id stringlengths 7 14 | test_class dict | test_case dict | focal_class dict | focal_method dict | repository dict |
|---|---|---|---|---|---|
37728390_13 | {
"fields": [
{
"declarator": "factory = new GeometryFactory()",
"modifier": "private",
"original_string": "private GeometryFactory factory = new GeometryFactory();",
"type": "GeometryFactory",
"var_name": "factory"
}
],
"file": "contrib/geomason/src/test/java/sim/field/geo/G... | {
"body": "@Test\n public void testClear()\n {\n System.out.println(\"clear\");\n\n MasonGeometry g = new MasonGeometry(createPoint(1,1));\n GeomVectorField instance = new GeomVectorField();\n instance.addGeometry(g);\n\n assertTrue(instance.getGeometries().size() == 1);\n ... | {
"fields": [
{
"declarator": "serialVersionUID = -754748817928825708L",
"modifier": "private static final",
"original_string": "private static final long serialVersionUID = -754748817928825708L;",
"type": "long",
"var_name": "serialVersionUID"
},
{
"declarator": "spati... | {
"body": "@Override\n public void clear()\n {\n super.clear();\n spatialIndex = new Quadtree();\n geometries.clear();\n\n needToRebuildIndex = false;\n }",
"class_method_signature": "GeomVectorField.clear()",
"constructor": false,
"full_signature": "@Override public void cl... | {
"created": "6/19/2015 3:04:41 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 37728390,
"size": null,
"stargazer_count": null,
"stars": 94,
"updates": "2020-01-06T15:38:11+00:00",
"url": "https://github.com/eclab/mason"
} |
37728390_7 | {
"fields": [],
"file": "contrib/geomason/src/test/java/sim/util/geo/AttributeValueTest.java",
"identifier": "AttributeValueTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testGetDouble()\n {\n System.out.println(\"getDouble\");\n AttributeValue instance = new AttributeValue(new Double(123.4));\n Double expResult = new Double(123.4);\n Double result = instance.getDouble();\n assertEquals(expResult, result);\n ... | {
"fields": [
{
"declarator": "serialVersionUID = -2342742107342686581L",
"modifier": "private static final",
"original_string": "private static final long serialVersionUID = -2342742107342686581L;",
"type": "long",
"var_name": "serialVersionUID"
},
{
"declarator": "val... | {
"body": "public Double getDouble()\n {\n return (Double) getValue();\n }",
"class_method_signature": "AttributeValue.getDouble()",
"constructor": false,
"full_signature": "public Double getDouble()",
"identifier": "getDouble",
"invocations": [
"getValue"
],
"modifiers": "public",
"p... | {
"created": "6/19/2015 3:04:41 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 37728390,
"size": null,
"stargazer_count": null,
"stars": 94,
"updates": "2020-01-06T15:38:11+00:00",
"url": "https://github.com/eclab/mason"
} |
37728390_6 | {
"fields": [],
"file": "contrib/geomason/src/test/java/sim/util/geo/AttributeValueTest.java",
"identifier": "AttributeValueTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testSetDouble()\n {\n System.out.println(\"setDouble\");\n Double value = new Double(123.4);\n AttributeValue instance = new AttributeValue();\n instance.setDouble(value);\n // TODO review the generated test code and remove the default call to fa... | {
"fields": [
{
"declarator": "serialVersionUID = -2342742107342686581L",
"modifier": "private static final",
"original_string": "private static final long serialVersionUID = -2342742107342686581L;",
"type": "long",
"var_name": "serialVersionUID"
},
{
"declarator": "val... | {
"body": "public void setDouble(double value)\n {\n setValue(new Double(value) );\n }",
"class_method_signature": "AttributeValue.setDouble(double value)",
"constructor": false,
"full_signature": "public void setDouble(double value)",
"identifier": "setDouble",
"invocations": [
"setValue"
... | {
"created": "6/19/2015 3:04:41 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 37728390,
"size": null,
"stargazer_count": null,
"stars": 94,
"updates": "2020-01-06T15:38:11+00:00",
"url": "https://github.com/eclab/mason"
} |
37728390_12 | {
"fields": [
{
"declarator": "factory = new GeometryFactory()",
"modifier": "private",
"original_string": "private GeometryFactory factory = new GeometryFactory();",
"type": "GeometryFactory",
"var_name": "factory"
}
],
"file": "contrib/geomason/src/test/java/sim/field/geo/G... | {
"body": "@Test\n public void testAddGeometry()\n {\n System.out.println(\"addGeometry\");\n MasonGeometry g = new MasonGeometry(createPoint(1,1));\n GeomVectorField instance = new GeomVectorField();\n instance.addGeometry(g);\n \n Bag geometries = instance.getGeometri... | {
"fields": [
{
"declarator": "serialVersionUID = -754748817928825708L",
"modifier": "private static final",
"original_string": "private static final long serialVersionUID = -754748817928825708L;",
"type": "long",
"var_name": "serialVersionUID"
},
{
"declarator": "spati... | {
"body": "public void addGeometry(final MasonGeometry g)\n {\n Envelope e = g.getGeometry().getEnvelopeInternal();\n MBR.expandToInclude(e);\n spatialIndex.insert(e, g);\n geometries.add(g);\n }",
"class_method_signature": "GeomVectorField.addGeometry(final MasonGeometry g)",
"c... | {
"created": "6/19/2015 3:04:41 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 37728390,
"size": null,
"stargazer_count": null,
"stars": 94,
"updates": "2020-01-06T15:38:11+00:00",
"url": "https://github.com/eclab/mason"
} |
56670932_6 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/InsetOperatorTest.java",
"identifier": "InsetOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testWithNullListInsetOperator() throws Exception {\n InsetOperator<Integer> insetOperator = new InsetOperator<>(\"in-set\", null);\n assertEquals(Flag.FlagResultStatus.DISABLED, insetOperator.appliesTo(2));\n assertEquals(Flag.FlagResultStatus.DISABLED, insetOper... | {
"fields": [
{
"declarator": "values",
"modifier": "private final",
"original_string": "private final List<T> values;",
"type": "List<T>",
"var_name": "values"
}
],
"file": "flaggr/src/main/java/com/comuto/flag/operators/InsetOperator.java",
"identifier": "InsetOperator",
... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable T value) {\n if (null != values) {\n for (T v : values) {\n if (v.equals(value))\n return Flag.FlagResultStatus.ENABLED;\n }\n }\n return Flag.FlagResultStatus.DISABL... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
56670932_0 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/PercentageOperatorTest.java",
"identifier": "PercentageOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testSimplePercentageOperator() throws Exception {\n PercentageOperator percentageOperator = new PercentageOperator(\"modulo\", 10, 0);\n assertEquals(Flag.FlagResultStatus.ENABLED, percentageOperator.appliesTo(\"8\"));\n assertEquals(Flag.FlagResultStatus.DISABLE... | {
"fields": [
{
"declarator": "MAX_PERCENTAGE = 100",
"modifier": "private static final",
"original_string": "private static final int MAX_PERCENTAGE = 100;",
"type": "int",
"var_name": "MAX_PERCENTAGE"
},
{
"declarator": "percentage",
"modifier": "private final",... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable String value) throws NumberFormatException {\n if (StringUtils.isEmpty(value)) {\n return DISABLED;\n }\n final int val = Integer.parseInt(value);\n\n //If there is no registration time\n if (val =... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
56670932_1 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/PercentageOperatorTest.java",
"identifier": "PercentageOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testSimplePercentageWithShiftOperator() throws Exception {\n PercentageOperator percentageOperator = new PercentageOperator(\"modulo\", 10, 5);\n assertEquals(Flag.FlagResultStatus.ENABLED, percentageOperator.appliesTo(\"12\"));\n assertEquals(Flag.FlagResultStat... | {
"fields": [
{
"declarator": "MAX_PERCENTAGE = 100",
"modifier": "private static final",
"original_string": "private static final int MAX_PERCENTAGE = 100;",
"type": "int",
"var_name": "MAX_PERCENTAGE"
},
{
"declarator": "percentage",
"modifier": "private final",... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable String value) throws NumberFormatException {\n if (StringUtils.isEmpty(value)) {\n return DISABLED;\n }\n final int val = Integer.parseInt(value);\n\n //If there is no registration time\n if (val =... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
56670932_2 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/PercentageOperatorTest.java",
"identifier": "PercentageOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testPercentageWithoutRegistrationValue() throws Exception {\n PercentageOperator percentageOperator = new PercentageOperator(\"modulo\", 10, 5);\n assertEquals(Flag.FlagResultStatus.DISABLED, percentageOperator.appliesTo(\"0\"));\n }",
"class_method_signature": "Pe... | {
"fields": [
{
"declarator": "MAX_PERCENTAGE = 100",
"modifier": "private static final",
"original_string": "private static final int MAX_PERCENTAGE = 100;",
"type": "int",
"var_name": "MAX_PERCENTAGE"
},
{
"declarator": "percentage",
"modifier": "private final",... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable String value) throws NumberFormatException {\n if (StringUtils.isEmpty(value)) {\n return DISABLED;\n }\n final int val = Integer.parseInt(value);\n\n //If there is no registration time\n if (val =... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
56670932_3 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/InsetOperatorTest.java",
