From: <ha...@us...> - 2008-12-01 06:50:09
|
Revision: 10396 http://jmol.svn.sourceforge.net/jmol/?rev=10396&view=rev Author: hansonr Date: 2008-12-01 06:50:05 +0000 (Mon, 01 Dec 2008) Log Message: ----------- # code: refactoring of method names in FileManager and Viewer # code: refactoring of method names to remove ambiguities between "openFile" and "createModelSet" Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2008-12-01 06:49:17 UTC (rev 10395) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2008-12-01 06:50:05 UTC (rev 10396) @@ -226,13 +226,12 @@ fail("Wrong type for " + file.getPath() + ": " + fileType + " instead of " + typeAllowed); } } - Object result = adapter.openBufferedReader(file.getName(), null, bReader, null); + Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, null); assertNotNull("Nothing read for " + file.getPath(), result); assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection); AtomSetCollection collection = (AtomSetCollection) result; assertTrue("No atoms loaded for " + file.getPath(), collection.atomCount > 0); - bReader.close(); } /* (non-Javadoc) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-05-17 03:26:49
|
Revision: 10885 http://jmol.svn.sourceforge.net/jmol/?rev=10885&view=rev Author: hansonr Date: 2009-05-17 03:26:41 +0000 (Sun, 17 May 2009) Log Message: ----------- Wien2k models Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2009-05-17 03:25:16 UTC (rev 10884) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2009-05-17 03:26:41 UTC (rev 10885) @@ -103,6 +103,7 @@ result.addDirectory(false, "sparchive", "sparchive", "Spartan"); result.addDirectory(false, "spinput", "spinput", "Odyssey"); result.addDirectory(false, "v3000", "sdf"); + result.addDirectory(false, "wien2k", "struct"); result.addDirectory(false, "xyz", "xyz"); return result; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-07 15:49:12
|
Revision: 11701 http://jmol.svn.sourceforge.net/jmol/?rev=11701&view=rev Author: hansonr Date: 2009-11-07 15:49:06 +0000 (Sat, 07 Nov 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2009-11-07 15:43:38 UTC (rev 11700) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2009-11-07 15:49:06 UTC (rev 11701) @@ -232,7 +232,7 @@ assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection); AtomSetCollection collection = (AtomSetCollection) result; - assertTrue("No atoms loaded for " + file.getPath(), collection.atomCount > 0); + assertTrue("No atoms loaded for " + file.getPath(), collection.getAtomCount() > 0); } /* (non-Javadoc) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-05 00:56:22
|
Revision: 12036 http://jmol.svn.sourceforge.net/jmol/?rev=12036&view=rev Author: hansonr Date: 2010-01-05 00:56:16 +0000 (Tue, 05 Jan 2010) Log Message: ----------- data file updates Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-01-05 00:55:31 UTC (rev 12035) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-01-05 00:56:16 UTC (rev 12036) @@ -60,13 +60,13 @@ result.addDirectory(false, "adf", "adf", "Adf"); result.addDirectory(false, "aminoacids", "mol"); result.addDirectory(false, "aminoacids", "pdb"); - result.addDirectory(false, "animations", "cml", "cml(xml)"); + result.addDirectory(false, "animations", "cml", "XmlCml"); result.addDirectory(false, "animations", "pdb"); result.addDirectory(true, "animations", "pdb.gz"); result.addDirectory(false, "animations", "xyz"); result.addDirectory(false, "cif", "cif"); - result.addDirectory(false, "c3xml", "c3xml", "chem3d(xml)"); - result.addDirectory(false, "cml", "cml", "cml(xml)"); + result.addDirectory(false, "c3xml", "c3xml", "XmlChem3d"); + result.addDirectory(false, "cml", "cml", "XmlCml"); result.addDirectory(false, "crystals", "mol"); result.addDirectory(false, "crystals", "pdb"); result.addDirectory(false, "csf", "csf", "Csf"); @@ -89,7 +89,7 @@ result.addDirectory(false, "mol", "mol"); result.addDirectory(false, "mol", "sdf"); result.addDirectory(false, "mol2", "mol2"); - result.addDirectory(false, "molpro", "xml", "molpro(xml)"); + result.addDirectory(false, "molpro", "xml", "XmlMolpro"); result.addDirectory(false, "mopac", "out"); result.addDirectory(false, "nwchem", "nwo", "NWChem"); result.addDirectory(false, "pdb", "pdb"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-06 20:19:55
