Maven xdoc Plugin - Checkstyle Results

Checkstyle Results

The following document contains the results of Checkstyle .

Summary

Files	Errors
422	609

Files

Files	Errors
org/mskcc/pathdb/action/BioPaxParentChild.java	1
org/mskcc/pathdb/action/DownloadSource.java	6
org/mskcc/pathdb/action/ExecuteSearch.java	1
org/mskcc/pathdb/action/FeedbackAction.java	2
org/mskcc/pathdb/action/IconRetriever.java	1
org/mskcc/pathdb/action/ShowBioPaxRecord2.java	35
org/mskcc/pathdb/action/ShowDataSourceDetails.java	1
org/mskcc/pathdb/action/StoreGlobalFilterSettings.java	11
org/mskcc/pathdb/action/admin/AdminHomeAction.java	1
org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteGetParentsXmlResponse.java	1
org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteHtmlResponse.java	1
org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteSearchXmlResponse.java	1
org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteTextResponse.java	6
org/mskcc/pathdb/bb/action/HomeAction.java	1
org/mskcc/pathdb/bb/action/WebService.java	1
org/mskcc/pathdb/bb/action/package.html	1
org/mskcc/pathdb/bb/model/BBGeneRecord.java	2
org/mskcc/pathdb/bb/model/BBPathwayRecord.java	6
org/mskcc/pathdb/bb/model/package.html	1
org/mskcc/pathdb/bb/sql/dao/DaoBBGene.java	5
org/mskcc/pathdb/bb/sql/dao/DaoBBInternalLink.java	1
org/mskcc/pathdb/bb/sql/dao/DaoBBPathway.java	1
org/mskcc/pathdb/bb/sql/dao/package.html	1
org/mskcc/pathdb/form/FeedbackForm.java	5
org/mskcc/pathdb/form/WebUIBean.java	1
org/mskcc/pathdb/lucene/BioPaxToIndex.java	1
org/mskcc/pathdb/lucene/IndexFactory.java	2
org/mskcc/pathdb/lucene/IndexRules.java	3
org/mskcc/pathdb/lucene/LuceneAutoFilter.java	1
org/mskcc/pathdb/lucene/LuceneQuery.java	1
org/mskcc/pathdb/lucene/LuceneReader.java	2
org/mskcc/pathdb/lucene/RecordIndexer.java	3
org/mskcc/pathdb/model/BioPaxEntityTypeMap.java	1
org/mskcc/pathdb/model/BioPaxTabs.java	4
org/mskcc/pathdb/model/Evidence.java	1
org/mskcc/pathdb/model/ExternalDatabaseRecord.java	5
org/mskcc/pathdb/model/GlobalFilterSettings.java	1
org/mskcc/pathdb/model/Reference.java	3
org/mskcc/pathdb/model/TypeCount.java	1
org/mskcc/pathdb/protocol/ProtocolConstants.java	1
org/mskcc/pathdb/protocol/ProtocolConstantsVersion2.java	1
org/mskcc/pathdb/protocol/ProtocolRequest.java	12
org/mskcc/pathdb/protocol/ProtocolValidatorVersion1.java	2
org/mskcc/pathdb/protocol/ProtocolValidatorVersion2.java	1
org/mskcc/pathdb/query/batch/PathwayBatchQuery.java	1
org/mskcc/pathdb/query/batch/PhysicalEntityWithPathwayList.java	1
org/mskcc/pathdb/query/batch/package.html	1
org/mskcc/path db/schemas/biopax/BioPaxUtil.java	1
org/mskcc/pathdb/schemas/biopax/ImportBioPaxToCPath.java	1
org/mskcc/pathdb/schemas/biopax/MemberMolecules.java	1
org/mskcc/pathdb/schemas/biopax/MemberPathways.java	1
org/mskcc/pathdb/schemas/biopax/TransformBioPaxToCPathRecords.java	9
org/mskcc/pathdb/schemas/biopax/UpdateRdfLinks.java	1
org/mskcc/pathdb/schemas/biopax/summary/BioPaxFeature.java	1
org/mskcc/pathdb/schemas/biopax/summary/BioPaxRecordSummaryUtils.java	1
org/mskcc/pathdb/schemas/biopax/summary/EntitySummaryParserNoCache.java	1
org/mskcc/pathdb/schemas/biopax/ summary/InteractionSummary.java	1
org/mskcc/pathdb/schemas/biopax/summary/InteractionSummaryUtils.java	7
org/mskcc/pathdb/schemas/biopax/summary/ParticipantSummaryComponent.java	1
org/mskcc/pathdb/schemas/biopax/summary/SummaryListUtil.java	1
org/mskcc/pathdb/servlet/CPathServletResponse.java	36
org/mskcc/pathdb/servlet/CPathUIConfig.java	1
org/mskcc/pathdb/servlet/CytoscapeJnlpServlet.java	157
org/mskcc/pathdb/sql/JdbcUtil.java	4
org/mskcc/pathdb/sql/assembly/PsiAssemblerStringOnly.java	3
org/mskcc/pathdb/sql/assembly/PsiAssembly.java	4
org/mskcc/pathdb/sql/assembly/PsiAssemblyStringOnly.java	3
org/mskcc/pathdb/sql/assembly/PsiAssemblyUtil.java	9
org/mskcc/pathdb/sql/dao/DaoCPath.java	1
org/mskcc/pathdb/sql/dao/DaoImport.java	1