"identifier": "InsetOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testStringInsetOperator() throws Exception {\n List<String> values = new ArrayList<>();\n values.add(\"1\");\n values.add(\"2\");\n values.add(\"3\");\n values.add(\"4\");\n values.add(\"5\");\n InsetOperator<String> insetOperator = ne... | {
"fields": [
{
"declarator": "values",
"modifier": "private final",
"original_string": "private final List<T> values;",
"type": "List<T>",
"var_name": "values"
}
],
"file": "flaggr/src/main/java/com/comuto/flag/operators/InsetOperator.java",
"identifier": "InsetOperator",
... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable T value) {\n if (null != values) {\n for (T v : values) {\n if (v.equals(value))\n return Flag.FlagResultStatus.ENABLED;\n }\n }\n return Flag.FlagResultStatus.DISABL... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
56670932_4 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/InsetOperatorTest.java",
"identifier": "InsetOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testIntegerInsetOperator() throws Exception {\n List<Integer> values = new ArrayList<>();\n values.add(1);\n values.add(2);\n values.add(3);\n values.add(4);\n values.add(5);\n InsetOperator<Integer> insetOperator = new InsetOperator<>... | {
"fields": [
{
"declarator": "values",
"modifier": "private final",
"original_string": "private final List<T> values;",
"type": "List<T>",
"var_name": "values"
}
],
"file": "flaggr/src/main/java/com/comuto/flag/operators/InsetOperator.java",
"identifier": "InsetOperator",
... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable T value) {\n if (null != values) {\n for (T v : values) {\n if (v.equals(value))\n return Flag.FlagResultStatus.ENABLED;\n }\n }\n return Flag.FlagResultStatus.DISABL... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
56670932_5 | {
"fields": [],
"file": "flaggr/src/test/java/com/comuto/flag/operators/InsetOperatorTest.java",
"identifier": "InsetOperatorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testEmptyInsetOperator() throws Exception {\n List<Integer> values = new ArrayList<>();\n InsetOperator<Integer> insetOperator = new InsetOperator<>(\"in-set\", values);\n assertEquals(Flag.FlagResultStatus.DISABLED, insetOperator.appliesTo(2));\n assertEq... | {
"fields": [
{
"declarator": "values",
"modifier": "private final",
"original_string": "private final List<T> values;",
"type": "List<T>",
"var_name": "values"
}
],
"file": "flaggr/src/main/java/com/comuto/flag/operators/InsetOperator.java",
"identifier": "InsetOperator",
... | {
"body": "@Override\n public Flag.FlagResultStatus appliesTo(@Nullable T value) {\n if (null != values) {\n for (T v : values) {\n if (v.equals(value))\n return Flag.FlagResultStatus.ENABLED;\n }\n }\n return Flag.FlagResultStatus.DISABL... | {
"created": null,
"fork": null,
"fork_count": 10,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 56670932,
"size": 134,
"stargazer_count": 91,
"stars": null,
"updates": null,
"url": "https://github.com/blablacar/flaggr-android"
} |
36819131_11 | {
"fields": [
{
"declarator": "builder",
"modifier": "private",
"original_string": "private CucumberReportBuilder builder;",
"type": "CucumberReportBuilder",
"var_name": "builder"
},
{
"declarator": "reports",
"modifier": "private",
"original_string": "priva... | {
"body": "@Test\n public void featureTagTest() {\n List<String> existingTags = new ArrayList<>();\n for (Feature f : reports.getFeatures()) {\n for (Tag t : f.getTags()) {\n existingTags.add(t.getName() + t.getLine());\n }\n }\n List<String> expecte... | {
"fields": [
{
"declarator": "pageTitle",
"modifier": "private",
"original_string": "private String pageTitle;",
"type": "String",
"var_name": "pageTitle"
},
{
"declarator": "features",
"modifier": "private",
"original_string": "private List<Feature> featur... | {
"body": "public List<Feature> getFeatures() {\n return features;\n }",
"class_method_signature": "AllFeatureReports.getFeatures()",
"constructor": false,
"full_signature": "public List<Feature> getFeatures()",
"identifier": "getFeatures",
"invocations": [],
"modifiers": "public",
"parameters... | {
"created": null,
"fork": null,
"fork_count": 14,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 36819131,
"size": 1256,
"stargazer_count": 16,
"stars": null,
"updates": null,
"url": "https://github.com/web-innovate/bootstraped-multi-test-results-report"
} |
36819131_0 | {
"fields": [],
"file": "junit-reporting-handlebars/src/test/java/com/github/bogdanlivadariu/reporting/junit/builder/JUnitReportBuilderTest.java",
"identifier": "JUnitReportBuilderTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void processedReportsTest() throws FileNotFoundException, JAXBException {\n List<String> xmlReports = new ArrayList<>();\n String report = this.getClass().getClassLoader().getResource(\"valid-report-1.xml\").getPath();\n xmlReports.add(report);\n JUnitReportBui... | {
"fields": [
{
"declarator": "SUITE_OVERVIEW = \"testSuitesOverview.html\"",
"modifier": "public static",
"original_string": "public static String SUITE_OVERVIEW = \"testSuitesOverview.html\";",
"type": "String",
"var_name": "SUITE_OVERVIEW"
},
{
"declarator": "TEST_OV... | {
"body": "public List<TestSuiteModel> getProcessedTestSuites() {\n return processedTestSuites;\n }",
"class_method_signature": "JUnitReportBuilder.getProcessedTestSuites()",
"constructor": false,
"full_signature": "public List<TestSuiteModel> getProcessedTestSuites()",
"identifier": "getProcessedTe... | {
"created": null,
"fork": null,
"fork_count": 14,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 36819131,
"size": 1256,
"stargazer_count": 16,
"stars": null,
"updates": null,
"url": "https://github.com/web-innovate/bootstraped-multi-test-results-report"
} |
36819131_1 | {
"fields": [],
"file": "junit-reporting-handlebars/src/test/java/com/github/bogdanlivadariu/reporting/junit/builder/JUnitReportBuilderTest.java",
"identifier": "JUnitReportBuilderTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void processedReportsSuitesTest() throws FileNotFoundException, JAXBException {\n List<String> xmlReports = new ArrayList<>();\n String report = this.getClass().getClassLoader().getResource(\"valid-report-2.xml\").getPath();\n xmlReports.add(report);\n JUnitRep... | {
"fields": [
{
"declarator": "SUITE_OVERVIEW = \"testSuitesOverview.html\"",
"modifier": "public static",
"original_string": "public static String SUITE_OVERVIEW = \"testSuitesOverview.html\";",
"type": "String",
"var_name": "SUITE_OVERVIEW"
},
{
"declarator": "TEST_OV... | {
"body": "public List<TestSuiteModel> getProcessedTestSuites() {\n return processedTestSuites;\n }",
"class_method_signature": "JUnitReportBuilder.getProcessedTestSuites()",
"constructor": false,
"full_signature": "public List<TestSuiteModel> getProcessedTestSuites()",
"identifier": "getProcessedTe... | {
"created": null,
"fork": null,
"fork_count": 14,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 36819131,
"size": 1256,
"stargazer_count": 16,
"stars": null,
"updates": null,
"url": "https://github.com/web-innovate/bootstraped-multi-test-results-report"
} |
36819131_10 | {
"fields": [
{
"declarator": "builder",
"modifier": "private",
"original_string": "private CucumberReportBuilder builder;",
"type": "CucumberReportBuilder",
"var_name": "builder"
},
{
"declarator": "reports",
"modifier": "private",
"original_string": "priva... | {
"body": "@Test\n public void featureSizeTest() {\n assertEquals(4, reports.getFeatures().size());\n }",
"class_method_signature": "AllFeatureReportsTest.featureSizeTest()",
"constructor": false,
"full_signature": "@Test public void featureSizeTest()",
"identifier": "featureSizeTest",
"invocat... | {
"fields": [
{
"declarator": "pageTitle",
"modifier": "private",
"original_string": "private String pageTitle;",
"type": "String",
"var_name": "pageTitle"
},
{
"declarator": "features",
"modifier": "private",
"original_string": "private List<Feature> featur... | {
"body": "public List<Feature> getFeatures() {\n return features;\n }",
"class_method_signature": "AllFeatureReports.getFeatures()",
"constructor": false,
"full_signature": "public List<Feature> getFeatures()",
"identifier": "getFeatures",
"invocations": [],
"modifiers": "public",
"parameters... | {
"created": null,
"fork": null,
"fork_count": 14,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 36819131,
"size": 1256,
"stargazer_count": 16,
"stars": null,
"updates": null,
"url": "https://github.com/web-innovate/bootstraped-multi-test-results-report"
} |
36819131_6 | {
"fields": [
{
"declarator": "xmlReports",
"modifier": "private",
"original_string": "private List<String> xmlReports;",
"type": "List<String>",
"var_name": "xmlReports"
},
{
"declarator": "reportPath = this.getClass().getClassLoader().getResource(\"valid-report-1.xml\... | {
"body": "@Test\n public void totalTestsTest() {\n assertEquals(reports.getTotalTests(), 13);\n }",
"class_method_signature": "AllJunitReportsTest.totalTestsTest()",
"constructor": false,
"full_signature": "@Test public void totalTestsTest()",
"identifier": "totalTestsTest",
"invocations": [
... | {
"fields": [
{
"declarator": "allTestSuites",
"modifier": "private",
"original_string": "private List<TestSuiteModel> allTestSuites;",
"type": "List<TestSuiteModel>",
"var_name": "allTestSuites"
},
{
"declarator": "suitesCount",
"modifier": "private",
"orig... | {
"body": "public int getTotalTests() {\n return totalTests;\n }",
