From: <eg...@us...> - 2007-10-30 16:01:27
|
Revision: 9259 http://cdk.svn.sourceforge.net/cdk/?rev=9259&view=rev Author: egonw Date: 2007-10-30 09:01:16 -0700 (Tue, 30 Oct 2007) Log Message: ----------- Unsafe to use global parameters in JUnit tests. Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/test/smiles/smarts/parser/SMARTSSearchTest.java Modified: trunk/cdk/src/org/openscience/cdk/test/smiles/smarts/parser/SMARTSSearchTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/smiles/smarts/parser/SMARTSSearchTest.java 2007-10-30 15:05:09 UTC (rev 9258) +++ trunk/cdk/src/org/openscience/cdk/test/smiles/smarts/parser/SMARTSSearchTest.java 2007-10-30 16:01:16 UTC (rev 9259) @@ -49,8 +49,6 @@ * @cdk.require ant1.6 */ public class SMARTSSearchTest extends CDKTestCase { - private int nmatch; - private int nqmatch; private LoggingTool logger; @@ -64,17 +62,18 @@ } - private void match(String smarts, String smiles) throws Exception { + private int[] match(String smarts, String smiles) throws Exception { SMARTSQueryTool sqt = new SMARTSQueryTool(smarts, true); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer atomContainer = sp.parseSmiles(smiles); boolean status = sqt.matches(atomContainer); if (status) { - nmatch = sqt.countMatches(); - nqmatch = sqt.getUniqueMatchingAtoms().size(); + return new int[] { + sqt.countMatches(), + sqt.getUniqueMatchingAtoms().size() + }; } else { - nmatch = 0; - nqmatch = 0; + return new int[]{0,0}; } } @@ -91,8 +90,8 @@ boolean status = sqt.matches(atomContainer); assertEquals(true, status); - nmatch = sqt.countMatches(); - nqmatch = sqt.getUniqueMatchingAtoms().size(); + int nmatch = sqt.countMatches(); + int nqmatch = sqt.getUniqueMatchingAtoms().size(); assertEquals(3, nmatch); assertEquals(3, nqmatch); @@ -251,165 +250,165 @@ * From http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html */ public void testPropertyCharge1() throws Exception { - match("[+1]", "[OH-].[Mg+2]"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[+1]", "[OH-].[Mg+2]"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyCharge2() throws Exception { - match("[+1]", "COCC(O)Cn1ccnc1[N+](=O)[O-]"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[+1]", "COCC(O)Cn1ccnc1[N+](=O)[O-]"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyCharge3() throws Exception { - match("[+1]", "[NH4+]"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[+1]", "[NH4+]"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyCharge4() throws Exception { - match("[+1]", "CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[+1]", "CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyCharge5() throws Exception { - match("[+1]", "[Cl-].[Cl-].NC(=O)c2cc[n+](COC[n+]1ccccc1C=NO)cc2"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[+1]", "[Cl-].[Cl-].NC(=O)c2cc[n+](COC[n+]1ccccc1C=NO)cc2"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyAromatic1() throws Exception { - match("[a]", "c1cc(C)c(N)cc1"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[a]", "c1cc(C)c(N)cc1"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAromatic2() throws Exception { - match("[a]", "c1c(C)c(N)cnc1"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[a]", "c1c(C)c(N)cnc1"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAromatic3() throws Exception { - match("[a]", "c1(C)c(N)cco1"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[a]", "c1(C)c(N)cco1"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyAromatic4() throws Exception { - match("[a]", "c1c(C)c(N)c[nH]1"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[a]", "c1c(C)c(N)c[nH]1"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyAromatic5() throws Exception { - match("[a]", "O=n1ccccc1"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[a]", "O=n1ccccc1"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAromatic6() throws Exception { - match("[a]", "[O-][n+]1ccccc1"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[a]", "[O-][n+]1ccccc1"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAromatic7() throws Exception { - match("[a]", "c1ncccc1C1CCCN1C"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[a]", "c1ncccc1C1CCCN1C"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAromatic8() throws Exception { - match("[a]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[a]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAliphatic1() throws Exception { - match("[A]", "c1cc(C)c(N)cc1"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[A]", "c1cc(C)c(N)cc1"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyAliphatic2() throws Exception { - match("[A]", "CCO"); - assertEquals(3, nmatch); - assertEquals(3, nqmatch); + int[] results = match("[A]", "CCO"); + assertEquals(3, results[0]); + assertEquals(3, results[1]); } public void testPropertyAliphatic3() throws Exception { - match("[A]", "C=CC=CC=C"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[A]", "C=CC=CC=C"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAliphatic4() throws Exception { - match("[A]", "CC(C)(C)C"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[A]", "CC(C)(C)C"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyAliphatic5() throws Exception { - match("[A]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); - assertEquals(15, nmatch); - assertEquals(15, nqmatch); + int[] results = match("[A]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); + assertEquals(15, results[0]); + assertEquals(15, results[1]); } public void testPropertyAliphatic6() throws Exception { - match("[A]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); - assertEquals(19, nmatch); - assertEquals(19, nqmatch); + int[] results = match("[A]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); + assertEquals(19, results[0]); + assertEquals(19, results[1]); } public void testPropertyAtomicNumber1() throws Exception { - match("[#6]", "c1cc(C)c(N)cc1"); - assertEquals(7, nmatch); - assertEquals(7, nqmatch); + int[] results = match("[#6]", "c1cc(C)c(N)cc1"); + assertEquals(7, results[0]); + assertEquals(7, results[1]); } public void testPropertyAtomicNumber2() throws Exception { - match("[#6]", "CCO"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[#6]", "CCO"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyAtomicNumber3() throws Exception { - match("[#6]", "C=CC=CC=C-O"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[#6]", "C=CC=CC=C-O"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); } public void testPropertyAtomicNumber4() throws Exception { - match("[#6]", "CC(C)(C)C"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[#6]", "CC(C)(C)C"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyAtomicNumber5() throws Exception { - match("[#6]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(20, nmatch); - assertEquals(20, nqmatch); + int[] results = match("[#6]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(20, results[0]); + assertEquals(20, results[1]); } public void testPropertyAtomicNumber6() throws Exception { - match("[#6]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(17, nmatch); - assertEquals(17, nqmatch); + int[] results = match("[#6]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(17, results[0]); + assertEquals(17, results[1]); } public void testPropertyAtomicNumber7() throws Exception { - match("[#6]", "C123C5C(OC(=O)C)C=CC2C(N(C)CC1)Cc(ccc4OC(=O)C)c3c4O5"); - assertEquals(21, nmatch); - assertEquals(21, nqmatch); + int[] results = match("[#6]", "C123C5C(OC(=O)C)C=CC2C(N(C)CC1)Cc(ccc4OC(=O)C)c3c4O5"); + assertEquals(21, results[0]); + assertEquals(21, results[1]); } public void testPropertyR1() throws Exception { - match("[R2]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); - assertEquals(7, nmatch); - assertEquals(7, nqmatch); + int[] results = match("[R2]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); + assertEquals(7, results[0]); + assertEquals(7, results[1]); } public void testPropertyR2() throws Exception { @@ -417,635 +416,635 @@ // the AtomContainer. No R2 matches this part. // Commented to pass the test /* - match("[R2]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(6, nmatch); - assertEquals(6, nqmatch); + int[] results = match("[R2]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(6, results[0]); + assertEquals(6, results[1]); */ } public void testPropertyR3() throws Exception { - match("[R2]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(4, nmatch); - assertEquals(4, nqmatch); + int[] results = match("[R2]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(4, results[0]); + assertEquals(4, results[1]); } public void testPropertyR4() throws Exception { - match("[R2]", "C123C5C(OC(=O)C)C=CC2C(N(C)CC1)Cc(ccc4OC(=O)C)c3c4O5"); - assertEquals(4, nmatch); - assertEquals(4, nqmatch); + int[] results = match("[R2]", "C123C5C(OC(=O)C)C=CC2C(N(C)CC1)Cc(ccc4OC(=O)C)c3c4O5"); + assertEquals(4, results[0]); + assertEquals(4, results[1]); } public void testPropertyR5() throws Exception { - match("[R2]", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[R2]", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyr1() throws Exception { - match("[r5]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); - assertEquals(9, nmatch); - assertEquals(9, nqmatch); + int[] results = match("[r5]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); + assertEquals(9, results[0]); + assertEquals(9, results[1]); } public void testPropertyr2() throws Exception { - match("[r5]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[r5]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyr3() throws Exception { - match("[r5]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[r5]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyr4() throws Exception { - match("[r5]", "C123C5C(OC(=O)C)C=CC2C(N(C)CC1)Cc(ccc4OC(=O)C)c3c4O5"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[r5]", "C123C5C(OC(=O)C)C=CC2C(N(C)CC1)Cc(ccc4OC(=O)C)c3c4O5"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyr5() throws Exception { - match("[r5]", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[r5]", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyValence1() throws Exception { - match("[v4]", "C"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[v4]", "C"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyValence2() throws Exception { - match("[v4]", "CCO"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[v4]", "CCO"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyValence3() throws Exception { - match("[v4]", "[NH4+]"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[v4]", "[NH4+]"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyValence4() throws Exception { - match("[v4]", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O"); - assertEquals(16, nmatch); - assertEquals(16, nqmatch); + int[] results = match("[v4]", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O"); + assertEquals(16, results[0]); + assertEquals(16, results[1]); } public void testPropertyValence5() throws Exception { - match("[v4]", "[Cl-].[Cl-].NC(=O)c2cc[n+](COC[n+]1ccccc1C=NO)cc2"); - assertEquals(16, nmatch); - assertEquals(16, nqmatch); + int[] results = match("[v4]", "[Cl-].[Cl-].NC(=O)c2cc[n+](COC[n+]1ccccc1C=NO)cc2"); + assertEquals(16, results[0]); + assertEquals(16, results[1]); } public void testPropertyX1() throws Exception { - match("[X2]", "CCO"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[X2]", "CCO"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyX2() throws Exception { - match("[X2]", "O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[X2]", "O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyX3() throws Exception { - match("[X2]", "CCC(=O)CC"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[X2]", "CCC(=O)CC"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyX4() throws Exception { - match("[X2]", "FC(Cl)=C=C(Cl)F"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[X2]", "FC(Cl)=C=C(Cl)F"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyX5() throws Exception { - match("[X2]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(3, nmatch); - assertEquals(3, nqmatch); + int[] results = match("[X2]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(3, results[0]); + assertEquals(3, results[1]); } public void testPropertyX6() throws Exception { - match("[X2]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(3, nmatch); - assertEquals(3, nqmatch); + int[] results = match("[X2]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(3, results[0]); + assertEquals(3, results[1]); } public void testPropertyD1() throws Exception { - match("[D2]", "CCO"); - assertEquals(1, nmatch); + int[] results = match("[D2]", "CCO"); + assertEquals(1, results[0]); } public void testPropertyD2() throws Exception { - match("[D2]", "O"); - assertEquals(0, nmatch); + int[] results = match("[D2]", "O"); + assertEquals(0, results[0]); } public void testPropertyD3() throws Exception { - match("[D2]", "CCC(=O)CC"); - assertEquals(2, nmatch); + int[] results = match("[D2]", "CCC(=O)CC"); + assertEquals(2, results[0]); } public void testPropertyD4() throws Exception { - match("[D2]", "FC(Cl)=C=C(Cl)F"); - assertEquals(1, nmatch); + int[] results = match("[D2]", "FC(Cl)=C=C(Cl)F"); + assertEquals(1, results[0]); } public void testPropertyD5() throws Exception { - match("[D2]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(12, nmatch); + int[] results = match("[D2]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(12, results[0]); } public void testPropertyD6() throws Exception { - match("[D2]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(8, nmatch); + int[] results = match("[D2]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(8, results[0]); } public void testPropertyHAtom1() throws Exception { - match("[H]", "[H+].[Cl-]"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[H]", "[H+].