org/mskcc/pathdb/sql/dao/DaoInternalFamily.java	1
org/mskcc/pathdb/sql/dao/DaoInternalLink.java	29
org/mskcc/pathdb/sql/dao/DaoOrganism.java	1
org/mskcc/pathdb/sql/dao/DaoReference.java	1
org/mskcc/pathdb/sql/dao/ManagedDAO.java	1
org/mskcc/pathdb/sql/query/GetBioPaxCommand.java	7
org/mskcc/pathdb/sql/query/GetNeighborsCommand.java	1
org/mskcc/pathdb/sql/query/QueryUtil.java	1
org/mskcc/pathdb/sql/references/BackgroundReferenceService.java	3
org/mskcc/pathdb/sql/snapshot/SnapshotReader.java	2
org/mskcc/pathdb/sql/snapshot/package.html	1
org/mskcc/pathdb/sql/transfer/PopulateInternalFamilyLookUpTable.java	11
org/mskcc/pathdb/sql/util/NeighborsUtil.java	1
org/mskcc/pathdb/sql/util/PhysicalEntitySetUtil.java	1
org/mskcc/pathdb/taglib/BioPaxParentChildTable.java	1
org/mskcc/pathdb/taglib/BioPaxShowFlag.java	2
org/mskcc/pathdb/taglib/CacheTable.java	1
org/mskcc/pathdb/taglib/DataSourceListTable.java	3
org/mskcc/pathdb/taglib/DbSnapshotInfo.java	4
org/mskcc/pathdb/taglib/ErrorMessage.java	3
org/mskcc/pathdb/taglib/EvidenceUtil.java	1
org/mskcc/pathdb/taglib/LogTable.java	2
org/mskcc/pathdb/taglib/OrganismTable.java	1
org/mskcc/pathdb/taglib/Pager.java	2
org/mskcc/pathdb/taglib/PathwayMembershipTable.java	5
org/mskcc/pathdb/taglib/PathwayMoleculesTable.java	1
org/mskcc/pathdb/taglib/ReactomeCommentUtil.java	1
org/mskcc/pathdb/taglib/ReferenceUtil.java	1
org/mskcc/pathdb/task/IndexLuceneTask.java	10
org/mskcc/pathdb/task/PopulateReferenceTableTask.java	1
org/mskcc/pathdb/task/PrecomputeTablesTask.java	2
org/mskcc/pathdb/test/form/FormSuite.java	2
org/mskcc/pathdb/test/form/TestFeedbackForm.java	5
org/mskcc/pathdb/test/form/package.html	1
org/mskcc/pathdb/test/lucene/TestItemToIndex.java	2
org/mskcc/pathdb/test/lucene/TestLuceneAutoFilter.java	2
org/mskcc/pathdb/test/query/QuerySuite.java	1
org/mskcc/pathdb/test/query/TestPhysicalEntitySetInteractionQuery.java	1
org/mskcc/pathdb/test/query/TestPhysicalEntitySetPathwayQuery.java	1
org/mskcc/pathdb/test/query/batch/BatchQuerySuite.java	1
org/mskcc/pathdb/test/query/batch/TestPathwayBatchQuery.java	8
org/mskcc/pathdb/test/query/batch/package.html	1
org/mskcc/pathdb/test/query/package.html	1
org/mskcc/pathdb/test/references/ReferencesSuite.java	1
org/mskcc/pathdb/test/references/TestPopulateReferenceTableTask.java	1
org/mskcc/pathdb/test/references/package.html	1
org/mskcc/pathdb/test/schemas/biopax/TestBioPaxElementFilter.java	1
org/mskcc/pathdb/test/schemas/biopax/TestBioPaxTransformToCPathRecords.java	1
org/mskcc/pathdb/test/schemas/biopax/TestBioPaxUtil.java	5
org/mskcc/pathdb/test/schemas/biopax/TestUpdateRdfLinks.java	3
org/mskcc/pathdb/test/sql/TestDaoCPath.java	3
org/mskcc/pathdb/test/sql/TestDaoExternalDbSnapshot.java	1
org/mskcc/pathdb/test/sql/TestDaoInternalFamily.java	3
org/mskcc/pathdb/test/sql/TestDaoInternalLink.java	4
org/mskcc/pathdb/test/sql/TestDaoSourceTracker.java	2
org/mskcc/pathdb/test/sql/TestSnapshotReader.java	1
org/mskcc/pathdb/test/sql/transfer/TestPopulateInternalFamilyLookUpTable.java	9
org/mskcc/pathdb/test/sql/transfer/TransferSuite.java	3
org/mskcc/pathdb/test/sql/transfer/package.html	1
org/mskcc/pathdb/test/taglib/TestBioPaxShowFlag.java	1
org/mskcc/pathdb/test/task/TestImportExternalDbTask.java	1
org/mskcc/pathdb/test/util/TestIdList.java	5
org/mskcc/pathdb/tool/Admin.java	8
org/mskcc/pathdb/tool/CreateSamplePValsFile.java	2
org/mskcc/pathdb/tool/LoadBioCartaPid.java	1
org/mskcc/pathdb/util /ExternalDatabaseConstants.java	9
org/mskcc/pathdb/util/IdList.java	9
org/mskcc/pathdb/util/Profile.java	5
org/mskcc/pathdb/util/biopax/BioPaxRecordUtil.java	1
org/mskcc/pathdb/util/email/SendMail.java	2
org/mskcc/pathdb/util/email/package.html	1
org/mskcc/pathdb/util/file/ZipUtil.java	1
org/mskcc/pathdb/util/rdf/RdfExtractor.java	1
org/mskcc/pathdb/util/tool/ConsoleUtil.java	1
org/mskcc/pathdb/xdebug/XDebugUtil.java	4

