test_class.file: base/silent/src/test/java/org/openscience/cdk/silent/BioPolymerTest.java
test_class.identifier: BioPolymerTest
test_class.superclass: extends AbstractBioPolymerTest
test_case.body: @Test
      public void testBioPolymer() {
          IBioPolymer oBioPolymer = new BioPolymer();
          Assert.assertNotNull(oBioPolymer);
          Assert.assertEquals(oBioPolymer.getMonomerCount(), 0);
  
          IStrand oStrand1 = oBioPolymer.getBuilder().newInstance(IStrand.class);
          oStrand1.setStrandName("A");
          IStrand oStrand2 = oBioPolymer.getBuilder().newInstance(IStrand.class);
          oStrand2.setStrandName("B");
          IMonomer oMono1 = oBioPolymer.getBuilder().newInstance(IMonomer.class);
          oMono1.setMonomerName(new String("TRP279"));
          IMonomer oMono2 = oBioPolymer.getBuilder().newInstance(IMonomer.class);
          oMono2.setMonomerName(new String("HOH"));
          IMonomer oMono3 = oBioPolymer.getBuilder().newInstance(IMonomer.class);
          oMono3.setMonomerName(new String("GLYA16"));
          IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C");
  
          oBioPolymer.addAtom(oAtom1);
          oBioPolymer.addAtom(oAtom2, oStrand1);
          oBioPolymer.addAtom(oAtom3, oMono1, oStrand1);
          oBioPolymer.addAtom(oAtom4, oMono2, oStrand2);
          oBioPolymer.addAtom(oAtom5, oMono3, oStrand2);
          Assert.assertNotNull(oBioPolymer.getAtom(0));
          Assert.assertNotNull(oBioPolymer.getAtom(1));
          Assert.assertNotNull(oBioPolymer.getAtom(2));
          Assert.assertNotNull(oBioPolymer.getAtom(3));
          Assert.assertNotNull(oBioPolymer.getAtom(4));
          Assert.assertEquals(oAtom1, oBioPolymer.getAtom(0));
          Assert.assertEquals(oAtom2, oBioPolymer.getAtom(1));
          Assert.assertEquals(oAtom3, oBioPolymer.getAtom(2));
          Assert.assertEquals(oAtom4, oBioPolymer.getAtom(3));
          Assert.assertEquals(oAtom5, oBioPolymer.getAtom(4));
  
          Assert.assertNull(oBioPolymer.getMonomer("0815", "A"));
          Assert.assertNull(oBioPolymer.getMonomer("0815", "B"));
          Assert.assertNull(oBioPolymer.getMonomer("0815", ""));
          Assert.assertNull(oBioPolymer.getStrand(""));
          Assert.assertNotNull(oBioPolymer.getMonomer("TRP279", "A"));
          Assert.assertEquals(oMono1, oBioPolymer.getMonomer("TRP279", "A"));
          Assert.assertEquals(oBioPolymer.getMonomer("TRP279", "A").getAtomCount(), 1);
          Assert.assertNotNull(oBioPolymer.getMonomer("HOH", "B"));
          Assert.assertEquals(oMono2, oBioPolymer.getMonomer("HOH", "B"));
          Assert.assertEquals(oBioPolymer.getMonomer("HOH", "B").getAtomCount(), 1);
          Assert.assertEquals(oBioPolymer.getStrand("B").getAtomCount(), 2);
          Assert.assertEquals(oBioPolymer.getStrand("B").getMonomerCount(), 2);
          Assert.assertNull(oBioPolymer.getStrand("C"));
          Assert.assertNotNull(oBioPolymer.getStrand("B"));
      }
test_case.class_method_signature: BioPolymerTest.testBioPolymer()
test_case.full_signature: @Test public void testBioPolymer()
test_case.identifier: testBioPolymer
test_case.invocations: assertNotNull assertEquals getMonomerCount newInstance getBuilder setStrandName newInstance getBuilder setStrandName newInstance getBuilder setMonomerName newInstance getBuilder setMonomerName newInstance getBuilder setMonomerName newInstance getBuilder newInstance getBuilder newInstance getBuilder newInstance getBuilder newInstance getBuilder addAtom addAtom addAtom addAtom addAtom assertNotNull getAtom assertNotNull getAtom assertNotNull getAtom assertNotNull getAtom assertNotNull getAtom assertEquals getAtom assertEquals getAtom assertEquals getAtom assertEquals getAtom assertEquals getAtom assertNull getMonomer assertNull getMonomer assertNull getMonomer assertNull getStrand assertNotNull getMonomer assertEquals getMonomer assertEquals getAtomCount getMonomer assertNotNull getMonomer assertEquals getMonomer assertEquals getAtomCount getMonomer assertEquals getAtomCount getStrand assertEquals getMonomerCount getStrand assertNull getStrand assertNotNull getStrand
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testBioPolymer()
focal_class.declarator: serialVersionUID = -5001873073769634393L
focal_class.modifier: private static final
focal_class.original_string: private static final long    serialVersionUID = -5001873073769634393L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: strands
focal_class.modifier: private
focal_class.original_string: private Map<String, IStrand> strands;
focal_class.type: Map<String, IStrand>
focal_class.var_name: strands
focal_class.file: base/silent/src/main/java/org/openscience/cdk/silent/BioPolymer.java
focal_class.identifier: BioPolymer
focal_class.interfaces: implements java.io.Serializable, IBioPolymer
focal_class.class_method_signature: BioPolymer.BioPolymer()
focal_class.full_signature: public  BioPolymer()
focal_class.identifier: BioPolymer
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  BioPolymer()
focal_class.class_method_signature: BioPolymer.addAtom(IAtom oAtom, IStrand oStrand)
focal_class.full_signature: @Override public void addAtom(IAtom oAtom, IStrand oStrand)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom oAtom, IStrand oStrand)
focal_class.return: void
focal_class.signature: void addAtom(IAtom oAtom, IStrand oStrand)
focal_class.class_method_signature: BioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.full_signature: @Override public void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.return: void
focal_class.signature: void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.class_method_signature: BioPolymer.getMonomerCount()
focal_class.full_signature: @Override public int getMonomerCount()
focal_class.identifier: getMonomerCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getMonomerCount()
focal_class.class_method_signature: BioPolymer.getMonomer(String monName, String strandName)
focal_class.full_signature: @Override public IMonomer getMonomer(String monName, String strandName)
focal_class.identifier: getMonomer
focal_class.modifiers: @Override public
focal_class.parameters: (String monName, String strandName)
focal_class.return: IMonomer
focal_class.signature: IMonomer getMonomer(String monName, String strandName)
focal_class.class_method_signature: BioPolymer.getMonomerNames()
focal_class.full_signature: @Override public Collection<String> getMonomerNames()
focal_class.identifier: getMonomerNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Collection<String>
focal_class.signature: Collection<String> getMonomerNames()
focal_class.class_method_signature: BioPolymer.getStrandCount()
focal_class.full_signature: @Override public int getStrandCount()
focal_class.identifier: getStrandCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getStrandCount()
focal_class.class_method_signature: BioPolymer.getStrand(String cName)
focal_class.full_signature: @Override public IStrand getStrand(String cName)
focal_class.identifier: getStrand
focal_class.modifiers: @Override public
focal_class.parameters: (String cName)
focal_class.return: IStrand
focal_class.signature: IStrand getStrand(String cName)
focal_class.class_method_signature: BioPolymer.getStrandNames()
focal_class.full_signature: @Override public Collection<String> getStrandNames()
focal_class.identifier: getStrandNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Collection<String>
focal_class.signature: Collection<String> getStrandNames()
focal_class.class_method_signature: BioPolymer.removeStrand(String name)
focal_class.full_signature: @Override public void removeStrand(String name)
focal_class.identifier: removeStrand
focal_class.modifiers: @Override public
focal_class.parameters: (String name)
focal_class.return: void
focal_class.signature: void removeStrand(String name)
focal_class.class_method_signature: BioPolymer.getStrands()
focal_class.full_signature: @Override public Map<String, IStrand> getStrands()
focal_class.identifier: getStrands
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<String, IStrand>
focal_class.signature: Map<String, IStrand> getStrands()
focal_class.class_method_signature: BioPolymer.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_class.class_method_signature: BioPolymer.clone()
focal_class.full_signature: @Override public IBioPolymer clone()
focal_class.identifier: clone
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IBioPolymer
focal_class.signature: IBioPolymer clone()
focal_class.superclass: extends Polymer
focal_method.body: public BioPolymer() {
          super();
          // Strand stuff
          strands = new Hashtable<String, IStrand>();
      }
focal_method.class_method_signature: BioPolymer.BioPolymer()
focal_method.full_signature: public  BioPolymer()
focal_method.identifier: BioPolymer
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  BioPolymer()