom(oAtom1, oMono1);
Assert.assertTrue(oStrand.getMonomerNames().contains(oMono1.getMonomerName()));
Expand All @@ -181,9 +181,9 @@ public void testRemoveMonomer_String() {
public void testGetMonomers() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
oStrand.addAtom(oAtom2, oMono1);
Expand All @@ -207,20 +207,16 @@ public void testGetMonomers() {
public void testToString() {
IStrand oStrand = (IStrand) newChemObject();
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
oMono1.setMonomerName("TRP279");
IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
oMono2.setMonomerName("HOH");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
oStrand.addAtom(oAtom2, oMono1);
oStrand.addAtom(oAtom3, oMono2);
Map<String, IMonomer> monomers = new Hashtable<String, IMonomer>();
IMonomer oMon = oStrand.getBuilder().newInstance(IMonomer.class);
oMon.setMonomerName("");
oMon.setMonomerType("UNKNOWN");
monomers.put("", oMon);
monomers.put("TRP279", oMono1);
monomers.put("HOH", oMono2);
String description = oStrand.toString();
for (int i = 0; i < description.length(); i++) {
Assert.assertTrue('\n' != description.charAt(i));
Expand All @@ -236,7 +232,7 @@ public void testToString() {
public void testClone() throws Exception {
IStrand strand = (IStrand) newChemObject();
Object clone = strand.clone();
Assert.assertTrue(clone instanceof IStrand);
Assert.assertNotNull(clone);
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}

}