|
Revision: 12057 http://jmol.svn.sourceforge.net/jmol/?rev=12057&view=rev Author: hansonr Date: 2010-01-06 20:19:48 +0000 (Wed, 06 Jan 2010) Log Message: ----------- reader update Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-01-06 19:37:32 UTC (rev 12056) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-01-06 20:19:48 UTC (rev 12057) @@ -58,12 +58,15 @@ //testOne = "csf"; result.addDirectory(false, "adf", "adf", "Adf"); + result.addDirectory(false, "adf", "out", "Adf"); + result.addDirectory(false, "aims", "in", "Aims"); result.addDirectory(false, "aminoacids", "mol"); result.addDirectory(false, "aminoacids", "pdb"); result.addDirectory(false, "animations", "cml", "XmlCml"); result.addDirectory(false, "animations", "pdb"); result.addDirectory(true, "animations", "pdb.gz"); result.addDirectory(false, "animations", "xyz"); + result.addDirectory(false, "castep", "cell", "Castep"); result.addDirectory(false, "cif", "cif"); result.addDirectory(false, "c3xml", "c3xml", "XmlChem3d"); result.addDirectory(false, "cml", "cml", "XmlCml"); @@ -72,6 +75,7 @@ result.addDirectory(false, "csf", "csf", "Csf"); result.addDirectory(true, "cube", "cub.gz"); result.addDirectory(true, "cube", "cube.gz"); + result.addDirectory(false, "dgrid", "adf", "Dgrid"); result.addDirectory(false, "folding", "xyz", "FoldingXyz"); result.addDirectory(true, "folding", "xyz.gz", "FoldingXyz"); result.addDirectory(false, "../Jmol-FAH/projects", "xyz", "FoldingXyz"); @@ -91,6 +95,8 @@ result.addDirectory(false, "mol2", "mol2"); result.addDirectory(false, "molpro", "xml", "XmlMolpro"); result.addDirectory(false, "mopac", "out"); + result.addDirectory(false, "odyssey", "odydata", "Odyssey"); + result.addDirectory(false, "odyssey", "xodydata", "XmlOdyssey"); result.addDirectory(false, "nwchem", "nwo", "NWChem"); result.addDirectory(false, "pdb", "pdb"); result.addDirectory(true, "pdb", "pdb.gz"); @@ -100,11 +106,14 @@ result.addDirectory(false, "shelx", "res"); result.addDirectory(false, "spartan", "smol", "SpartanSmol"); result.addDirectory(false, "spartan", "txt", "Spartan"); + result.addDirectory(false, "spartan", "sp4", "Spartan"); result.addDirectory(false, "sparchive", "sparchive", "Spartan"); - result.addDirectory(false, "spinput", "spinput", "Odyssey"); + result.addDirectory(false, "sparchive", "spartan", "Spartan"); result.addDirectory(false, "v3000", "sdf"); result.addDirectory(false, "wien2k", "struct"); + result.addDirectory(false, "webmo", "mo", "WebMO"); result.addDirectory(false, "xyz", "xyz"); + result.addDirectory(false, "vasp", "dat", "Vasp"); return result; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-22 12:59:28
|
Revision: 12182 http://jmol.svn.sourceforge.net/jmol/?rev=12182&view=rev Author: hansonr Date: 2010-01-22 12:59:03 +0000 (Fri, 22 Jan 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-01-22 12:58:07 UTC (rev 12181) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-01-22 12:59:03 UTC (rev 12182) @@ -110,10 +110,10 @@ result.addDirectory(false, "sparchive", "spartan", "Spartan"); result.addDirectory(false, "v3000", "mol", "V3000"); result.addDirectory(false, "v3000", "sdf", "V3000"); + result.addDirectory(false, "vasp", "xml", "XmlVasp"); result.addDirectory(false, "wien2k", "struct", "Wien2k"); result.addDirectory(false, "webmo", "mo", "WebMO"); result.addDirectory(false, "xyz", "xyz", "Xyz"); - result.addDirectory(false, "vasp", "dat", "Vasp"); return result; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-25 18:38:53
|
Revision: 12477 http://jmol.svn.sourceforge.net/jmol/?rev=12477&view=rev Author: hansonr Date: 2010-02-25 18:38:47 +0000 (Thu, 25 Feb 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-02-25 18:30:16 UTC (rev 12476) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-02-25 18:38:47 UTC (rev 12477) @@ -69,6 +69,7 @@ result.addDirectory(false, "cif", "cif", "Cif"); result.addDirectory(false, "c3xml", "c3xml", "XmlChem3d"); result.addDirectory(false, "cml", "cml", "XmlCml"); + result.addDirectory(false, "crystal", "out", "Crystal"); result.addDirectory(false, "crystals", "mol", "Mol"); result.addDirectory(false, "crystals", "pdb", "Pdb"); result.addDirectory(false, "csf", "csf", "Csf"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-06-18 19:41:33
|
Revision: 13430 http://jmol.svn.sourceforge.net/jmol/?rev=13430&view=rev Author: hansonr Date: 2010-06-18 19:41:27 +0000 (Fri, 18 Jun 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-06-18 19:40:54 UTC (rev 13429) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-06-18 19:41:27 UTC (rev 13430) @@ -115,6 +115,7 @@ result.addDirectory(false, "vasp", "xml", "XmlVasp"); result.addDirectory(false, "wien2k", "struct", "Wien2k"); result.addDirectory(false, "webmo", "mo", "WebMO"); + result.addDirectory(false, "xsd", "xsd", "XmlXsd"); result.addDirectory(false, "xyz", "xyz", "Xyz"); return result; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-11-04 14:10:29
|
Revision: 14575 http://jmol.svn.sourceforge.net/jmol/?rev=14575&view=rev Author: hansonr Date: 2010-11-04 14:10:23 +0000 (Thu, 04 Nov 2010) Log Message: ----------- VASP reader test Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-11-04 14:09:11 UTC (rev 14574) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-11-04 14:10:23 UTC (rev 14575) @@ -113,6 +113,7 @@ result.addDirectory(false, "v3000", "mol", "V3000"); result.addDirectory(false, "v3000", "sdf", "V3000"); result.addDirectory(false, "vasp", "xml", "XmlVasp"); + result.addDirectory(false, "vasp", "dat", "Vasp"); result.addDirectory(false, "wien2k", "struct", "Wien2k"); result.addDirectory(false, "webmo", "mo", "WebMO"); result.addDirectory(false, "xsd", "xsd", "XmlXsd"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-01 13:01:49
|
Revision: 14743 http://jmol.svn.sourceforge.net/jmol/?rev=14743&view=rev Author: hansonr Date: 2010-12-01 13:01:43 +0000 (Wed, 01 Dec 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-01 12:58:33 UTC (rev 14742) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-01 13:01:43 UTC (rev 14743) @@ -85,7 +85,6 @@ result.addDirectory(false, "gaussian", "log", "Gaussian"); result.addDirectory(false, "gaussian", "out", "Gaussian"); result.addDirectory(false, "ghemical", "gpr", "GhemicalMM"); - result.addDirectory(false, "gpt2", "gpt2","MopacGraphf"); result.addDirectory(false, "gromacs", "gro", "Gromacs"); result.addDirectory(false, "hin", "hin", "HyperChem"); result.addDirectory(false, "jaguar", "out", "Jaguar"); @@ -96,6 +95,8 @@ result.addDirectory(false, "mol2", "mol2", "Mol2"); result.addDirectory(false, "molpro", "xml", "XmlMolpro"); result.addDirectory(false, "mopac", "out", "Mopac"); + result.addDirectory(false, "mopac", "gpt2","MopacGraphf"); + result.addDirectory(false, "mopac", "mgf","MopacGraphf"); result.addDirectory(false, "odyssey", "odydata", "Odyssey"); result.addDirectory(false, "odyssey", "xodydata", "XmlOdyssey"); result.addDirectory(false, "nwchem", "nwo", "NWChem"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-17 14:49:30
|
Revision: 14799 http://jmol.svn.sourceforge.net/jmol/?rev=14799&view=rev Author: hansonr Date: 2010-12-17 14:49:24 +0000 (Fri, 17 Dec 2010) Log Message: ----------- version=12.1.26_dev # code: JUnit test for file reading GenNBO and CIF files lacks viewer object Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-17 14:49:00 UTC (rev 14798) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-17 14:49:24 UTC (rev 14799) @@ -13,6 +13,7 @@ import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; +import java.util.Hashtable; import java.util.zip.GZIPInputStream; import org.jmol.util.JUnitLogger; @@ -84,6 +85,9 @@ result.addDirectory(false, "gamess", "out", ";Gamess;GamessUS;GamessUK;"); result.addDirectory(false, "gaussian", "log", "Gaussian"); result.addDirectory(false, "gaussian", "out", "Gaussian"); + result.addDirectory(false, "gennbo", "out", "GenNBO"); + result.addDirectory(false, "gennbo", "36", "GenNBO"); + result.addDirectory(false, "gennbo", "37", "GenNBO"); result.addDirectory(false, "ghemical", "gpr", "GhemicalMM"); result.addDirectory(false, "gromacs", "gro", "Gromacs"); result.addDirectory(false, "hin", "hin", "HyperChem"); @@ -223,7 +227,9 @@ fail("Wrong type for " + file.getPath() + ": " + fileType + " instead of " + typeAllowed); } } - Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, null); + Hashtable<String, Object> htParams = new Hashtable<String, Object>(); + htParams.put("fullPathName", file.getAbsolutePath()); + Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, htParams); assertNotNull("Nothing read for " + file.getPath(), result); assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-17 22:58:38
|
Revision: 14816 http://jmol.svn.sourceforge.net/jmol/?rev=14816&view=rev Author: hansonr Date: 2010-12-17 22:58:31 +0000 (Fri, 17 Dec 2010) Log Message: ----------- V3000 moved to mol directory Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-17 22:54:46 UTC (rev 14815) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-17 22:58:31 UTC (rev 14816) @@ -115,8 +115,6 @@ result.addDirectory(false, "spartan", "sp4", "Spartan"); result.addDirectory(false, "sparchive", "sparchive", "Spartan"); result.addDirectory(false, "sparchive", "spartan", "Spartan"); - result.addDirectory(false, "v3000", "mol", "V3000"); - result.addDirectory(false, "v3000", "sdf", "V3000"); result.addDirectory(false, "vasp", "xml", "XmlVasp"); result.addDirectory(false, "vasp", "dat", "VaspOutcar"); result.addDirectory(false, "wien2k", "struct", "Wien2k"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-17 23:05:12
|
Revision: 14819 http://jmol.svn.sourceforge.net/jmol/?rev=14819&view=rev Author: hansonr Date: 2010-12-17 23:05:06 +0000 (Fri, 17 Dec 2010) Log Message: ----------- V3000 moved to mol directory Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-17 23:01:54 UTC (rev 14818) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-17 23:05:06 UTC (rev 14819) @@ -94,6 +94,7 @@ result.addDirectory(false, "jaguar", "out", "Jaguar"); result.addDirectory(false, "modifiedGroups", "cif", "Cif"); result.addDirectory(false, "modifiedGroups", "pdb", "Pdb"); + result.addDirectory(false, "mol", "v3000", "Mol"); result.addDirectory(false, "mol", "mol", "Mol"); result.addDirectory(false, "mol", "sdf", "Mol"); result.addDirectory(false, "mol2", "mol2", "Mol2"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-18 19:28:34
|
Revision: 14830 http://jmol.svn.sourceforge.net/jmol/?rev=14830&view=rev Author: hansonr Date: 2010-12-18 19:28:27 +0000 (Sat, 18 Dec 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-18 19:20:19 UTC (rev 14829) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-18 19:28:27 UTC (rev 14830) @@ -227,7 +227,7 @@ } } Hashtable<String, Object> htParams = new Hashtable<String, Object>(); - htParams.put("fullPathName", file.getAbsolutePath()); + htParams.put("fullPathName", file.getCanonicalPath()); Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, htParams); assertNotNull("Nothing read for " + file.getPath(), result); assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-22 13:53:39
|
Revision: 14871 http://jmol.svn.sourceforge.net/jmol/?rev=14871&view=rev Author: hansonr Date: 2010-12-22 13:53:33 +0000 (Wed, 22 Dec 2010) Log Message: ----------- GULP reader addition Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-22 13:51:04 UTC (rev 14870) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-22 13:53:33 UTC (rev 14871) @@ -90,6 +90,8 @@ result.addDirectory(false, "gennbo", "37", "GenNBO"); result.addDirectory(false, "ghemical", "gpr", "GhemicalMM"); result.addDirectory(false, "gromacs", "gro", "Gromacs"); + result.addDirectory(false, "gulp", "gout", "Gulp"); + result.addDirectory(false, "gulp", "got", "Gulp"); result.addDirectory(false, "hin", "hin", "HyperChem"); result.addDirectory(false, "jaguar", "out", "Jaguar"); result.addDirectory(false, "modifiedGroups", "cif", "Cif"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-22 14:32:28
|
Revision: 14873 http://jmol.svn.sourceforge.net/jmol/?rev=14873&view=rev Author: hansonr Date: 2010-12-22 14:32:22 +0000 (Wed, 22 Dec 2010) Log Message: ----------- test will not continue on assert failure Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-22 14:31:30 UTC (rev 14872) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-22 14:32:22 UTC (rev 14873) @@ -206,6 +206,8 @@ testFile(); } + private static boolean continuing = true; + /** * Tests reading of one file. * @@ -213,6 +215,8 @@ * @throws IOException */ public void testFile() throws FileNotFoundException, IOException { + if (!continuing) + return; JUnitLogger.setInformation(file.getPath()); InputStream iStream = new FileInputStream(file); iStream = new BufferedInputStream(iStream); @@ -225,17 +229,20 @@ if (typeAllowed != null) { String fileType = adapter.getFileTypeName(bReader); if (!typeAllowed.equals(fileType) && typeAllowed.indexOf(";"+ fileType + ";") < 0) { + continuing = false; fail("Wrong type for " + file.getPath() + ": " + fileType + " instead of " + typeAllowed); } } Hashtable<String, Object> htParams = new Hashtable<String, Object>(); htParams.put("fullPathName", file.getCanonicalPath()); Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, htParams); + continuing = (result != null && result instanceof AtomSetCollection); assertNotNull("Nothing read for " + file.getPath(), result); assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection); - AtomSetCollection collection = (AtomSetCollection) result; - assertTrue("No atoms loaded for " + file.getPath(), collection.getAtomCount() > 0); + int nAtoms = ((AtomSetCollection) result).getAtomCount(); + continuing &= (nAtoms > 0); + assertTrue("No atoms loaded for " + file.getPath(), nAtoms > 0); } /* (non-Javadoc) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-22 19:52:44
|
Revision: 14882 http://jmol.svn.sourceforge.net/jmol/?rev=14882&view=rev Author: hansonr Date: 2010-12-22 19:52:37 +0000 (Wed, 22 Dec 2010) Log Message: ----------- version=12.1.27_dev # new feature: QuantumEspresso reader Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-22 19:51:41 UTC (rev 14881) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2010-12-22 19:52:37 UTC (rev 14882) @@ -110,6 +110,7 @@ result.addDirectory(false, "pdb", "pdb", "Pdb"); result.addDirectory(true, "pdb", "pdb.gz", "Pdb"); // result.pmesh files are not molecular data files + result.addDirectory(false, "quantumEspresso", "out", "Espresso"); result.addDirectory(false, "psi3", "out", "Psi"); result.addDirectory(false, "qchem", "out", "Qchem"); result.addDirectory(false, "shelx", "res", "Shelx"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-11 12:07:53
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Revision: 16056 http://jmol.svn.sourceforge.net/jmol/?rev=16056&view=rev Author: hansonr Date: 2011-09-11 12:07:47 +0000 (Sun, 11 Sep 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2011-09-11 12:07:24 UTC (rev 16055) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2011-09-11 12:07:47 UTC (rev 16056) @@ -65,7 +65,7 @@ result.addDirectory("animations", "cml", "XmlCml"); result.addDirectory("animations", "pdb;pdb.gz", "Pdb"); result.addDirectory("animations", "xyz", "Xyz"); - result.addDirectory("castep", "cell", "Castep"); + result.addDirectory("castep", "cell;phonon", "Castep"); result.addDirectory("cif", "cif", "Cif"); result.addDirectory("c3xml", "c3xml", "XmlChem3d"); result.addDirectory("cml", "cml", "XmlCml"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-11-21 01:29:03
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Revision: 16494 http://jmol.svn.sourceforge.net/jmol/?rev=16494&view=rev Author: hansonr Date: 2011-11-21 01:28:56 +0000 (Mon, 21 Nov 2011) Log Message: ----------- zmatrix data JUnit test Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2011-11-20 21:53:43 UTC (rev 16493) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2011-11-21 01:28:56 UTC (rev 16494) @@ -113,6 +113,7 @@ result.addDirectory("webmo", "mo", "WebMO"); result.addDirectory("xsd", "xsd", "XmlXsd"); result.addDirectory("xyz", "xyz", "Xyz"); + result.addDirectory("zmatrix", "txt;zmat", "ZMatrix"); return result; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-06-04 09:05:57
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Revision: 17255 http://jmol.svn.sourceforge.net/jmol/?rev=17255&view=rev Author: hansonr Date: 2012-06-04 09:05:46 +0000 (Mon, 04 Jun 2012) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2012-06-04 08:51:14 UTC (rev 17254) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2012-06-04 09:05:46 UTC (rev 17255) @@ -91,6 +91,7 @@ result.addDirectory("mol", "v3000;mol;sdf", "Mol"); result.addDirectory("mol2", "mol2", "Mol2"); result.addDirectory("molpro", "xml", "XmlMolpro"); + result.addDirectory("mopac", "arc;archive", "MopacArchive"); result.addDirectory("mopac", "out", "Mopac"); result.addDirectory("mopac", "gpt2", "MopacGraphf"); result.addDirectory("mopac", "mgf", "MopacGraphf"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-06-06 04:20:32
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Revision: 18290 http://sourceforge.net/p/jmol/code/18290 Author: hansonr Date: 2013-06-06 04:20:29 +0000 (Thu, 06 Jun 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2013-06-06 04:06:20 UTC (rev 18289) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2013-06-06 04:20:29 UTC (rev 18290) @@ -110,6 +110,7 @@ result.addDirectory("sparchive", "sparchive;spartan", "Spartan"); result.addDirectory("vasp", "xml", "XmlVasp"); result.addDirectory("vasp", "dat", "VaspOutcar"); + result.addDirectory("vasp", "poscar", "VaspPoscar"); result.addDirectory("wien2k", "struct", "Wien2k"); result.addDirectory("webmo", "mo", "WebMO"); result.addDirectory("xsd", "xsd", "XmlXsd"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-10-29 18:41:55
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Revision: 18855 http://sourceforge.net/p/jmol/code/18855 Author: hansonr Date: 2013-10-29 18:41:50 +0000 (Tue, 29 Oct 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2013-10-29 18:25:29 UTC (rev 18854) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2013-10-29 18:41:50 UTC (rev 18855) @@ -16,7 +16,7 @@ import java.util.Hashtable; import java.util.zip.GZIPInputStream; -import javajs.util.ParserJS; +import javajs.util.Parser; import org.jmol.util.JUnitLogger; import org.jmol.util.Logger; @@ -135,7 +135,7 @@ if (testOne != null && !directory.equals(testOne)) return; File dir = new File(datafileDirectory, directory); - String[] exts = ParserJS.split(ext, ";"); + String[] exts = Parser.split(ext, ";"); for (int ie = 0; ie < exts.length; ie++) { final String e = exts[ie]; String[] files = dir.list(new FilenameFilter() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-01-10 22:46:29
|
Revision: 19166 http://sourceforge.net/p/jmol/code/19166 Author: hansonr Date: 2014-01-10 22:46:26 +0000 (Fri, 10 Jan 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2014-01-10 22:45:46 UTC (rev 19165) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2014-01-10 22:46:26 UTC (rev 19166) @@ -231,7 +231,7 @@ assertNotNull("Nothing read for " + file.getPath(), result); assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection); - int nAtoms = ((AtomSetCollection) result).getAtomCount(); + int nAtoms = ((AtomSetCollection) result).atomCount; continuing &= (nAtoms > 0); assertTrue("No atoms loaded for " + file.getPath(), nAtoms > 0); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-03-21 18:46:33
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Revision: 19505 http://sourceforge.net/p/jmol/code/19505 Author: hansonr Date: 2014-03-21 18:46:30 +0000 (Fri, 21 Mar 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2014-03-21 18:45:51 UTC (rev 19504) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2014-03-21 18:46:30 UTC (rev 19505) @@ -231,7 +231,7 @@ assertNotNull("Nothing read for " + file.getPath(), result); assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String); assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection); - int nAtoms = ((AtomSetCollection) result).atomCount; + int nAtoms = ((AtomSetCollection) result).ac; continuing &= (nAtoms > 0); assertTrue("No atoms loaded for " + file.getPath(), nAtoms > 0); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-01-21 12:55:01
|
Revision: 20219 http://sourceforge.net/p/jmol/code/20219 Author: hansonr Date: 2015-01-21 12:54:58 +0000 (Wed, 21 Jan 2015) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java =================================================================== --- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2015-01-21 12:50:07 UTC (rev 20218) +++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java 2015-01-21 12:54:58 UTC (rev 20219) @@ -67,8 +67,8 @@ result.addDirectory("animations", "pdb;pdb.gz", "Pdb"); result.addDirectory("animations", "xyz", "Xyz"); result.addDirectory("castep", "cell;phonon", "Castep"); + result.addDirectory("cif", "mmcif", "MMCif"); result.addDirectory("cif", "cif", "Cif"); - result.addDirectory("cif", "mmcif", "MMCif"); result.addDirectory("c3xml", "c3xml", "XmlChem3d"); result.addDirectory("cml", "cml", "XmlCml"); result.addDirectory("crystal", "out;outp", "Crystal"); @@ -80,7 +80,7 @@ result.addDirectory("dmol", "outmol", "Dmol"); result.addDirectory("folding", "xyz;xyz.gz", "FoldingXyz"); result.addDirectory("../Jmol-FAH/projects", "xyz;xyz.gz", "FoldingXyz"); - result.addDirectory("gamess", "log;out;txt", ";Gamess;GamessUS;GamessUK;"); + result.addDirectory("gamess", "log;out", ";Gamess;GamessUS;GamessUK;"); result.addDirectory("gaussian", "log;out", "Gaussian"); result.addDirectory("gennbo", "out;36;37", "GenNBO"); result.addDirectory("ghemical", "gpr", "GhemicalMM"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |