test_class.file: base/silent/src/test/java/org/openscience/cdk/silent/StrandTest.java
test_class.identifier: StrandTest
test_class.superclass: extends AbstractStrandTest
test_case.body: @Test
      public void testStrand() {
          IStrand oStrand = new Strand();
          Assert.assertNotNull(oStrand);
          Assert.assertEquals(oStrand.getMonomerCount(), 0);
  
          IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
          oMono1.setMonomerName(new String("TRP279"));
          IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
          oMono2.setMonomerName(new String("HOH"));
          IMonomer oMono3 = oStrand.getBuilder().newInstance(IMonomer.class);
          oMono3.setMonomerName(new String("GLYA16"));
          IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C");
          IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C");
  
          oStrand.addAtom(oAtom1);
          oStrand.addAtom(oAtom2);
          oStrand.addAtom(oAtom3, oMono1);
          oStrand.addAtom(oAtom4, oMono2);
          oStrand.addAtom(oAtom5, oMono3);
          Assert.assertNotNull(oStrand.getAtom(0));
          Assert.assertNotNull(oStrand.getAtom(1));
          Assert.assertNotNull(oStrand.getAtom(2));
          Assert.assertNotNull(oStrand.getAtom(3));
          Assert.assertNotNull(oStrand.getAtom(4));
          Assert.assertEquals(oAtom1, oStrand.getAtom(0));
          Assert.assertEquals(oAtom2, oStrand.getAtom(1));
          Assert.assertEquals(oAtom3, oStrand.getAtom(2));
          Assert.assertEquals(oAtom4, oStrand.getAtom(3));
          Assert.assertEquals(oAtom5, oStrand.getAtom(4));
  
          Assert.assertNull(oStrand.getMonomer("0815"));
          Assert.assertNotNull(oStrand.getMonomer(""));
          Assert.assertNotNull(oStrand.getMonomer("TRP279"));
          Assert.assertEquals(oMono1, oStrand.getMonomer("TRP279"));
          Assert.assertEquals(oStrand.getMonomer("TRP279").getAtomCount(), 1);
          Assert.assertNotNull(oStrand.getMonomer("HOH"));
          Assert.assertEquals(oMono2, oStrand.getMonomer("HOH"));
          Assert.assertEquals(oStrand.getMonomer("HOH").getAtomCount(), 1);
          Assert.assertEquals(oStrand.getMonomer("").getAtomCount(), 2);
          Assert.assertEquals(oStrand.getAtomCount(), 5);
          Assert.assertEquals(oStrand.getMonomerCount(), 3);
      }
test_case.class_method_signature: StrandTest.testStrand()
test_case.full_signature: @Test public void testStrand()
test_case.identifier: testStrand
test_case.invocations: assertNotNull assertEquals getMonomerCount 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 assertNotNull getMonomer assertNotNull getMonomer assertEquals getMonomer assertEquals getAtomCount getMonomer assertNotNull getMonomer assertEquals getMonomer assertEquals getAtomCount getMonomer assertEquals getAtomCount getMonomer assertEquals getAtomCount assertEquals getMonomerCount
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testStrand()
focal_class.declarator: serialVersionUID = 4200943086350928356L
focal_class.modifier: private static final
focal_class.original_string: private static final long     serialVersionUID = 4200943086350928356L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: monomers
focal_class.modifier: private
focal_class.original_string: private Map<String, IMonomer> monomers;
focal_class.type: Map<String, IMonomer>
focal_class.var_name: monomers
focal_class.declarator: strandName
focal_class.modifier: private
focal_class.original_string: private String                strandName;
focal_class.type: String
focal_class.var_name: strandName
focal_class.declarator: strandType
focal_class.modifier: private
focal_class.original_string: private String                strandType;
focal_class.type: String
focal_class.var_name: strandType
focal_class.file: base/silent/src/main/java/org/openscience/cdk/silent/Strand.java
focal_class.identifier: Strand
focal_class.interfaces: implements java.io.Serializable, IStrand
focal_class.class_method_signature: Strand.Strand()
focal_class.full_signature: public  Strand()
focal_class.identifier: Strand
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  Strand()
focal_class.class_method_signature: Strand.getStrandName()
focal_class.full_signature: @Override public String getStrandName()
focal_class.identifier: getStrandName
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getStrandName()
focal_class.class_method_signature: Strand.getStrandType()
focal_class.full_signature: @Override public String getStrandType()
focal_class.identifier: getStrandType
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getStrandType()
focal_class.class_method_signature: Strand.setStrandName(String cStrandName)
focal_class.full_signature: @Override public void setStrandName(String cStrandName)
focal_class.identifier: setStrandName
focal_class.modifiers: @Override public
focal_class.parameters: (String cStrandName)
focal_class.return: void
focal_class.signature: void setStrandName(String cStrandName)
focal_class.class_method_signature: Strand.setStrandType(String cStrandType)
focal_class.full_signature: @Override public void setStrandType(String cStrandType)
focal_class.identifier: setStrandType
focal_class.modifiers: @Override public
focal_class.parameters: (String cStrandType)
focal_class.return: void
focal_class.signature: void setStrandType(String cStrandType)
focal_class.class_method_signature: Strand.addAtom(IAtom oAtom)
focal_class.full_signature: @Override public void addAtom(IAtom oAtom)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom oAtom)
focal_class.return: void
focal_class.signature: void addAtom(IAtom oAtom)
focal_class.class_method_signature: Strand.addAtom(IAtom oAtom, IMonomer oMonomer)
focal_class.full_signature: @Override public void addAtom(IAtom oAtom, IMonomer oMonomer)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom oAtom, IMonomer oMonomer)
focal_class.return: void
focal_class.signature: void addAtom(IAtom oAtom, IMonomer oMonomer)
focal_class.class_method_signature: Strand.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: Strand.getMonomer(String cName)
focal_class.full_signature: @Override public IMonomer getMonomer(String cName)
focal_class.identifier: getMonomer
focal_class.modifiers: @Override public
focal_class.parameters: (String cName)
focal_class.return: IMonomer
focal_class.signature: IMonomer getMonomer(String cName)
focal_class.class_method_signature: Strand.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: Strand.removeMonomer(String name)
focal_class.full_signature: @Override public void removeMonomer(String name)
focal_class.identifier: removeMonomer
focal_class.modifiers: @Override public
focal_class.parameters: (String name)
focal_class.return: void
focal_class.signature: void removeMonomer(String name)
focal_class.class_method_signature: Strand.getMonomers()
focal_class.full_signature: @Override public Map<String, IMonomer> getMonomers()
focal_class.identifier: getMonomers
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<String, IMonomer>
focal_class.signature: Map<String, IMonomer> getMonomers()
focal_class.class_method_signature: Strand.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: Strand.clone()
focal_class.full_signature: @Override public IStrand clone()
focal_class.identifier: clone
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IStrand
focal_class.signature: IStrand clone()
focal_class.superclass: extends AtomContainer
focal_method.body: public Strand() {
          super();
          // Stand stuff
          monomers = new Hashtable<String, IMonomer>();
          Monomer oMonomer = new Monomer();
          oMonomer.setMonomerName("");
          oMonomer.setMonomerType("UNKNOWN");
          monomers.put("", oMonomer);
          strandName = "";
      }
focal_method.class_method_signature: Strand.Strand()
focal_method.full_signature: public  Strand()
focal_method.identifier: Strand
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  Strand()