org/mskcc/pathdb/action/BioPaxParentChild.java

Error	Line
Got an exception - expecting EOF, f ound 'if'	0

org/mskcc/pathdb/action/DownloadSource.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused import - java.util.zip.ZipOutputStream.	13
Unused import - java.util.zip.ZipEntry.	14
Missing a Javadoc comment.	19
' & gt;=' is not followed by whitespace.	42
',' is not followed by whitespace.	47

org/mskcc/pathdb/action/ExecuteSearch.java

Error	Line
Got an exception - expecting EOF, found 'GlobalFilterSettings'	0

org/mskcc/pathdb/action/FeedbackAction.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'+' should be on a new line.	53

org/mskcc/pathdb/action/IconRetriever.java

Error	Line
Name 'BUF_SIZE' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	109

org/mskcc/pathdb/action/ShowBioPaxRecord2.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused import - javax.servlet.http.HttpSession.	24
Unused import - java.util.Iterator.	27
Name 'BP_SUMMARY' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	38
Variable 'BP_SUMMARY' must be private and have accessor methods.	38
Name 'ENTITY_SUMMARY' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	43
Variable 'ENTITY_SUMMARY' must be private and have accessor methods.	43
Name 'EXTERNAL_LINKS' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	48
Variable 'EXTERNAL_LINKS' must be private and have accessor methods.	48
Name 'TYPES_LIST' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	53
Variable 'TYPES_LIST' must be private and have accessor methods.	53
Name 'OUT_OF_SCOPE' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	58
Variable 'OUT_OF_SCOPE' must be private and have accessor methods.	58
Name 'ID_PARAMETER' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	63
Variable 'ID_PARAMETER' must be private and have accessor methods.	63
' & amp; & amp;' should be on a new line.	124
'=' is not preceeded with whitespace.	252
'=' is not followed by whitespace.	252
' & lt;' is not preceeded with whitespace.	252
' & lt;' is not followed by whitespace.	252
'+=' is not preceeded with whitespace.	254
'==' is not followed by whitespace.	266
'=' is not preceeded with whitespace.	269
'=' is not followed by whitespace.	269
' & lt;' is not preceeded with whitespace.	269
' & lt;' is not followed by whitespace.	269
'==' is not followed by whitespace.	290
'=' is not preceeded with whitespace.	293
'=' is not followed by whitespace.	293
' & lt;' is not preceeded with whitespace.	293
' & lt;' is not followed by whitespace.	293
'=' is not preceeded with whitespace.	312
'=' is not followed by whitespace.	312
' & lt;' is not preceeded with whitespace.	312
' & lt;' is not followed by whitespace.	312

org/mskcc/pathdb/action/ShowDataSourceDetails.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1

org/mskcc/pathdb/action/StoreGlobalFilterSettings.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'==' is not followed by whitespace.	46
'==' is not followed by whitespace.	54
'=' is not preceeded with whitespace.	71
'=' is not followed by whitespace.	71
'=' is not preceeded with whitespace.	79
'=' is not followed by whitespace.	79
'+' is not preceeded with whitespace.	91
'+' is not followed by whitespace.	91
'+' is not preceeded with whitespace.	93
'+' is not followed by whitespace.	93

org/mskcc/pathdb/action/admin/AdminHomeAction.java

Error	Line
Unused import - org.mskcc.pathdb.form.WebUIBean.	40

org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteGetParentsXmlResponse.java

Error	Line
Got an exception - expecting EOF, found 'ArrayList'	0

org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteHtmlResponse.java

Error	Line
Got an exception - expecting EOF, found 'GlobalFilterSettings'	0

org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteSearchXmlResponse.java

Error	Line
Got an exception - expecting EOF, found 'entityTypes'	0

org/mskcc/pathdb/action/web_api/biopax_mode/ExecuteTextResponse.java

Error	Line
' & lt;' is not preceeded with whitespace.	94
' & lt;' is not followed by whitespace.	94
' & gt;' is not preceeded with whitespace.	94
' & lt;' is not preceeded with whitespace.	112
' & lt;' is not followed by whitespace.	112
' & gt;' is not preceeded with whitespace.	112

org/mskcc/pathdb/bb/action/HomeAction.java

Error	Line
Got an exception - expecting EOF, found 'DaoCPath'	0

org/mskcc/pathdb/bb/action/WebService.java

Error	Line
Got an exception - expecting EOF, found 'if'	0

org/mskcc/pathdb/bb/action/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/bb/model/BBGeneRecord.java

Error	Line
Expected @param tag for 'entrezGeneID'.	60
Expected @param tag for 'geneName'.	60

org/mskcc/pathdb/bb/model/BBPathwayRecord.java

Error	Line
Expected @param tag for 'pathwayID'.	72
Expected @param tag for 'pathwayName'.	72
Ex pected @param tag for 'source'.	72
Expected @param tag for 'url'.	72
Unused @param tag for 'source'.	147
Expected @param tag for 'url'.	149

org/mskcc/pathdb/bb/model/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/bb/sql/dao/DaoBBGene.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Expected @throws tag for 'DaoException'.	56
'if' construct must use '{}'s.	59
'if' construct must use '{}'s.	63
Expected @throws tag for 'DaoException'.	95

org/mskcc/pathdb/bb/sql/dao/DaoBBInternalLink.java

Error	Line
Got an exception - expecting EOF, found 'PreparedStatement'	0

org/mskcc/pathdb/bb/sql/dao/DaoBBPathway.java

Error	Line
Got an exception - expecting EOF, found 'PreparedStatement'	0

org/mskcc/pathdb/bb/sql/dao/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/form/FeedbackForm.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'=' is not preceeded with whitespace.	104
'=' is not followed by whitespace.	104
' & lt;' is not preceeded with whitespace.	104
' & lt;' is not followed by whitespace.	104

org/mskcc/pathdb/form/WebUIBean.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/lucene/BioPaxToIndex.java

Error	Line
Got an exception - expecting EOF, found 'if'	0

org/mskcc/pathdb/lucene/IndexFactory.java

Error	Line
Expected @throws tag for 'DaoException'.	61
Expected @throws tag for 'BioPaxRecordSummaryException'.	61

org/mskcc/pathdb/lucene/IndexRules.java

Error	Line
'if' construct must use '{}'s.	70
'if' construct must use '{}'s.	72
' & amp; & amp;' should be on a new line.	72

org/mskcc/pathdb/lucene/LuceneAutoFilter.java

Error	Line
Got an exception - expecting EOF, found 'break'	0

org/mskcc/pathdb/lucene/LuceneQuery.java

Error	Line
Got an exception - expecting EOF, found 'this'	0

org/mskcc/pathdb/lucene/LuceneReader.java

Error	Line
Unused import - java.util.List.	45
'cast' is not followed by whitespace.	100

org/mskcc/pathdb/lucene/RecordIndexer.java

Error	Line
Line is longer than 125 characters.	154
Expected @throws tag for 'DaoException'.	154
Expected @throws tag for 'BioPaxRecordSummaryException'.	154

org/mskcc/pathdb/model/BioPaxEntityTypeMap.java

Error	Line
Unused import - org.mskcc.pathdb.action.BioPaxParentChild.	34

org/mskcc/pathdb/model/BioPaxTabs.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Variable 'childMap' must be private and have accessor methods.	13
Variable 'parentMap' must be private and have accessor methods.	14
Missing a Javadoc comment.	42

org/mskcc/pathdb/model/Evidence.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/model/ExternalDatabaseRecord.java

Error	Line
Unused import - org.apache.log4j.Logger.	34
'?' should be on a new line.	351
':' should be on a new line.	352
'?' should be on a new line.	374
':' should be on a new line.	375

org/mskcc/pathdb/model/GlobalFilterSettings.java

Error	Line
Got an exception - expecting EOF, found 'ArrayList'	0

org/mskcc/pathdb/model/Reference.java

Error	Line
'?' should be on a new line.	178
':' should be on a new line.	179
Expected @param tag for 'isEvidenceReference'.	188

org/mskcc/pathdb/model/TypeCount.java

Error	Line
Line does not match exp ected header line of '^// \$[I ] [d ] : .*\$$'.	1

org/mskcc/pathdb/protocol/ProtocolConstants.java

Error	Line
Missing a header - not enough lines in file.	1

org/mskcc/pathdb/protocol/ProtocolConstantsVersion2.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1

org/mskcc/pathdb/protocol/ProtocolRequest.java

Error	Line
'cast' is not followed by whitespace.	320
'cast' is not followed by whitespace.	321
'cast' is not followed by whitespace.	322
'cast' is not followed by whitespace.	323
'cast' is not followed by whitespace.	324
'{' is not preceeded with whitespace.	499
'=' is not preceeded with whitespace.	607
'=' is not followed by whitespace.	607
' & lt;' is not preceeded with whitespace.	607
' & lt;' is not followed by whitespace.	607
Expression can be simplified.	696
Expression can be simplified.	699

org/mskcc/pathdb/protocol/ProtocolValidatorVersion1.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'}' should be on the same line.	179

org/mskcc/pathdb/protocol/ProtocolValidatorVersion2.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/query/batch/PathwayBatchQuery.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/query/batch/PhysicalEntityWithPathwayList.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/query/batch/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/schemas/biopax/BioPaxUtil.java

Error	Line
Got an exception - expecting EOF, found 'xpath'	0

org/mskcc/pathdb/schemas/biopax/ImportBioPaxToCPath.java

Error	Line
Got an exception - expecting EOF, found 'if'	0

org/mskcc/pathdb/schemas/biopax/MemberMolecules.java

Error	Line
Got an exception - expecting EOF, found 'DaoInternalFamily'	0

org/mskcc/pathdb/schemas/biopax/MemberPathways.java

Error	Line
Got an exception - expecting EOF, found 'DaoInternalFamily'	0

org/mskcc/pathdb/schemas/biopax/TransformBioPaxToCPathRecords.java

Error	Line
Unused import - org.mskcc.pathdb.schemas.biopax.summary.BioPaxRecordSummary.	42
Expected @param tag for 'resource'.	71
Expected an @return tag.	86
Expected @param tag for 'resource'.	86
Expected @throws tag for 'JDOMException'.	86
'=' is not preceeded with whitespace.	146
'=' is not followed by whitespace.	146
' & lt;' is not preceeded with whitespace.	146
' & lt;' is not followed by whitespace.	146

org/mskcc/pathdb/schemas/biopax/UpdateRdfLinks.java

Error	Line
'?' should be on a new line.	84

org/mskcc/pathdb/schemas/biopax/summary/BioPaxFeature.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1

org/mskcc/pathdb/schemas/biopax/summary/BioPaxRecordSummaryUtils.java

Error	Line
Got an exception - expecting EOF, found 'for'	0

org/mskcc/pathdb/schemas/biopax/summary/EntitySummaryParserNoCache.java

Error	Line
Got an exception - expecting EOF, found 'XPath'	0

org/mskcc/pathdb/schemas/biopax/summary/InteractionSummary.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/schemas/biopax/summary/InteractionSummaryUtils.java

Error	Line
'==' is not followed by whitespace.	118
'==' is not followed by whitespace.	246
'=' is not preceeded with whitespace.	310
'=' is not followed by whitespace.	310
' & lt;' is not preceeded with whitespace.	310
' & lt;' is not followed by whitespace.	310
'if' is not followed by whitespace.	313

org/mskcc/pathdb/schemas/biopax/summary/ParticipantSummaryComponent.java

Error	Line
Got an exception - expecting EOF, found 'type'	0

org/mskcc/pathdb/schemas/biopax/summary/SummaryListUtil.java

Error	Line
Expected @param tag for 'filterSettings'.	77

org/mskcc/pathdb/servlet/CPathServletResponse.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Missing a Javadoc comment.	11
Missing a Javadoc comment.	16
Missing a Javadoc comment.	20
'{' is not followed by whitespace.	20
'}' is not preceeded with whitespace.	20
Missing a Javadoc comment.	21
Missing a Javadoc comment.	22
Missing a Javadoc comment.	23
Missing a Javadoc comment.	24
Missing a Javadoc comment.	25
Missing a Javadoc comment.	26
Missing a Javadoc comment.	27
Missing a Javadoc comment.	28
Missing a Javadoc comment.	29
Missing a Javadoc comment.	30
Missing a Javadoc comment.	31
Missing a Javadoc comment.	32
Missing a Javadoc comment.	33
Missing a Javadoc comment.	34
Missing a Javadoc comment.	35
Missing a Javadoc comment.	36
Missing a Javadoc comment .	37
Missing a Javadoc comment.	38
Missing a Javadoc comment.	39
Missing a Javadoc comment.	40
Missing a Javadoc comment.	41
Missing a Javadoc comment.	42
Line is longer than 125 characters.	43
Missing a Javadoc comment.	43
Missing a Javadoc comment.	44
Missing a Javadoc comment.	45
Missing a Javadoc commen t.	46
Missing a Javadoc comment.	47
Missing a Javadoc comment.	48
Missing a Javadoc comment.	49