"class_method_signature": "AllJUnitReports.getTotalTests()",
"constructor": false,
"full_signature": "public int getTotalTests()",
"identifier": "getTotalTests",
"invocations": [],
"modifiers": "public",
"parameters": "()",
"... | {
"created": null,
"fork": null,
"fork_count": 14,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 36819131,
"size": 1256,
"stargazer_count": 16,
"stars": null,
"updates": null,
"url": "https://github.com/web-innovate/bootstraped-multi-test-results-report"
} |
36819131_7 | {
"fields": [
{
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36819131_8 | {
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36819131_4 | {
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36819131_15 | {
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36819131_14 | {
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36819131_5 | {
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36819131_9 | {
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36819131_2 | {
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36819131_13 | {
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36819131_12 | {
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36819131_3 | {
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49632464_3 | {
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49632464_2 | {
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49632464_5 | {
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49632464_4 | {
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49632464_1 | {
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"body": "@Test\n public void testJSONBBoxDeserializer() throws IOException, DecodingException {\n try (ByteArrayInputStream input = new ByteArrayInputStream(BBOX_JSON.getBytes(StandardCharsets.UTF_8))) {\n Data<?> data = handler.parse(null, input, FORMAT);\n assertThat(data, is(insta... | {
"fields": [
{
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"type": "Set<Format>",
"var... | {
"body": "@Override\n public Data<?> parse(TypedProcessInputDescription<?> description, InputStream input, Format format)\n throws IOException, DecodingException {\n\n JsonNode bboxNode = objectMapper.readTree(input);\n\n ArrayNode arrayNode = (ArrayNode) bboxNode.get(BBOX);\n\n Js... | {
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"url": "https://github.com/52North/javaPS"
} |
49632464_0 | {
"fields": [
{
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"var_name": "X_MIN"
},
{
"declarator": "Y_MIN = 7.1",
"modifier": "private static final",
"ori... | {
"body": "@Test\n public void testJSONBBoxSerializer() throws IOException, EncodingException {\n OwsBoundingBox bbox = new OwsBoundingBox(new double[] { X_MIN, Y_MIN }, new double[] { X_MAX, Y_MAX },\n EPSG_4326);\n BoundingBoxData data = new BoundingBoxData(bbox);\n\n try (Inp... | {
"fields": [
{
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"type": "Set<Format>",
"var... | {
"body": "@Override\n public InputStream generate(TypedProcessOutputDescription<?> description, Data<?> data, Format format)\n throws IOException, EncodingException {\n\n InputStream result = null;\n\n if (data instanceof BoundingBoxData) {\n OwsBoundingBox boundingBox = ((Boun... | {
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"url": "https://github.com/52North/javaPS"
} |
31202652_16 | {
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{
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},
{
"declarator": "msScan1 = new SimpleMsScan(123, msFunctio... | {
"body": "@Test\n public void testScanNumber() throws MSDKException {\n // Verify scan number\n Assert.assertEquals(new Integer(123), msScan1.getScanNumber());\n }",
"class_method_signature": "SimpleMsScanTest.testScanNumber()",
"constructor": false,
"full_signature": "@Test public void testScanNumber(... | {
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{
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{
"declarator": "scanNumber",
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"constructor": false,
"full_signature": "@Override @Nonnull public Integer getScanNumber()",
"identifier": "getScanNumber",
"invocations": [],
"modi... | {
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"url": "https://github.com/msdk/msdk"
} |
31202652_41 | {
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{
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"original_string": "@Rule\n public final RestoreSystemProperties restoreSystemProperties = new RestoreSystemProperties();",
"type": "RestoreSystemProperties",
... | {
"body": "@Test\n public void testVersionWithLastUsed() {\n PiVersionsAction action = mock(PiVersionsAction.class);\n when(action.getLastUsedVersion()).thenReturn(\"1.3\");\n when(action.getCurrentVersion()).thenReturn(\"2.0\");\n\n PeakInvestigatorOptionsProvider provider =\n factory.createOptio... | {
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}
],
"file": "msdk-spectra-peakinvestigator/src/main/java/io/g... | {
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"url": "https://github.com/msdk/msdk"
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31202652_57 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCentroided4() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided4.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDat... | {
"fields": [],
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_4 | {
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{
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},
{
"declarator": "objSliceSparseMatrix",
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"body": "@Test\n public void testRemoveDataPoints() throws MSDKException, IOException {\n List<Triplet> updatedTripletList = objSliceSparseMatrix.removeDataPoints(1810596, 50, 77);\n for (int i = 0; i < updatedTripletList.size(); i++) {\n SliceSparseMatrix.Triplet triplet = updatedTripletList.get(i);\n ... | {
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{
"declarator": "sortListAccordingToMzScan",
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"body": "public List<Triplet> removeDataPoints(int roundedmz, int lowerScanBound, int upperScanBound) {\n\n Triplet searchTriplet = new Triplet();\n\n for (int i = lowerScanBound; i <= upperScanBound; i++) {\n\n searchTriplet.mz = roundedmz;\n searchTriplet.scanListIndex = i;\n int index = Coll... | {
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} |
31202652_82 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n @Ignore(\"Algorithm fails on this test, need a better algorithm\")\n public void testThresholded3() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"thresholded3.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFile... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_8 | {
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{
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}
],
"file": "msdk-io-filet... | {
"body": "@Test\n public void testMzXML() throws MSDKException, IOException {\n File fileName = new File(TEST_DATA_PATH + \"A1-0_A2.mzXML\");\n FileType fileType = FileTypeDetectionAlgorithm.detectDataFileType(fileName);\n Assert.assertEquals(FileType.MZXML, fileType);\n }",
"class_method_signature": "F... | {
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{
"declarator": "CDF_HEADER = \"CDF\"",
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},
{
"declarator": "MZML_HEADER = \"<mzML\"",
"modifier": "... | {
"body": "public static @Nullable FileType detectDataFileType(@Nonnull File fileName) throws IOException {\n\n // Parameter check\n Preconditions.checkNotNull(fileName);\n\n if (fileName.isDirectory()) {\n // To check for Waters .raw directory, we look for _FUNC[0-9]{3}.DAT\n for (File f : fileNam... | {
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31202652_77 | {
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} | {
"body": "@Test\n public void testProfile8() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile8.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDataFile ... | {
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_20 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testC10() throws MSDKException {\n\n String formula = \"C10\";\n\n MsSpectrum pattern =\n IsotopePatternGeneratorAlgorithm.generateIsotopes(formula, 0.0001, 1000.0f, 0.001);\n\n Assert.assertEquals(new Integer(4), pattern.getNumberOfDataPoints());\n Assert.assertEqua... | {
"fields": [
{
"declarator": "ELECTRON_MASS = 5.4857990943E-4",
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"type": "double",
"var_name": "ELECTRON_MASS"
},
{
"declarator": "formulaPattern =\n ... | {
"body": "public static @Nonnull MsSpectrum generateIsotopes(@Nonnull String chemicalFormula,\n @Nonnull Double minAbundance, @Nonnull Float intensityScale, @Nonnull Double mzTolerance) {\n\n Matcher m = formulaPattern.matcher(chemicalFormula);\n if (!m.matches())\n throw new IllegalArgumentException... | {
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31202652_36 | {
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{
"declarator": "mzValues1 = {100.0, 200.0}",
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"type": "double[]",
"var_name": "mzValues1"
},
{
"declarator": "intensityValues1 = {10.0f, 20.... | {
"body": "@Test\n public void testSpectrumToString() {\n MsSpectrum spectrum = mockSpectrum(mzValues1, intensityValues1);\n\n String result = TxtExportAlgorithm.spectrumToString(spectrum);\n String lines[] = result.split(\"\\\\r?\\\\n\");\n assertThat(lines, arrayContaining(expectedSimple));\n }",
"c... | {
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{
"class_method_signature": "TxtExportAlgorithm.exportSpectrum(@Nonnull File exportFile, @Nonnull MsSpectrum spectrum)",
"constr... | {
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"class_method_signature": "TxtExportAlgorithm.spectrumToString(@Nonnull MsSpectrum spectrum)",
"constructor": false,
"full_signature": "public static @Nonnull String sp... | {
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31202652_61 | {
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} | {
"body": "@Test\n public void testCentroided8() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided8.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDat... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_60 | {
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} | {
"body": "@Test\n public void testCentroided7() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided7.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDat... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_37 | {
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{
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"type": "double[]",
"var_name": "mzValues1"
},
{
"declarator": "intensityValues1 = {10.0f, 20.... | {
"body": "@Test\n public void testSpectrumToStringWithTabs() {\n MsSpectrum spectrum = mockSpectrum(mzValues1, intensityValues1);\n\n String result = TxtExportAlgorithm.spectrumToString(spectrum, \"\\t\");\n String lines[] = result.split(\"\\\\r?\\\\n\");\n assertThat(lines, arrayContaining(expectedSimp... | {
"fields": [],
"file": "msdk-io-txt/src/main/java/io/github/msdk/io/txt/TxtExportAlgorithm.java",
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{
"class_method_signature": "TxtExportAlgorithm.exportSpectrum(@Nonnull File exportFile, @Nonnull MsSpectrum spectrum)",
"constr... | {
"body": "public static @Nonnull String spectrumToString(@Nonnull MsSpectrum spectrum) {\n return spectrumToString(spectrum, \" \");\n }",
"class_method_signature": "TxtExportAlgorithm.spectrumToString(@Nonnull MsSpectrum spectrum)",
"constructor": false,
"full_signature": "public static @Nonnull String sp... | {
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31202652_21 | {
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"superclass": ""
} | {
"body": "@Test\n public void testC39H60N14O14() throws MSDKException {\n String formula = \"C39H60N14O14\";\n\n MsSpectrum pattern =\n IsotopePatternGeneratorAlgorithm.generateIsotopes(formula, 0.01, 1.0f, 0.1);\n\n Assert.assertEquals(new Integer(4), pattern.getNumberOfDataPoints());\n Assert.a... | {
"fields": [
{
"declarator": "ELECTRON_MASS = 5.4857990943E-4",
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{
"declarator": "formulaPattern =\n ... | {
"body": "public static @Nonnull MsSpectrum generateIsotopes(@Nonnull String chemicalFormula,\n @Nonnull Double minAbundance, @Nonnull Float intensityScale, @Nonnull Double mzTolerance) {\n\n Matcher m = formulaPattern.matcher(chemicalFormula);\n if (!m.matches())\n throw new IllegalArgumentException... | {
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31202652_76 | {
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} | {
"body": "@Test\n public void testProfile7() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile7.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDataFile ... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_9 | {
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{
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}
],
"file": "msdk-io-filet... | {
"body": "@Test\n public void testMzML() throws MSDKException, IOException {\n File fileName = new File(TEST_DATA_PATH + \"RawCentriodCidWithMsLevelInRefParamGroup.mzML\");\n FileType fileType = FileTypeDetectionAlgorithm.detectDataFileType(fileName);\n Assert.assertEquals(FileType.MZML, fileType);\n }",
... | {
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{
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},
{
"declarator": "MZML_HEADER = \"<mzML\"",
"modifier": "... | {
"body": "public static @Nullable FileType detectDataFileType(@Nonnull File fileName) throws IOException {\n\n // Parameter check\n Preconditions.checkNotNull(fileName);\n\n if (fileName.isDirectory()) {\n // To check for Waters .raw directory, we look for _FUNC[0-9]{3}.DAT\n for (File f : fileNam... | {
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"url": "https://github.com/msdk/msdk"
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31202652_83 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n @Ignore(\"Algorithm fails on this test, need a better algorithm\")\n public void testThresholded4() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"thresholded4.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFile... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
"identifier": "SpectrumTypeDetectionAlgorithm",
"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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"url": "https://github.com/msdk/msdk"
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31202652_5 | {
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{
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"var_name": "rawFile"
},
{
"declarator": "objSliceSparseMatrix",
"modifier": "private static",
"original_s... | {
"body": "@Test\n public void testgetBiGaussianValue() throws MSDKException {\n List<Triplet> horizontalSlice = objSliceSparseMatrix.getHorizontalSlice(1810596, 50, 77);\n BiGaussian objBiGaussian = new BiGaussian(horizontalSlice, 1810596, 50, 77);\n double biGaussianValue = objBiGaussian.get... | {
"fields": [
{
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},
{
"declarator": "mu",
"modifier": "public final",
"original_string": "public final int mu... | {
"body": "public double getValue(int x) {\n\n double sigma = x >= mu ? sigmaRight : sigmaLeft;\n double exponentialTerm = Math.exp(-1 * Math.pow(x - mu, 2) / (2 * Math.pow(sigma, 2)));\n return maxHeight * exponentialTerm;\n\n }",
"class_method_signature": "BiGaussian.getValue(int x)",
"c... | {
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31202652_56 | {
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"identifier": "SpectrumTypeDetectionAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCentroided3() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided3.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDat... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_40 | {
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{
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"modifier": "@Rule\n public final",
"original_string": "@Rule\n public final RestoreSystemProperties restoreSystemProperties = new RestoreSystemProperties();",
"type": "RestoreSystemProperties",
... | {
"body": "@Test\n public void testVersionNoLastUsed() {\n PiVersionsAction action = mock(PiVersionsAction.class);\n when(action.getLastUsedVersion()).thenReturn(\"\");\n when(action.getCurrentVersion()).thenReturn(\"1.3\");\n\n PeakInvestigatorOptionsProvider provider =\n factory.createOptionsPro... | {
"fields": [
{
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"var_name": "DEFAULT_RTO"
}
],
"file": "msdk-spectra-peakinvestigator/src/main/java/io/g... | {
"body": "@Override\n public PeakInvestigatorOptionsProvider createOptionsProvider(PiVersionsAction action,\n final int dataStart, final int dataEnd) {\n\n final String version = action.getLastUsedVersion().isEmpty() ? action.getCurrentVersion()\n : action.getLastUsedVersion();\n\n return new Peak... | {
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31202652_17 | {
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{
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},
{
"declarator": "msScan1 = new SimpleMsScan(123, msFunctio... | {
"body": "@Test\n public void testIsolationInfo() throws MSDKException {\n // Verify isolation info\n Assert.assertEquals(new LinkedList<>(), msScan1.getIsolations());\n\n // Change isolation info\n final @Nonnull List<IsolationInfo> newIsolations = msScan1.getIsolations();\n newIsolations.add(new Si... | {
"fields": [
{
"declarator": "dataFile",
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"type": "RawDataFile",
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},
{
"declarator": "scanNumber",
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"original_... | {
"body": "@Override\n @Nonnull\n public List<IsolationInfo> getIsolations() {\n return isolations;\n }",
"class_method_signature": "SimpleMsScan.getIsolations()",
"constructor": false,
"full_signature": "@Override @Nonnull public List<IsolationInfo> getIsolations()",
"identifier": "getIsolations",
"i... | {
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31202652_71 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testProfile2() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile2.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDataFile ... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_26 | {
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"identifier": "IsotopePatternGeneratorAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCharge2Neg() throws MSDKException {\n\n String formula = \"[C]2-\";\n\n MsSpectrum pattern =\n IsotopePatternGeneratorAlgorithm.generateIsotopes(formula, 0.01, 1000.0f, 0.0);\n\n Assert.assertEquals(new Integer(2), pattern.getNumberOfDataPoints());\n Assert.asser... | {
"fields": [
{
"declarator": "ELECTRON_MASS = 5.4857990943E-4",
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"type": "double",
"var_name": "ELECTRON_MASS"
},
{
"declarator": "formulaPattern =\n ... | {
"body": "public static @Nonnull MsSpectrum generateIsotopes(@Nonnull String chemicalFormula,\n @Nonnull Double minAbundance, @Nonnull Float intensityScale, @Nonnull Double mzTolerance) {\n\n Matcher m = formulaPattern.matcher(chemicalFormula);\n if (!m.matches())\n throw new IllegalArgumentException... | {
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"url": "https://github.com/msdk/msdk"
} |
31202652_30 | {
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{
"declarator": "folder = new TemporaryFolder()",
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"type": "TemporaryFolder",
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},
{
"declarator": "spectrumText = \"10.0... | {
"body": "@Test\n public void testSpectrumWithHeader() {\n StringBuilder builder = new StringBuilder();\n builder.append(\"# header line 1\\n\");\n builder.append(\"header line 2\\n\");\n builder.append(spectrumText);\n\n Collection<SimpleMsSpectrum> spectra =\n TxtImportAlgorithm.parseMsSpect... | {
"fields": [
{
"declarator": "linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\.\\\\d+)?)\")",
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"original_string": "private static final Pattern linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\... | {
"body": "public static @Nonnull Collection<SimpleMsSpectrum> parseMsSpectra(@Nonnull Reader reader) {\n\n Collection<SimpleMsSpectrum> result = new ArrayList<>();\n Scanner scanner = new Scanner(reader);\n\n while (scanner.hasNextLine()) {\n SimpleMsSpectrum spectrum = parseMsSpectrum(scanner);\n ... | {
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31202652_67 | {
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"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
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} | {
"body": "@Test\n public void testCentroided14() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided14.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawD... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_10 | {
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{
"declarator": "TEST_DATA_PATH = \"src/test/resources/\"",
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}
],
"file": "msdk-io-filet... | {
"body": "@Test\n public void testMzData() throws MSDKException, IOException {\n File fileName = new File(TEST_DATA_PATH + \"test.mzData\");\n FileType fileType = FileTypeDetectionAlgorithm.detectDataFileType(fileName);\n Assert.assertEquals(FileType.MZDATA, fileType);\n }",
"class_method_signature": "F... | {
"fields": [
{
"declarator": "CDF_HEADER = \"CDF\"",
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},
{
"declarator": "MZML_HEADER = \"<mzML\"",
"modifier": "... | {
"body": "public static @Nullable FileType detectDataFileType(@Nonnull File fileName) throws IOException {\n\n // Parameter check\n Preconditions.checkNotNull(fileName);\n\n if (fileName.isDirectory()) {\n // To check for Waters .raw directory, we look for _FUNC[0-9]{3}.DAT\n for (File f : fileNam... | {
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} |
31202652_47 | {
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} | {
"body": "@Test\n public void multipleMgfImportTest() throws IOException, MSDKException {\n final int expectedSize = 10;\n final String expectedTitles[] = {\n \"PRIDE_Exp_mzData_Ac_9266.xml_id_1\",\n \"PRIDE_Exp_mzData_Ac_9266.xml_id_2\",\n \"PRIDE_Exp_mzData_Ac_9266.xml_id_3\",\n ... | {
"fields": [
{
"declarator": "PEPMASS_PATTERN = Pattern.compile(\"(?<=PEPMASS=)(\\\\d+\\\\.\\\\d+)\")",
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"original_string": "private final Pattern PEPMASS_PATTERN = Pattern.compile(\"(?<=PEPMASS=)(\\\\d+\\\\.\\\\d+)\");",
"type": "Pattern",
"var_name": "P... | {
"body": "@Nullable\n @Override\n public List<MgfMsSpectrum> execute() throws MSDKException {\n logger.info(\"Started MGF import from {}\", target);\n spectra = new LinkedList<>();\n\n String line;\n try (final BufferedReader reader = new BufferedReader(new FileReader(target))) {\n while (!cancell... | {
"created": null,
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"url": "https://github.com/msdk/msdk"
} |
31202652_51 | {
"fields": [],
"file": "msdk-spectra-centroiding/src/test/java/io/github/msdk/spectra/centroiding/WaveletCentroidingAlgorithmTest.java",
"identifier": "WaveletCentroidingAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testOrbitrap() throws Exception {\n\n // Import the file\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile_orbitrap.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMeth... | {
"fields": [
{
"declarator": "NPOINTS = 60000",
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"original_string": "private static final double NPOINTS = 60000;",
"type": "double",
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},
{
"declarator": "WAVELET_ESL = -5",
"modifier": "private static final... | {
"body": "@Override\n public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) {\n\n // Copy all scan properties\n SimpleMsScan newScan = MsScanUtil.clone(inputScan, false);\n\n // Load data points\n double[] mzBuffer = inputScan.getMzValues();\n float[] intensityBuffer = inputScan.getIntensity... | {
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"url": "https://github.com/msdk/msdk"
} |
31202652_2 | {
"fields": [
{
"declarator": "rawFile",
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"type": "RawDataFile",
"var_name": "rawFile"
},
{
"declarator": "objSliceSparseMatrix",
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"body": "@Test\n public void getVerticalSlice() throws MSDKException, IOException {\n List<SliceSparseMatrix.VerticalSliceDataPoint> slice = objSliceSparseMatrix.getVerticalSlice(5);\n Assert.assertEquals(5389, slice.size());\n }",
"class_method_signature": "SliceSparseMatrixTest.getVerticalSlice()",
"c... | {
"fields": [
{
"declarator": "rtMap",
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"type": "HashMap<Integer, Float>",
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{
"declarator": "sortListAccordingToMzScan",
"modifier": "private final... | {
"body": "public List<VerticalSliceDataPoint> getVerticalSlice(int scanNumber) {\n\n List<Triplet> oneScanTriplet = new ArrayList<Triplet>();\n List<VerticalSliceDataPoint> datapointList = new ArrayList<VerticalSliceDataPoint>();\n\n Triplet searchTriplet = new Triplet();\n searchTriplet.scanListIndex = ... | {
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"url": "https://github.com/msdk/msdk"
} |
31202652_84 | {
"fields": [],
"file": "msdk-spectra-splash/src/test/java/io/github/msdk/spectra/splash/SplashCalculationAlgorithmTest.java",
"identifier": "SplashCalculationAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testSplash1() throws MSDKException {\n\n double mzValues[] = new double[] {100.0, 101.0, 102.0};\n float intValues[] = new float[] {1.0f, 2.0f, 3.0f};\n\n final String correctSplash = \"splash10-0udi-0900000000-f5bf6f6a4a1520a35d4f\";\n final String calculatedSplash =\n ... | {
"fields": [
{
"declarator": "splashFactory = SplashFactory.create()",
"modifier": "private static final",
"original_string": "private static final Splash splashFactory = SplashFactory.create();",
"type": "Splash",
"var_name": "splashFactory"
}
],
"file": "msdk-spectra-splas... | {
"body": "public static @Nonnull String calculateSplash(@Nonnull MsSpectrum spectrum) {\n\n return calculateSplash(spectrum.getMzValues(), spectrum.getIntensityValues(),\n spectrum.getNumberOfDataPoints());\n }",
"class_method_signature": "SplashCalculationAlgorithm.calculateSplash(@Nonnull MsSpectrum s... | {
"created": null,
"fork": null,
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"is_fork": false,
"language": "Java",
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"stars": null,
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"url": "https://github.com/msdk/msdk"
} |
31202652_85 | {
"fields": [],
"file": "msdk-spectra-splash/src/test/java/io/github/msdk/spectra/splash/SplashCalculationAlgorithmTest.java",
"identifier": "SplashCalculationAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testSplash2() throws MSDKException {\n\n double mzValues[] = new double[] {100.0};\n float intValues[] = new float[] {50f};\n\n final String correctSplash = \"splash10-0udi-0900000000-cc0ed451a7eca3bcb4a6\";\n final String calculatedSplash =\n SplashCalculationAlgori... | {
"fields": [
{
"declarator": "splashFactory = SplashFactory.create()",
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"original_string": "private static final Splash splashFactory = SplashFactory.create();",
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],
"file": "msdk-spectra-splas... | {
"body": "public static @Nonnull String calculateSplash(@Nonnull MsSpectrum spectrum) {\n\n return calculateSplash(spectrum.getMzValues(), spectrum.getIntensityValues(),\n spectrum.getNumberOfDataPoints());\n }",
"class_method_signature": "SplashCalculationAlgorithm.calculateSplash(@Nonnull MsSpectrum s... | {
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31202652_3 | {
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{
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31202652_50 | {
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"body": "@Test\n public void testOrbitrap() throws Exception {\n\n // Import the file\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile_orbitrap.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMeth... | {
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"declarator": "mzBuffer[] = new double[10000]",
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31202652_46 | {
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} | {
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"body": "@Nullable\n @Override\n public List<MgfMsSpectrum> execute() throws MSDKException {\n logger.info(\"Started MGF import from {}\", target);\n spectra = new LinkedList<>();\n\n String line;\n try (final BufferedReader reader = new BufferedReader(new FileReader(target))) {\n while (!cancell... | {
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31202652_11 | {
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{
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31202652_66 | {
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"body": "@Test\n public void testCentroided13() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided13.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawD... | {
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{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_31 | {
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31202652_27 | {
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{
"declarator": "spectrumText = \"10.0... | {
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{
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31202652_70 | {
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} | {
"body": "@Test\n public void testProfile1() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile1.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDataFile ... | {
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"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
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31202652_65 | {
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"body": "@Test\n public void testCentroided12() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided12.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawD... | {
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{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_32 | {
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{
"declarator": "spectrumText = \"10.0... | {
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"class_method_signature": "TxtImportAlgorithmTest.testNoSpectrumAsString()",
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{
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"body": "private static @Nonnull SimpleMsSpectrum parseMsSpectrum(@Nonnull Scanner scanner) {\n\n double mzValues[] = new double[16];\n float intensityValues[] = new float[16];\n int size = 0;\n\n while (scanner.hasNextLine()) {\n String line = scanner.nextLine();\n Matcher m = linePattern.mat... | {
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31202652_24 | {
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} | {
"body": "@Test\n public void testCharge1Pos() throws MSDKException {\n\n String formula = \"C+\";\n\n MsSpectrum pattern =\n IsotopePatternGeneratorAlgorithm.generateIsotopes(formula, 0.01, 1000.0f, 0.005);\n\n Assert.assertEquals(new Integer(2), pattern.getNumberOfDataPoints());\n Assert.assert... | {
"fields": [
{
"declarator": "ELECTRON_MASS = 5.4857990943E-4",
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{
"declarator": "formulaPattern =\n ... | {
"body": "public static @Nonnull MsSpectrum generateIsotopes(@Nonnull String chemicalFormula,\n @Nonnull Double minAbundance, @Nonnull Float intensityScale, @Nonnull Double mzTolerance) {\n\n Matcher m = formulaPattern.matcher(chemicalFormula);\n if (!m.matches())\n throw new IllegalArgumentException... | {
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31202652_73 | {
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} | {
"body": "@Test\n public void testProfile4() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile4.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDataFile ... | {
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{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
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31202652_49 | {
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} | {
"body": "@Test(expected = MSDKException.class)\n public void malformedInputRegexpTest() throws MSDKException {\n final String file = \"malformed_query.mgf\";\n File inputFile = getResourcePath(file).toFile();\n MgfFileImportMethod importMethod = new MgfFileImportMethod(inputFile);\n\n importMethod.exec... | {
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{
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31202652_86 | {
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"body": "@Test\n public void testValidmzMLfile() throws Exception {\n\n File inputFile = new File(this.getClass().getClassLoader().getResource(\"msms.mzML\").toURI());\n\n Assert.assertNotNull(inputFile);\n FeatureFinderMetaboDetector mzDetector = new FeatureFinderMetaboDetector(inputFile);\n Assert.as... | {
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{
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"... | {
"body": "public List<Double> execute() throws XMLStreamException, IOException, MSDKException {\n\t\tList<Double> mzValuesResult = new ArrayList<Double>();\n\t\tcreateTempFeatureXMLFile();\n\n\t\tXMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();\n\t\tXMLEventReader xmlEventReader = xmlInputFactory.cre... | {
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31202652_69 | {
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} | {
"body": "@Test\n @Ignore(\"Algorithm fails on this test, need a better algorithm\")\n public void testCentroided16() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided16.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFile... | {
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{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_28 | {
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{
"declarator": "spectrumText = \"10.0... | {
"body": "@Test\n public void test4PeaksFromFile() throws IOException {\n File file = folder.newFile();\n FileWriter writer = new FileWriter(file);\n writer.write(spectrumText);\n writer.close();\n\n MsSpectrum spectrum = TxtImportAlgorithm.parseMsSpectrum(new FileReader(file));\n\n assertThat(spe... | {
"fields": [
{
"declarator": "linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\.\\\\d+)?)\")",
"modifier": "private static final",
"original_string": "private static final Pattern linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\... | {
"body": "private static @Nonnull SimpleMsSpectrum parseMsSpectrum(@Nonnull Scanner scanner) {\n\n double mzValues[] = new double[16];\n float intensityValues[] = new float[16];\n int size = 0;\n\n while (scanner.hasNextLine()) {\n String line = scanner.nextLine();\n Matcher m = linePattern.mat... | {
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31202652_0 | {
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}
],
"file": "msdk-featuredetection-adap3d/src/test/java/io/github/msdk/featuredetection/adap3d/ADAP3D... | {
"body": "@Test\n @Ignore(\"Temporarily ignored, until ADAP3D work is resumed\")\n public void testPeakDetection() throws MSDKException, IOException {\n\n ADAP3DFeatureDetectionMethod ob =\n new ADAP3DFeatureDetectionMethod(rawFile, new ADAP3DFeatureDetectionParameters());\n List<Feature> featureList ... | {
"fields": [
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"declarator": "logger = LoggerFactory.getLogger(this.getClass())",
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{
"declarator": "rawFi... | {
"body": "public List<Feature> execute() {\n\n logger.info(\"Starting ADAP3D feature detection on file \" + rawFile.getName());\n \n // Create SliceSparseMatrix\n logger.debug(\"Loading the raw data into SliceSparceMatrix\");\n this.objSliceSparseMatrix = new SliceSparseMatrix(rawFile, msScanPredicate... | {
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31202652_53 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testOrbitrap() throws Exception {\n\n // Import the file\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile_orbitrap.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMeth... | {
"fields": [
{
"declarator": "binSize",
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{
"declarator": "newScan",
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"original_string": "priva... | {
"body": "@Override\n public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) {\n\n // Copy all scan properties\n this.newScan = MsScanUtil.clone(inputScan, false);\n\n // Load data points\n mzBuffer = inputScan.getMzValues();\n intensityBuffer = inputScan.getIntensityValues();\n numOfDataP... | {
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"url": "https://github.com/msdk/msdk"
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31202652_45 | {
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} | {
"body": "@Test\n public void testExportMSP() throws MSDKException, IOException {\n\n File tmpFile = File.createTempFile(\"msdktest\", \"msp\");\n tmpFile.deleteOnExit();\n\n MsSpectrum testSpectrum = new SimpleMsSpectrum(new double[] {10.0, 20.0, 30.0},\n new float[] {100f, 200f, 300f}, 3, MsSpectr... | {
"fields": [],
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{
"class_method_signature": "MspExportAlgorithm.exportSpectrum(@Nonnull File exportFile, @Nonnull MsSpectrum spectrum)",
"constr... | {
"body": "public static void exportSpectrum(@Nonnull File exportFile, @Nonnull MsSpectrum spectrum)\n throws IOException, MSDKException {\n exportSpectra(exportFile, Collections.singleton(spectrum));\n }",
"class_method_signature": "MspExportAlgorithm.exportSpectrum(@Nonnull File exportFile, @Nonnull MsSp... | {
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"url": "https://github.com/msdk/msdk"
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31202652_12 | {
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{
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"file": "msdk-io-filet... | {
"body": "@Test\n public void testWatersRaw() throws MSDKException, IOException {\n File fileName = new File(TEST_DATA_PATH + \"20150813-63.raw\");\n FileType fileType = FileTypeDetectionAlgorithm.detectDataFileType(fileName);\n Assert.assertEquals(FileType.WATERS_RAW, fileType);\n }",
"class_method_sig... | {
"fields": [
{
"declarator": "CDF_HEADER = \"CDF\"",
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{
"declarator": "MZML_HEADER = \"<mzML\"",
"modifier": "... | {
"body": "public static @Nullable FileType detectDataFileType(@Nonnull File fileName) throws IOException {\n\n // Parameter check\n Preconditions.checkNotNull(fileName);\n\n if (fileName.isDirectory()) {\n // To check for Waters .raw directory, we look for _FUNC[0-9]{3}.DAT\n for (File f : fileNam... | {
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31202652_13 | {
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],
"file": "msdk-io-filet... | {
"body": "@Test\n public void testMzTAB() throws MSDKException, IOException {\n File fileName = new File(TEST_DATA_PATH + \"lipidomics-HFD-LD-study-PL-DG-SM.mzTab\");\n FileType fileType = FileTypeDetectionAlgorithm.detectDataFileType(fileName);\n Assert.assertEquals(FileType.MZTAB, fileType);\n }",
"cl... | {
"fields": [
{
"declarator": "CDF_HEADER = \"CDF\"",
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{
"declarator": "MZML_HEADER = \"<mzML\"",
"modifier": "... | {
"body": "public static @Nullable FileType detectDataFileType(@Nonnull File fileName) throws IOException {\n\n // Parameter check\n Preconditions.checkNotNull(fileName);\n\n if (fileName.isDirectory()) {\n // To check for Waters .raw directory, we look for _FUNC[0-9]{3}.DAT\n for (File f : fileNam... | {
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31202652_44 | {
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{
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],
"file": "msdk-io-msp/s... | {
"body": "@Test\n public void testSampleMSP() throws MSDKException, IOException {\n\n // Import the file\n File inputFile = new File(TEST_DATA_PATH + \"sample.msp\");\n\n MspSpectrum spectrum = MspImportAlgorithm.parseMspFromFile(inputFile);\n\n Assert.assertEquals(new Integer(18), spectrum.getNumberOfD... | {
"fields": [
{
"declarator": "propertyPattern = Pattern.compile(\"^([A-Z]+): (.+)\")",
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"original_string": "private static final Pattern propertyPattern = Pattern.compile(\"^([A-Z]+): (.+)\");",
"type": "Pattern",
"var_name": "propertyPattern"
... | {
"body": "public static @Nonnull MspSpectrum parseMspFromFile(@Nonnull File mspFile)\n throws IOException, MSDKException {\n\n String str = Files.toString(mspFile, Charsets.ISO_8859_1);\n\n if (Strings.isNullOrEmpty(str))\n throw new IOException(\"Could not parse content of file \" + mspFile);\n\n ... | {
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"url": "https://github.com/msdk/msdk"
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31202652_52 | {
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"file": "msdk-spectra-centroiding/src/test/java/io/github/msdk/spectra/centroiding/LocalMaximaCentroidingAlgorithmTest.java",
"identifier": "LocalMaximaCentroidingAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testOrbitrap() throws Exception {\n\n // Import the file\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile_orbitrap.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMeth... | {
"fields": [
{
"declarator": "newScan",
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"type": "SimpleMsScan",
"var_name": "newScan"
},
{
"declarator": "mzBuffer[] = new double[10000]",
"modifier": "private @Nonnull",
"original_s... | {
"body": "@Override\n public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) {\n\n // Copy all scan properties\n this.newScan = MsScanUtil.clone(inputScan, false);\n\n // Load data points\n mzBuffer = inputScan.getMzValues();\n intensityBuffer = inputScan.getIntensityValues();\n final int ... | {
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"url": "https://github.com/msdk/msdk"
} |
31202652_1 | {
"fields": [
{
"declarator": "rawFile",
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"var_name": "rawFile"
},
{
"declarator": "objSliceSparseMatrix",
"modifier": "private static",
"original_s... | {
"body": "@Test\n public void getHorizontalSlice() throws MSDKException, IOException {\n List<Triplet> slice = objSliceSparseMatrix.getHorizontalSlice(181.0596, 50, 77);\n Assert.assertEquals(28, slice.size());\n }",
"class_method_signature": "SliceSparseMatrixTest.getHorizontalSlice()",
"constructor": f... | {
"fields": [
{
"declarator": "rtMap",
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"original_string": "private final HashMap<Integer, Float> rtMap;",
"type": "HashMap<Integer, Float>",
"var_name": "rtMap"
},
{
"declarator": "sortListAccordingToMzScan",
"modifier": "private final... | {
"body": "public List<Triplet> getHorizontalSlice(double mz, int lowerScanBound, int upperScanBound) {\n\n int roundedmz = roundMZ(mz);\n List<Triplet> sliceList = new ArrayList<Triplet>();\n\n for (int i = lowerScanBound; i <= upperScanBound; i++) {\n Triplet searchTriplet = new Triplet();\n sear... | {
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} |
31202652_29 | {
"fields": [
{
"declarator": "folder = new TemporaryFolder()",
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"type": "TemporaryFolder",
"var_name": "folder"
},
{
"declarator": "spectrumText = \"10.0... | {
"body": "@Test\n public void testTwoSpetra() {\n\n Collection<SimpleMsSpectrum> spectra =\n TxtImportAlgorithm.parseMsSpectra(new StringReader(spectraText));\n assertThat(spectra.size(), equalTo(2));\n\n Iterator<SimpleMsSpectrum> iterator = spectra.iterator();\n\n MsSpectrum spectrum = iterator... | {
"fields": [
{
"declarator": "linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\.\\\\d+)?)\")",
"modifier": "private static final",
"original_string": "private static final Pattern linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\... | {
"body": "public static @Nonnull Collection<SimpleMsSpectrum> parseMsSpectra(@Nonnull Reader reader) {\n\n Collection<SimpleMsSpectrum> result = new ArrayList<>();\n Scanner scanner = new Scanner(reader);\n\n while (scanner.hasNextLine()) {\n SimpleMsSpectrum spectrum = parseMsSpectrum(scanner);\n ... | {
"created": null,
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} |
31202652_87 | {
"fields": [],
"file": "msdk-featuredetection-openms/src/test/java/io/github/msdk/featuredetection/openms/FeatureFinderMetaboDetectorTest.java",
"identifier": "FeatureFinderMetaboDetectorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test(expected = MSDKException.class)\n public void testInvalidmzMLFile() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"truncated.mzML\").toURI());\n\n Assert.assertNotNull(inputFile);\n FeatureFinderMetaboDetector mzDetector3 = new Featu... | {
"fields": [
{
"declarator": "OPENMS_FEATURE_FINDER_METABO_LIBRARY_NAME",
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"type": "String",
"var_name": "OPENMS_FEATURE_FINDER_METABO_LIBRARY_NAME"
},
{
"... | {
"body": "public List<Double> execute() throws XMLStreamException, IOException, MSDKException {\n\t\tList<Double> mzValuesResult = new ArrayList<Double>();\n\t\tcreateTempFeatureXMLFile();\n\n\t\tXMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();\n\t\tXMLEventReader xmlEventReader = xmlInputFactory.cre... | {
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} |
31202652_68 | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
"identifier": "SpectrumTypeDetectionAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCentroided15() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided15.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawD... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
"identifier": "SpectrumTypeDetectionAlgorithm",
"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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} |
31202652_48 | {
"fields": [],
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void levelsTest() throws MSDKException {\n final String fname = \"levels.mgf\";\n final File inputFile = getResourcePath(fname).toFile();\n final Integer[] expectedLevels = {1, 2, null};\n\n MgfFileImportMethod importMethod = new MgfFileImportMethod(inputFile);\n List<MgfMsSp... | {
"fields": [
{
"declarator": "PEPMASS_PATTERN = Pattern.compile(\"(?<=PEPMASS=)(\\\\d+\\\\.\\\\d+)\")",
"modifier": "private final",
"original_string": "private final Pattern PEPMASS_PATTERN = Pattern.compile(\"(?<=PEPMASS=)(\\\\d+\\\\.\\\\d+)\");",
"type": "Pattern",
"var_name": "P... | {
"body": "@Nullable\n @Override\n public List<MgfMsSpectrum> execute() throws MSDKException {\n logger.info(\"Started MGF import from {}\", target);\n spectra = new LinkedList<>();\n\n String line;\n try (final BufferedReader reader = new BufferedReader(new FileReader(target))) {\n while (!cancell... | {
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31202652_72 | {
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"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
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} | {
"body": "@Test\n public void testProfile3() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile3.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDataFile ... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
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"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
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31202652_25 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCharge2Pos() throws MSDKException {\n\n String formula = \"[C]2+\";\n\n MsSpectrum pattern =\n IsotopePatternGeneratorAlgorithm.generateIsotopes(formula, 0.01, 1000.0f, 0.0);\n\n Assert.assertEquals(new Integer(2), pattern.getNumberOfDataPoints());\n Assert.asser... | {
"fields": [
{
"declarator": "ELECTRON_MASS = 5.4857990943E-4",
"modifier": "private static final",
"original_string": "private static final double ELECTRON_MASS = 5.4857990943E-4;",
"type": "double",
"var_name": "ELECTRON_MASS"
},
{
"declarator": "formulaPattern =\n ... | {
"body": "public static @Nonnull MsSpectrum generateIsotopes(@Nonnull String chemicalFormula,\n @Nonnull Double minAbundance, @Nonnull Float intensityScale, @Nonnull Double mzTolerance) {\n\n Matcher m = formulaPattern.matcher(chemicalFormula);\n if (!m.matches())\n throw new IllegalArgumentException... | {
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} |
31202652_33 | {
"fields": [
{
"declarator": "folder = new TemporaryFolder()",
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"type": "TemporaryFolder",
"var_name": "folder"
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{
"declarator": "spectrumText = \"10.0... | {
"body": "@Test\n public void testNoSpectrumAsReader() {\n MsSpectrum spectrum = TxtImportAlgorithm.parseMsSpectrum(new StringReader(\"not a spectrum\"));\n assertThat(spectrum, nullValue());\n }",
"class_method_signature": "TxtImportAlgorithmTest.testNoSpectrumAsReader()",
"constructor": false,
"full_... | {
"fields": [
{
"declarator": "linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\.\\\\d+)?)\")",
"modifier": "private static final",
"original_string": "private static final Pattern linePattern =\n Pattern.compile(\"(\\\\d+(\\\\.\\\\d+)?)[^\\\\d]+(\\\\d+(\\\\... | {
"body": "private static @Nonnull SimpleMsSpectrum parseMsSpectrum(@Nonnull Scanner scanner) {\n\n double mzValues[] = new double[16];\n float intensityValues[] = new float[16];\n int size = 0;\n\n while (scanner.hasNextLine()) {\n String line = scanner.nextLine();\n Matcher m = linePattern.mat... | {
"created": null,
"fork": null,
"fork_count": 40,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 31202652,
"size": 213452,
"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
31202652_64 | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
"identifier": "SpectrumTypeDetectionAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCentroided11() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided11.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawD... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
"identifier": "SpectrumTypeDetectionAlgorithm",
"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
"created": null,
"fork": null,
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"language": "Java",
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"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
31202652_80 | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
"identifier": "SpectrumTypeDetectionAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testThresholded1() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"thresholded1.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawD... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
"identifier": "SpectrumTypeDetectionAlgorithm",
"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
"created": null,
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"is_fork": false,
"language": "Java",
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"repo_id": 31202652,
"size": 213452,
"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
31202652_38 | {
"fields": [
{
"declarator": "restoreSystemProperties = new RestoreSystemProperties()",
"modifier": "@Rule\n public final",
"original_string": "@Rule\n public final RestoreSystemProperties restoreSystemProperties = new RestoreSystemProperties();",
"type": "RestoreSystemProperties",
... | {
"body": "@Test\n public void testProjectInfoMissing() {\n PeakInvestigatorProjectProvider provider = factory.createProjectProvider();\n assertThat(provider.show(), equalTo(PeakInvestigatorProvider.Status.CANCEL));\n }",
"class_method_signature": "PeakInvestigatorDefaultProviderFactoryTest.testProjectInfoM... | {
"fields": [
{
"declarator": "DEFAULT_RTO = \"RTO-24\"",
"modifier": "private final static",
"original_string": "private final static String DEFAULT_RTO = \"RTO-24\";",
"type": "String",
"var_name": "DEFAULT_RTO"
}
],
"file": "msdk-spectra-peakinvestigator/src/main/java/io/g... | {
"body": "@Override\n public PeakInvestigatorProjectProvider createProjectProvider() {\n return new PeakInvestigatorProjectProvider() {\n\n @Override\n public Status show() {\n if (System.getProperty(\"peakinvestigator.username\") == null\n || System.getProperty(\"peakinvestigator.pas... | {
"created": null,
"fork": null,
"fork_count": 40,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 31202652,
"size": 213452,
"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
31202652_79 | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
"identifier": "SpectrumTypeDetectionAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n @Ignore(\"Algorithm fails on this test, need a better algorithm\")\n public void testProfile10() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"profile10.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImport... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
"identifier": "SpectrumTypeDetectionAlgorithm",
"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
"created": null,
"fork": null,
"fork_count": 40,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 31202652,
"size": 213452,
"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
31202652_6 | {
"fields": [
{
"declarator": "rawFile",
"modifier": "private static",
"original_string": "private static RawDataFile rawFile;",
"type": "RawDataFile",
"var_name": "rawFile"
},
{
"declarator": "objSliceSparseMatrix",
"modifier": "private static",
"original_s... | {
"body": "@Test\n public void testInterpolationX() {\n\n final int numTriplets = 5;\n List<Triplet> triplets = new ArrayList<>(numTriplets);\n for (int i = 0; i < numTriplets; ++i) triplets.add(new Triplet());\n triplets.get(0).mz = 40;\n triplets.get(0).scanListIndex = 1;\n ... | {
"fields": [
{
"declarator": "maxHeight",
"modifier": "public final",
"original_string": "public final double maxHeight;",
"type": "double",
"var_name": "maxHeight"
},
{
"declarator": "mu",
"modifier": "public final",
"original_string": "public final int mu... | {
"body": "private double InterpolationX(List<Triplet> horizontalSlice, int mu, double halfHeight,\n int leftBound, int rightBound, int roundedmz, Direction direction) {\n\n int step = direction == Direction.RIGHT ? 1 : -1;\n\n Comparator<Triplet> compareMzScan = (t1, t2... | {
"created": null,
"fork": null,
"fork_count": 40,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 31202652,
"size": 213452,
"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
31202652_55 | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/test/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithmTest.java",
"identifier": "SpectrumTypeDetectionAlgorithmTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCentroided2() throws Exception {\n\n File inputFile =\n new File(this.getClass().getClassLoader().getResource(\"centroided2.mzML\").toURI());\n Assert.assertTrue(inputFile.canRead());\n MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);\n RawDat... | {
"fields": [],
"file": "msdk-spectra-centroidprofiledetection/src/main/java/io/github/msdk/spectra/centroidprofiledetection/SpectrumTypeDetectionAlgorithm.java",
"identifier": "SpectrumTypeDetectionAlgorithm",
"interfaces": "",
"methods": [
{
"class_method_signature": "SpectrumTypeDetectionAlgorith... | {
"body": "public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) {\n double mzValues[] = msSpectrum.getMzValues();\n float intensityValues[] = msSpectrum.getIntensityValues();\n Integer size = msSpectrum.getNumberOfDataPoints();\n return detectSpectrumType(mzValues, intensityValu... | {
"created": null,
"fork": null,
"fork_count": 40,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 31202652,
"size": 213452,
"stargazer_count": 26,
"stars": null,
"updates": null,
"url": "https://github.com/msdk/msdk"
} |
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