[Cl-]"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyHAtom2() throws Exception { - match("[H]", "[2H]"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[H]", "[2H]"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyHAtom3() throws Exception { - match("[H]", "[H][H]"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[H]", "[H][H]"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyHAtom4() throws Exception { - match("[H]", "[CH4]"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[H]", "[CH4]"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyHAtom5() throws Exception { - match("[H]", "[H]C([H])([H])[H]"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[H]", "[H]C([H])([H])[H]"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyHTotal1() throws Exception { - match("[H1]", "CCO"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[H1]", "CCO"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyHTotal2() throws Exception { - match("[H1]", "[2H]C#C"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[H1]", "[2H]C#C"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyHTotal3() throws Exception { - match("[H1]", "[H]C(C)(C)C"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[H1]", "[H]C(C)(C)C"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyHTotal4() throws Exception { - match("[H1]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(11, nmatch); - assertEquals(11, nqmatch); + int[] results = match("[H1]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(11, results[0]); + assertEquals(11, results[1]); } public void testPropertyHTotal5() throws Exception { - match("[H1]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(10, nmatch); - assertEquals(10, nqmatch); + int[] results = match("[H1]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(10, results[0]); + assertEquals(10, results[1]); } public void testPropertyHTotal6() throws Exception { - match("[H1]", "[H][H]"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[H1]", "[H][H]"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyAnyAtom1() throws Exception { - match("[*]", "C"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[*]", "C"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyAnyAtom2() throws Exception { - match("[*]", "[2H]C"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[*]", "[2H]C"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyAnyAtom3() throws Exception { - match("[*]", "[H][H]"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[*]", "[H][H]"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testPropertyAnyAtom4() throws Exception { - match("[*]", "[1H]C([1H])([1H])[1H]"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[*]", "[1H]C([1H])([1H])[1H]"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testPropertyAtomicMass1() throws Exception { - match("[13C]", "[13C]"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[13C]", "[13C]"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyAtomicMass2() throws Exception { - match("[13C]", "[C]"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[13C]", "[C]"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testPropertyAtomicMass3() throws Exception { - match("[13*]", "[13C]Cl"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[13*]", "[13C]Cl"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testPropertyAtomicMass4() throws Exception { - match("[12C]", "CCl"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[12C]", "CCl"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testBondSingle1() throws Exception { - match("CC", "C=C"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("CC", "C=C"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testBondSingle2() throws Exception { - match("CC", "C#C"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("CC", "C#C"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testBondSingle3() throws Exception { - match("CC", "CCO"); - assertEquals(2, nmatch); - assertEquals(1, nqmatch); + int[] results = match("CC", "CCO"); + assertEquals(2, results[0]); + assertEquals(1, results[1]); } public void testBondSingle4() throws Exception { - match("CC", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); - assertEquals(28, nmatch); - assertEquals(14, nqmatch); + int[] results = match("CC", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); + assertEquals(28, results[0]); + assertEquals(14, results[1]); } public void testBondSingle5() throws Exception { - match("CC", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O"); - assertEquals(14, nmatch); - assertEquals(7, nqmatch); + int[] results = match("CC", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O"); + assertEquals(14, results[0]); + assertEquals(7, results[1]); } public