org/mskcc/pathdb/servlet/CPathUIConfig.java

Error	Line
Missing a Javadoc comment.	199

org/mskcc/pathdb/servlet/CytoscapeJnlpServlet.java

Error	Line
Unused import - org.apache.log4j.Logger.	43
Unused @param tag for 'req'.	76
Unused @param tag for 'res'.	77
Expected @param tag for 'request'.	81
Expected @param tag for 'response'.	81
'if' construct must use '{}'s.	86
'if' construct must use '{}'s.	90
'}' should be on the same line.	104
'cast' is not followed by whitespace.	115
'+' should be on a new line.	119
'+' should be on a new line.	120
Line is longer than 125 characters.	121
'+' should be on a new line.	121
'+' should be on a new line.	122
Line is longer than 125 characters.	123
'+' should be on a new line.	123
'+' should be on a new line.	124
Line is longer than 125 characters.	125
'+' should be on a new line.	148
'+' should be on a new line.	149
'+' should be on a new line.	150
'+' should be on a new line.	151
'+' should be on a new line.	152
'+' should be on a new line.	153
'+' should be on a new line.	154
'+' should be on a new line.	155
'+' should be on a new line.	156
'+' should be on a new line.	157
'+' should be on a new line.	158
'+' should be on a new line.	159
'+' should be on a new line.	160
Line is longer than 125 characters.	161
'+' should be on a new line.	161
Line is longer than 125 characters.	162
'+' should be on a new line.	162
'+' should be on a new line.	163
'+' should be on a new line.	164
'+' should be on a new line.	165
'+' should be on a new line.	166
'+' should be on a new line.	167
'+' should be on a new line.	168
'+' should be on a new line.	169
'+' sho uld be on a new line.	170
'+' should be on a new line.	171
'+' should be on a new line.	172
'+' should be on a new line.	173
'+' should be on a new line.	174
'+' should be on a new line.	175
'+' should be on a new line.	176
'+' should be on a new line.	177
'+' should be on a new line.	178
'+' should be on a new line.	179
'+' should be on a new line.	180
'+' should be on a new line.	181
'+' should be on a new line.	182
'+' should be on a new line.	183
'+' should be on a new line.	184
'+' should be on a new line.	185
'+' should be on a new line.	186
'+' should be on a new line.	187
'+' should be on a new line.	188
'+' should be on a new line.	189
'+' should be on a new line.	190
'+' should be on a new line.	191
'+' should be on a new line.	192
'+' should be on a new line.	193
'+' should be on a new line.	194
'+' should be on a new line.	195
'+' should be on a new line.	196
'+' should be on a new line.	197
'+' should be on a new line.	198
'+' should be on a new line.	199
'+' should be on a new line.	200
'+' should be on a new line.	201
'+' should be on a new line.	202
'+' should be on a new line.	203
'+' should be on a new line.	204
'+' should be on a new line.	205
'+' should be on a new line.	206
'+' should be on a new line.	207
'+' should be on a new line.	208
'+' should be on a new line.	209
'+' should be on a new line.	210
'+' should be on a new line.	211
'+' should be on a new line.	212
'+' should be on a new line.	213
'+' should be on a new line.	214
'+' should be on a new line.	215
'+' should be on a new line.	216
'+' should be on a new line.	217
'+' should be on a new line.	218
'+' should be on a new line.	219
'+' should be on a new line.	220
'+' should be on a new line.	221
'+' should be on a new line.	222
'+' should be on a new line.	223
'+' should be on a new line.	224
'+' should be on a new line.	225
'+' should be on a new line.	226
'+' should be on a new line.	227
'+' should be on a new line.	228
'+' should be on a new line.	229
'+' should be on a new line.	230
'+' should be on a new line.	231
'+' should be on a new line.	232
'+' should be on a new line.	233
'+' should be on a new line.	234
'+' should be on a new line.	235
'+' should be on a new line.	236
'+' should be on a new line.	237
'+' should be on a new line.	238
'+' should be on a new line.	239
'+' should be on a new line.	240
'+' should be on a new line.	241
'+' should be on a new line.	242
'+' should be on a new line.	243
'+' should be on a new line.	244
'+' should be on a new line.	245
'+' should be on a new line.	246
'+' should be on a new line.	247
'+' should be on a new line.	248
Line is longer than 125 characters.	249
'+' should be on a new line.	249
'+' should be on a new line.	250
'+' should be on a new line.	251
'+' should be on a new line.	252
'+' should be on a new line.	253
'+' should be on a new line.	254
'+' should be on a new line.	255
'+' should be on a new line.	256
'+' should be on a new line.	257
'+' should be on a new line.	258
'+' should be on a new line.	259
'+' should be on a new line.	260
'+' should be on a new line.	261
'+' should be on a new line.	262
'+' should be on a new line.	263
'+' should be on a new line.	264
'+' should be on a new line.	265
'+' should be on a new line.	266
'+' should be on a new line.	267
'+' should be on a new line.	268
'+' should be on a new line.	269
'+' should be on a new line.	270
'+' should be on a new line.	271
'+' should be on a new line.	272
'+' should be on a new line.	273
'+' should be on a new line.	274
'+' should be on a new line.	275
'+' should be on a new line.	276
'+' should be on a new line.	277
'+' should be on a new line.	278
'+' should be on a new line.	279
'+' should be on a new line.	280
'+' should be on a new line.	281
'+' should be on a new line.	282
'+' should be on a new line.	283

org/mskcc/pathdb/sql/JdbcUtil.java

Error	Line
Unused import - org.apache.commons.pool.impl.GenericObjectPool.	35
Unused import - org.apache.commons.pool.impl.GenericKeyedObjectPool.	36
Unused import - javax.sql.DataSource.	40
'!' is followed by whitespace.	102

org/mskcc/pathdb/sql/assembly/PsiAssemblerStringOnly.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Variable 'xmlDoc' must be private and have accessor methods.	21
'+' is not followed by whitespace.	100

org/mskcc/pathdb/sql/assembly/PsiAssembly.java

Error	Line
Unused import - org.mskcc.pathdb.model.CPathRecord.	41
Unused import - org.mskcc.pathdb.model.InternalLinkRecord.	42
Unused import - org.ms kcc.pathdb.sql.dao.DaoCPath.	44
Unused import - org.mskcc.pathdb.sql.dao.DaoInternalLink.	46

org/mskcc/pathdb/sql/assembly/PsiAssemblyStringOnly.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused @throws tag for 'org.mskcc.pathdb.sql.assembly.AssemblyException'.	108
Expected @throws tag for 'AssemblyException'.	110

org/mskcc/pathdb/sql/assembly/PsiAssemblyUtil.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'=' is not preceeded with whitespace.	58
'=' is not followed by whitespace.	58
' & lt;' is not preceeded with whitespace.	58
' & lt;' is not followed by whitespace.	58
'=' is not preceeded with whitespace.	62
'=' is not followed by whitespace.	62
' & lt;' is not preceeded with whitespace.	62
' & lt;' is not followed by whitespace.	62

org/mskcc/pathdb/sql/dao/DaoCPath.java

Error	Line
Got an exception - expecting EOF, found 'ArrayList'	0

org/mskcc/pathdb/sql/dao/DaoImport.java

Error	Line
Expected @param tag for 'snapshotId'.	190

org/mskcc/pathdb/sql/dao/DaoInternalFamily.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/sql/dao/DaoInternalLink.java

Error	Line
' & gt;' is not followed by whitespace.	231
'=' is not preceeded with whitespace.	237
'=' is not followed by whitespace.	237
' & lt;' is not preceeded with whitespace.	237
' & lt;' is not followed by whitespace.	237
'+' is not followed by whitespace.	246
'+' is not preceeded with whitespace.	248
'+' is not followed by whitespace.	299
'+' is not preceeded with whitespace.	301
' & gt;' is not followed by whitespace.	354
'=' is not preceeded with whitespace.	360
'=' is not followed by whitespace.	360
' & lt;' is not preceeded with whitespace.	360
' & lt;' is not followed by whitespace.	360
'+' is not followed by whitespace.	369
'+' is not preceeded with whitespace.	371
' & gt;' is not followed by whitespace.	427
'=' is not preceeded with whitespace.	433
'=' is not followed by whitespace.	433
' & lt;' is not preceeded with whitespace.	433
' & lt;' is not followed by whitespace.	433
'+' is not followed by whitespace.	441
'+' is not followed by whitespace.	485
' & gt;' is not followed by whitespace.	534
'=' is not prece eded with whitespace.	540
'=' is not followed by whitespace.	540
' & lt;' is not preceeded with whitespace.	540
' & lt;' is not followed by whitespace.	540
'+' is not followed by whitespace.	548

org/mskcc/pathdb/sql/dao/DaoOrganism.java

Error	Line
Expected @param tag for 'ncbiTaxonomyId'.	93

org/mskcc/pathdb/sql/dao/DaoReference.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/sql/dao/ManagedDAO.java

Error	Line
Unused import - java.util.Hashtable.	41

org/mskcc/pathdb/sql/query/GetBioPaxCommand.java

Error	Line
Unused import - org.mskcc.pathdb.model.CPathRecord.	34
Unused import - org.mskcc.pathdb.protocol.ProtocolException.	37
Unused import - org.mskcc.pathdb.protocol.ProtocolStatusCode.	38
Unused import - org.mskcc.pathdb.sql.dao.DaoCPath.	42
'=' is not preceeded with whitespace.	89
'=' is not followed by whitespace.	89
' & lt;' is not preceeded with whitespace.	89

org/mskcc/pathdb/sql/query/GetNeighborsCommand.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/sql/query/QueryUtil.java

Error	Line
Got an exception - expecting EOF, found 'List'	0

org/mskcc/pathdb/sql/references/BackgroundReferenceService.java

Error	Line
Expected an @return tag.	225
Expected @param tag for 'xrefs'.	225
Expected @throws tag for 'DaoException'.	226

org/mskcc/pathdb/sql/snapshot/SnapshotReader.java

Error	Line
Expected @param tag for 'fileName'.	68
'=' is not followed by whitespace.	97

org/mskcc/pathdb/sql/snapshot/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/sql/transfer/PopulateInternalFamilyLookUpTable.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused import - org.mskcc.pathdb.model.Organism.	3
Unused import - org.mskcc.pathdb.util.CPathConstants.	16
Line is longer than 125 characters.	36
Expected @throws tag for 'BioPaxRecordSummaryException'.	58
Line is longer than 125 characters.	99
Line is longer than 125 characters.	100
Line is longer than 125 characters.	101
Missing a Javadoc comment.	112
'\|\|' should be on a new line.	309
'\|\|' should be on a new line.	313

org/mskcc/pathdb/sql/util/NeighborsUtil.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/sql/util/PhysicalEntitySetUtil.java

Error	Line
Got an exception - expecting EOF, found 'DaoInternalLink'	0

org/mskcc/pathdb/taglib/BioPaxParentChildTable.java

Error	Line
Unused import - org.mskcc.pathdb.schemas.biopax.summary.SummaryListUtil.	40

org/mskcc/pathdb/taglib/BioPaxShowFlag.java

Error	Line
'}' should be on the same line.	140
Expected @param tag for 'anchorName'.	198

org/mskcc/pathdb/taglib/CacheTable.java

Error	Line
Unused import - java.util.StringTokenizer.	46

org/mskcc/pathdb/taglib/DataSourceListTable.java

Er ror	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused import - org.mskcc.pathdb.model.CPathRecord.	3
Line is longer than 125 characters.	68

org/mskcc/pathdb/taglib/DbSnapshotInfo.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Type Javadoc comment is missing an @author tag.	14
Expected @param tag for 'showAllDetails'.	50
'!' is followed by whitespace.	58

org/mskcc/pathdb/taglib/ErrorMessage.java

Error	Line
'+' should be on a new line.	165
'+' should be on a new line.	175
'+' is not followed by whitespace.	180

org/mskcc/pathdb/taglib/EvidenceUtil.java

Error	Line
Got an exception - expecting EOF, found 'Map'	0

org/mskcc/pathdb/taglib/LogTable.java

Error	Line
Unused import - org.mskcc.pathdb.util.html.HtmlUtil.	37
'+' is not followed by whitespace.	83

org/mskcc/pathdb/taglib/OrganismTable.java

Error	Line
Unused import - org.mskcc.pathdb.protocol.ProtocolConstantsVersion1.	38

org/mskcc/pathdb/taglib/Pager.java

Error	Line
Expected @param tag for 'color'.	179
Expected @param tag for 'entityTypeParameter'.	179

org/mskcc/pathdb/taglib/PathwayMembershipTable.java

Error	Line
Unused import - org.mskcc.pathdb.model.CPathRecord.	35
Unused import - org.mskcc.pathdb.util.biopax.BioPaxRecordUtil.	37
Expected @param tag for 'totalNumPathways'.	90
'cast' is not followed by whitespace.	146
'?' should be on a new line.	148

org/mskcc/pathdb/taglib/PathwayMoleculesTable.java

Error	Line
Expected @param tag for 'totalNumMolecules'.	101

org/mskcc/pathdb/taglib/ReactomeCommentUtil.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1

org/mskcc/pathdb/taglib/ReferenceUtil.java

Error	Line
Got an exception - expecting EOF, found 'for'	0

org/mskcc/pathdb/task/IndexLuceneTask.java

Error	Line
Unused import - org.mskcc.pathdb.sql.transfer.PopulateInternalFamilyLookUpTable.	46
'if' construct must use '{}'s.	188
'=' is not preceeded with white space.	227
'=' is not followed by whitespace.	227
' & lt;' is not preceeded with whitespace.	227
' & lt;' is not followed by whitespace.	227
'=' is not preceeded with whitespace.	230
'=' is not followed by whitespace.	230
' & lt;' is not preceeded with whitespace.	230
' & lt;' is not followed by whitespace.	230

org/mskcc/pathdb/task/PopulateReferenceTableTask.java

Error	Line
Got an exception - expecting EOF, found 'DaoReference'	0

org/mskcc/pathdb/task/PrecomputeTablesTask.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Expected @throws tag for 'BioPaxRecordSummaryException'.	46

org/mskcc/pathdb/test/form/FormSuite.java

Error	Line
Missing a header - not enough lines in file.	1
Unused import - org.mskcc.pathdb.test.model.TestBackgroundReferencePair.	6

org/mskcc/pathdb/test/form/TestFeedbackForm.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused import - org.apache.struts.action.ActionMessage.	8
Unused import - java.util.Iterator.	10
'+' should be on a new line.	84
'+' should be on a new line.	85

org/mskcc/pathdb/test/form/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/test/lucene/TestItemToIndex.java

Error	Line
'+' is not followed by whitespace.	118
'+' should be on a new line.	119

org/mskcc/pathdb/test/lucene/TestLuceneAutoFilter.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'+' should be on a new line.	26

org/mskcc/pathdb/test/query/QuerySuite.java

Error	Line
Expected @param tag for 'args'.	64

org/mskcc/pathdb/test/query/TestPhysicalEntitySetInteractionQuery.java

Error	Line
Got an exception - expecting EOF, found 'long'	0

org/mskcc/pathdb/test/query/TestPhysicalEntitySetPathwayQuery.java

Error	Line
Got an exception - expecting EOF, found '}'	0

org/mskcc/pathdb/test/query/batch/BatchQuerySuite.java

Error	Line
Missing a header - not enough lines in file.	1

org/mskcc/pathdb/test/query/batch/TestPathwayBatchQuery.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Name 'ATF2_REF_SEQ_ID' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	25
' & lt;' is not preceeded with whitespace.	58
' & lt;' is not followed by whitespace.	58
' & gt;' is not preceeded with whitespace.	58
' & lt;' is not preceeded with whitespace.	64
' & lt;' is not followed by whitespace.	64
' & gt;' is not preceeded with whitespace.	64

org/mskcc/pathdb/test/query/batch/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/test/query/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/test/references/ReferencesSuite.java

Error	Line
Expected @param tag for 'args'.	61

org/mskcc/pathdb/test/references/TestPopulateReferenceTableTask.java

Error	Line
Got an exception - expecting EOF, found 'recordsToFetch'	0

org/mskcc/pathdb/test/references/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/test/schemas/biopax/TestBioPaxElementFilter.java

Error	Line
Unused import - java.util.ArrayList.	42

org/mskcc/pathdb/test/schemas/biopax/TestBioPaxTransformToCPathRecords.java

Error	Line
Unused import - java.util.ArrayList.	45

org/mskcc/pathdb/test/schemas/biopax/TestBioPaxUtil.java

Error	Line
Unused import - org.mskcc.pathdb.schemas.biopax.OwlConstants.	45
Unused import - org.mskcc.pathdb.util.rdf.RdfUtil.	48
Missing a Javadoc comment.	69
Missing a Javadoc comment.	75
'+' should be on a new line.	200

org/mskcc/pathdb/test/schemas/biopax/TestUpdateRdfLinks.java

Error	Line
Unused import - org.jdom.Document.	37
Unused import - org.mskcc.pathdb.util.xml.XmlUtil.	44
Unused import - java.util.ArrayList.	47

org/mskcc/pathdb/test/sql/TestDaoCPath.java

Error	Line
' & lt;' is not preceeded with whitespace.	106
' & lt;' is not followed by whitespace.	106
' & gt;' is not preceeded with whitespace.	106

org/mskcc/pathdb/test/sql/TestDaoExternalDbSnapshot.java

Error	Line
Unused import - org.mskcc.pathdb.sql.dao.DaoException.	36

org/mskcc/pathdb/test/sql/TestDaoInternalFamily.java

Error	Line
Line is longer than 125 characters.	67
Line is longer than 125 characters.	68
Line is longer than 125 characters.	69

org/mskcc/pathdb/test/sql/TestDaoInternalLink.java

Error	Line
'=' is not preceeded with whitespace.	174
'=' is not followed by whitespace.	174
' & lt;' is not prece eded with whitespace.	174
' & lt;' is not followed by whitespace.	174

org/mskcc/pathdb/test/sql/TestDaoSourceTracker.java

Error	Line
Unused import - org.mskcc.pathdb.sql.dao.DaoException.	36
Unused import - java.util.Date.	44

org/mskcc/pathdb/test/sql/TestSnapshotReader.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1

org/mskcc/pathdb/test/sql/transfer/TestPopulateInternalFamilyLookUpTable.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Unused import - org.mskcc.pathdb.sql.JdbcUtil.	7
Unused import - org.mskcc.pathdb.util.Profile.	10
Expected @throws tag for 'BioPaxRecordSummaryException'.	25
Missing a Javadoc comment.	43
'=' is not preceeded with whitespace.	50
'=' is not followed by whitespace.	50
' & lt;' is not preceeded with whitespace.	50
' & lt;' is not followed by whitespace.	50

org/mskcc/pathdb/test/sql/transfer/TransferSuite.java

Error	Line
Missing a header - not enough lines in file.	1
Unused import - org.mskcc.pathdb.test.sql.references.ReferencesSuite.	7
Unused import - org.mskcc.pathdb.test.sql.assembly.AssemblySuite.	8

org/mskcc/pathdb/test/sql/transfer/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/test/taglib/TestBioPaxShowFlag.java

Error	Line
Unused import - org.mskcc.pathdb.taglib.BioPaxParentChildTable.	36

org/mskcc/pathdb/test/task/TestImportExternalDbTask.java

Error	Line
Unused import - org.mskcc.pathdb.sql.dao.DaoException.	36

org/mskcc/pathdb/test/util/TestIdList.java

Error	Line
Unused import - junit.framework.TestResult.	43
Expected an @return tag.	55
Expected @param tag for 'args'.	62
'cast' is not followed by whitespace.	86
'cast' is not followed by whitespace.	86

org/mskcc/pathdb/tool/Admin.java

Error	Line
Unused import - org.mskcc.pathdb.sql.JdbcUtil.	38
'if' construct must use '{}'s.	257
'?' should be on a new line.	516
'if' construct must use '{}'s.	540
'if' construct must use '{}'s.	541
'if' construct must use '{}'s.	542
'if' construct must use '{}'s.	543
'}' should be on the same line.	544

org/mskcc/pathdb/tool/CreateSamplePValsFile.java

Error	Line
Unused import - org.jdom.JDOMException.	35
Unused import - org.mskcc.pathdb.sql.dao.ExternalDatabaseNotFoundException.	41

org/mskcc/pathdb/tool/LoadBioCartaPid.java

Error	Line
Got an exception - expecting EOF, found 'for'	0

org/mskcc/pathdb/util/ExternalDatabaseConstants.java

Error	Line
Missing a header - not enough lines in file.	1
Name 'REF_SEQ' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	13
Variable 'REF_SEQ' must be private and have accessor methods.	13
Name 'UNIPROT' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	18
Variable 'UNIPROT' must be private and have accessor methods.	18
Name 'REACTOME' must match pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	23
Variable 'REACTOME' must be private and have accessor methods.	23
Name 'INTERNAL_DATABASE' must ma tch pattern '^[a-z ] [a-zA-Z0-9 ] *$'.	28
Variable 'INTERNAL_DATABASE' must be private and have accessor methods.	28

org/mskcc/pathdb/util/IdList.java

Error	Line
'cast' is not followed by whitespace.	69
'if' construct must use '{}'s.	70
'cast' is not followed by whitespace.	135
'if' construct must use '{}'s.	136
'cast' is not followed by whitespace.	152
'cast' is not followed by whitespace.	152
'{' is not preceeded with whitespace.	187
'{' is not followed by whitespace.	187
'}' is not preceeded with whitespace.	187

org/mskcc/pathdb/util/Profile.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
Variable 'startTime' must be private and have accessor methods.	9
Variable 'totalTime' must be private and have accessor methods.	10
'-' is not preceeded with whitespace.	32
'-' is not followed by whitespace.	32

org/mskcc/pathdb/util/biopax/BioPaxRecordUtil.java

Error	Line
Got an exception - expecting EOF, found 'XPath'	0

org/mskcc/pathdb/util/email/SendMail.java

Error	Line
Line does not match expected header line of '^// \$[I ] [d ] : .*\$$'.	1
'{' is not preceeded with whitespace.	25

org/mskcc/pathdb/util/email/package.html

Error	Line
Missing package documentation file.	0

org/mskcc/pathdb/util/file/ZipUtil.java

Error	Line
Expected @param tag for 'fileName'.	53

org/mskcc/pathdb/util/rdf/RdfExtractor.java

Error	Line
'?' should be on a new line.	140

org/mskcc/pathdb/util/tool/ConsoleUtil.java

Error	Line
'static' modifier out of order with the JLS suggestions.	55

org/mskcc/pathdb/xdebug/XDebugUtil.java

Error	Line
Missing a header - not enough lines in file.	1
Type Javadoc comment is missing an @author tag.	11
'{' is not preceeded with whitespace.	20
'cast' is not followed by whitespace.	24