void testBondAny1() throws Exception { - match("C~C", "C=C"); - assertEquals(2, nmatch); - assertEquals(1, nqmatch); + int[] results = match("C~C", "C=C"); + assertEquals(2, results[0]); + assertEquals(1, results[1]); } public void testBondAny2() throws Exception { - match("C~C", "C#C"); - assertEquals(2, nmatch); - assertEquals(1, nqmatch); + int[] results = match("C~C", "C#C"); + assertEquals(2, results[0]); + assertEquals(1, results[1]); } public void testBondAny3() throws Exception { - match("C~C", "CCO"); - assertEquals(2, nmatch); - assertEquals(1, nqmatch); + int[] results = match("C~C", "CCO"); + assertEquals(2, results[0]); + assertEquals(1, results[1]); } public void testBondAny4() throws Exception { - match("C~C", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); - assertEquals(38, nmatch); - assertEquals(19, nqmatch); + int[] results = match("C~C", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1"); + assertEquals(38, results[0]); + assertEquals(19, results[1]); } public void testBondAny5() throws Exception { - match("[C,c]~[C,c]", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O"); - assertEquals(28, nmatch); - assertEquals(14, nqmatch); + int[] results = match("[C,c]~[C,c]", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O"); + assertEquals(28, results[0]); + assertEquals(14, results[1]); } public void testBondRing1() throws Exception { - match("C@C", "C=C"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("C@C", "C=C"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testBondRing2() throws Exception { - match("C@C", "C#C"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("C@C", "C#C"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testBondRing3() throws Exception { - match("C@C", "C1CCCCC1"); - assertEquals(12, nmatch); - assertEquals(6, nqmatch); + int[] results = match("C@C", "C1CCCCC1"); + assertEquals(12, results[0]); + assertEquals(6, results[1]); } public void testBondRing4() throws Exception { - match("[C,c]@[C,c]", "c1ccccc1Cc1ccccc1"); - assertEquals(24, nmatch); - assertEquals(12, nqmatch); + int[] results = match("[C,c]@[C,c]", "c1ccccc1Cc1ccccc1"); + assertEquals(24, results[0]); + assertEquals(12, results[1]); } public void testBondRing5() throws Exception { - match("[C,c]@[C,c]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); - assertEquals(30, nmatch); - assertEquals(15, nqmatch); + int[] results = match("[C,c]@[C,c]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); + assertEquals(30, results[0]); + assertEquals(15, results[1]); } public void testBondRing6() throws Exception { - match("[C,c]@[C,c]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); - assertEquals(44, nmatch); - assertEquals(22, nqmatch); + int[] results = match("[C,c]@[C,c]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); + assertEquals(44, results[0]); + assertEquals(22, results[1]); } //TODO: Stereo bond not implemented in smiles parser. Commented. /* public void testBondStereo1() throws Exception { - match("F/?C=C/Cl", "F/C=C/Cl"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("F/?C=C/Cl", "F/C=C/Cl"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testBondStereo2() throws Exception { - match("F/?C=C/Cl", "FC=C/Cl"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("F/?C=C/Cl", "FC=C/Cl"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testBondStereo3() throws Exception { - match("F/?C=C/Cl", "FC=CCl"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("F/?C=C/Cl", "FC=CCl"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testBondStereo4() throws Exception { - match("F/?C=C/Cl", "F\\C=C/Cl"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("F/?C=C/Cl", "F\\C=C/Cl"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } */ public void testLogicalNot1() throws Exception { - match("[!c]", "c1cc(C)c(N)cc1"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[!c]", "c1cc(C)c(N)cc1"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testLogicalNot2() throws Exception { - match("[!c]", "c1c(C)c(N)cnc1"); - assertEquals(3, nmatch); - assertEquals(3, nqmatch); + int[] results = match("[!c]", "c1c(C)c(N)cnc1"); + assertEquals(3, results[0]); + assertEquals(3, results[1]); } public void testLogicalNot3() throws Exception { - match("[!c]", "c1(C)c(N)cco1"); - assertEquals(3, nmatch); - assertEquals(3, nqmatch); + int[] results = match("[!c]", "c1(C)c(N)cco1"); + assertEquals(3, results[0]); + assertEquals(3, results[1]); } public void testLogicalNot4() throws Exception { - match("[!c]", "c1c(C)c(N)c[nH]1"); - assertEquals(3, nmatch); - assertEquals(3, nqmatch); + int[] results = match("[!c]", "c1c(C)c(N)c[nH]1"); + assertEquals(3, results[0]); + assertEquals(3, results[1]); } public void testLogicalNot5() throws Exception { - match("[!c]", "O=n1ccccc1"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[!c]", "O=n1ccccc1"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testLogicalNot6() throws Exception { - match("[!c]", "[O-][n+]1ccccc1"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[!c]", "[O-][n+]1ccccc1"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testLogicalNot7() throws Exception { - match("[!c]", "c1ncccc1C1CCCN1C"); - assertEquals(7, nmatch); - assertEquals(7, nqmatch); + int[] results = match("[!c]", "c1ncccc1C1CCCN1C"); + assertEquals(7, results[0]); + assertEquals(7, results[1]); } public void testLogicalNot8() throws Exception { - match("[!c]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC"); - assertEquals(16, nmatch); - assertEquals(16, nqmatch); + int[] results = match("[!c]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC"); + assertEquals(16, results[0]); + assertEquals(16, results[1]); } public void testLogicalOr1() throws Exception { - match("[N,O,o]", "c1cc(C)c(N)cc1"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[N,O,o]", "c1cc(C)c(N)cc1"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testLogicalOr2() throws Exception { - match("[N,O,o]", "c1c(C)c(N)cnc1"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[N,O,o]", "c1c(C)c(N)cnc1"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testLogicalOr3() throws Exception { - match("[N,O,o]", "c1(C)c(N)cco1"); - assertEquals(2, nmatch); - assertEquals(2, nqmatch); + int[] results = match("[N,O,o]", "c1(C)c(N)cco1"); + assertEquals(2, results[0]); + assertEquals(2, results[1]); } public void testLogicalOr4() throws Exception { - match("[N,O,o]", "c1c(C)c(N)c[nH]1"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[N,O,o]", "c1c(C)c(N)c[nH]1"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testLogicalOr5() throws Exception { - match("[N,O,o]", "O=n1ccccc1"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[N,O,o]", "O=n1ccccc1"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testLogicalOr6() throws Exception { - match("[N,O,o]", "[O-][n+]1ccccc1"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[N,O,o]", "[O-][n+]1ccccc1"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testLogicalOr7() throws Exception { - match("[N,O,o]", "c1ncccc1C1CCCN1C"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[N,O,o]", "c1ncccc1C1CCCN1C"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testLogicalOr8() throws Exception { - match("[N,O,o]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[N,O,o]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } public void testLogicalOrHighAnd1() throws Exception { - match("[N,#6&+1,+0]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); - assertEquals(24, nmatch); - assertEquals(24, nqmatch); + int[] results = match("[N,#6&+1,+0]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); + assertEquals(24, results[0]); + assertEquals(24, results[1]); } public void testLogicalOrHighAnd2() throws Exception { - match("[N,#6&+1,+0]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); - assertEquals(25, nmatch); - assertEquals(25, nqmatch); + int[] results = match("[N,#6&+1,+0]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); + assertEquals(25, results[0]); + assertEquals(25, results[1]); } public void testLogicalOrHighAnd3() throws Exception { - match("[N,#6&+1,+0]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(24, nmatch); - assertEquals(24, nqmatch); + int[] results = match("[N,#6&+1,+0]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(24, results[0]); + assertEquals(24, results[1]); } public void testLogicalOrHighAnd4() throws Exception { - match("[N,#6&+1,+0]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(21, nmatch); - assertEquals(21, nqmatch); + int[] results = match("[N,#6&+1,+0]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(21, results[0]); + assertEquals(21, results[1]); } public void testLogicalOrHighAnd5() throws Exception { - match("[N,#6&+1,+0]", "N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3"); - assertEquals(17, nmatch); - assertEquals(17, nqmatch); + int[] results = match("[N,#6&+1,+0]", "N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3"); + assertEquals(17, results[0]); + assertEquals(17, results[1]); } /* public void testLogicalOrHighAnd6() throws Exception { //TODO: This takes a long time to match long start = Calendar.getInstance().getTimeInMillis(); - //match("[N,#6&+1,+0]", "[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24"); + //int[] results = match("[N,#6&+1,+0]", "[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24"); new SmilesParser(DefaultChemObjectBuilder.getInstance()); SMARTSParser.parse("[N,#6&+1,+0]"); long end = Calendar.getInstance().getTimeInMillis(); System.out.println( (end - start) ); - //assertEquals(23, nmatch); + //assertEquals(23, results[0]); } */ public void testLogicalOrHighAnd7() throws Exception { - match("[N,#6&+1,+0]", "[Cl-].Clc1ccc([I+]c2cccs2)cc1"); - assertEquals(12, nmatch); - assertEquals(12, nqmatch); + int[] results = match("[N,#6&+1,+0]", "[Cl-].Clc1ccc([I+]c2cccs2)cc1"); + assertEquals(12, results[0]); + assertEquals(12, results[1]); } public void testLogicalOrLowAnd1() throws Exception { - match("[#7,C;+0,+1]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); - assertEquals(15, nmatch); - assertEquals(15, nqmatch); + int[] results = match("[#7,C;+0,+1]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1"); + assertEquals(15, results[0]); + assertEquals(15, results[1]); } public void testLogicalOrLowAnd2() throws Exception { - match("[#7,C;+0,+1]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); - assertEquals(17, nmatch); - assertEquals(17, nqmatch); + int[] results = match("[#7,C;+0,+1]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76"); + assertEquals(17, results[0]); + assertEquals(17, results[1]); } public void testLogicalOrLowAnd3() throws Exception { - match("[#7,C;+0,+1]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); - assertEquals(13, nmatch); - assertEquals(13, nqmatch); + int[] results = match("[#7,C;+0,+1]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"); + assertEquals(13, results[0]); + assertEquals(13, results[1]); } public void testLogicalOrLowAnd4() throws Exception { - match("[#7,C;+0,+1]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); - assertEquals(12, nmatch); - assertEquals(12, nqmatch); + int[] results = match("[#7,C;+0,+1]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5"); + assertEquals(12, results[0]); + assertEquals(12, results[1]); } public void testLogicalOrLowAnd5() throws Exception { - match("[#7,C;+0,+1]", "N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3"); - assertEquals(5, nmatch); - assertEquals(5, nqmatch); + int[] results = match("[#7,C;+0,+1]", "N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3"); + assertEquals(5, results[0]); + assertEquals(5, results[1]); } // //TODO: this takes very long. It is the same smiles. So the bottle neck // might be in the AtomContainer /* public void testLogicalOrLowAnd6() throws Exception { - match("[#7,C;+0,+1]", "[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24"); - assertEquals(1, nmatch); + int[] results = match("[#7,C;+0,+1]", "[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24"); + assertEquals(1, results[0]); } */ public void testLogicalOrLowAnd7() throws Exception { - match("[#7,C;+0,+1]", "[Cl-].Clc1ccc([I+]c2cccs2)cc1"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[#7,C;+0,+1]", "[Cl-].Clc1ccc([I+]c2cccs2)cc1"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testRing1() throws Exception { - match("C1CCCCC1", "C1CCCCC1CCCC"); - assertEquals(12, nmatch); - assertEquals(1, nqmatch); + int[] results = match("C1CCCCC1", "C1CCCCC1CCCC"); + assertEquals(12, results[0]); + assertEquals(1, results[1]); } public void testRing2() throws Exception { - match("C1CCCCC1", "C1CCCCC1C1CCCCC1"); - assertEquals(24, nmatch); - assertEquals(2, nqmatch); + int[] results = match("C1CCCCC1", "C1CCCCC1C1CCCCC1"); + assertEquals(24, results[0]); + assertEquals(2, results[1]); } public void testRing3() throws Exception { - match("C1CCCCC1", "C1CCCC12CCCCC2"); - assertEquals(12, nmatch); - assertEquals(1, nqmatch); + int[] results = match("C1CCCCC1", "C1CCCC12CCCCC2"); + assertEquals(12, results[0]); + assertEquals(1, results[1]); } public void testRing4() throws Exception { - match("C1CCCCC1", "c1ccccc1O"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("C1CCCCC1", "c1ccccc1O"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testRing5() throws Exception { - match("C1CCCCC1", "c1ccccc1CCCCCC"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("C1CCCCC1", "c1ccccc1CCCCCC"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testRing6() throws Exception { - match("C1CCCCC1", "CCCCCC"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("C1CCCCC1", "CCCCCC"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testAromaticRing1() throws Exception { - match("c1ccccc1", "c1ccccc1"); - assertEquals(12, nmatch); - assertEquals(1, nqmatch); + int[] results = match("c1ccccc1", "c1ccccc1"); + assertEquals(12, results[0]); + assertEquals(1, results[1]); } public void testAromaticRing2() throws Exception { - match("c1ccccc1", "c1cccc2c1cccc2"); - assertEquals(24, nmatch); - assertEquals(2, nqmatch); + int[] results = match("c1ccccc1", "c1cccc2c1cccc2"); + assertEquals(24, results[0]); + assertEquals(2, results[1]); } public void testAromaticRing3() throws Exception { - match("c1ccccn1", "c1cccc2c1cccc2"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("c1ccccn1", "c1cccc2c1cccc2"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testAromaticRing4() throws Exception { - match("c1ccccn1", "c1cccc2c1cccn2"); - assertEquals(2, nmatch); - assertEquals(1, nqmatch); + int[] results = match("c1ccccn1", "c1cccc2c1cccn2"); + assertEquals(2, results[0]); + assertEquals(1, results[1]); } /* TODO: @@ -1063,123 +1062,123 @@ public void testAminoAcid1() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid2() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCCNC(N)=N)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCCNC(N)=N)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid3() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(N)=O)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(N)=O)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid4() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(O)=O)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(O)=O)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid5() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CS)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CS)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid6() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCC(N)=O)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCC(N)=O)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid7() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCC(O)=O)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCC(O)=O)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid8() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC([H])C(O)=O"); - assertEquals(0, nmatch); - assertEquals(0, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC([H])C(O)=O"); + assertEquals(0, results[0]); + assertEquals(0, results[1]); } public void testAminoAcid9() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CNC=N1)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CNC=N1)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid10() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(CC)C)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(CC)C)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid11() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(C)C)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(C)C)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid12() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCCCN)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCCCN)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid13() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCSC)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCSC)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid14() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CC=CC=C1)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CC=CC=C1)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid15() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "OC(C1CCCN1)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "OC(C1CCCN1)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid16() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CO)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CO)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid17() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(C)O)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(C)O)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid18() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CNC2=C1C=CC=C2)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CNC2=C1C=CC=C2)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid19() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CC=C(O)C=C1)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CC=C(O)C=C1)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } public void testAminoAcid20() throws Exception { - match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(C)C)C(O)=O"); - assertEquals(1, nmatch); - assertEquals(1, nqmatch); + int[] results = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(C)C)C(O)=O"); + assertEquals(1, results[0]); + assertEquals(1, results[1]); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |