ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java (11 lines): - line 18: // TODO Auto-generated method stub - line 24: // TODO Auto-generated method stub - line 30: // TODO Auto-generated method stub - line 36: // TODO Auto-generated method stub - line 43: // TODO Auto-generated method stub - line 50: // TODO Auto-generated method stub - line 57: // TODO Auto-generated method stub - line 62: // TODO Auto-generated method stub - line 67: // TODO Auto-generated method stub - line 73: // TODO Auto-generated method stub - line 79: // TODO Auto-generated method stub ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/DomUtil.java (9 lines): - line 70: // TODO Auto-generated catch block - line 89: // TODO Auto-generated catch block - line 92: // TODO Auto-generated catch block - line 95: // TODO Auto-generated catch block - line 116: // TODO Auto-generated catch block - line 119: // TODO Auto-generated catch block - line 122: // TODO Auto-generated catch block - line 143: // TODO Auto-generated catch block - line 146: // TODO Auto-generated catch block ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java (8 lines): - line 361: // TODO with syntax - line 372: // TODO optimize with Stringbuffer instead of concatenation - line 380: // FIXME This should be an AND ? - line 421: // return "N"; //TODO: sketch - line 425: // return "N"; //TODO: sketch - line 429: // return "N"; //TODO: sketch - line 433: // return "NA"; //TODO: sketch - line 583: // FIXME - Based on gpl'd code so can't be released (marginal to no effect on performance) ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java (8 lines): - line 6: // TODO Auto-generated method stub - line 11: // TODO Auto-generated method stub - line 16: // TODO Auto-generated method stub - line 21: // TODO Auto-generated method stub - line 26: // TODO Auto-generated method stub - line 31: // TODO Auto-generated method stub - line 36: // TODO Auto-generated method stub - line 41: // TODO Auto-generated method stub ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java (7 lines): - line 59: // TODO https://www.w3schools.com/howto/howto_css_switch.asp - line 60: // TODO https://www.w3schools.com/html/tryit.asp?filename=tryhtml_layout_flexbox - line 61: // TODO https://www.w3schools.com/html/html5_new_elements.asp - line 63: // TODO https://css-tricks.com/snippets/css/a-guide-to-flexbox/ - line 64: // TODO https://www.quackit.com/css/flexbox/tutorial/nested_flex_containers.cfm - line 135: // TODO at each paragraph end index add a newline unless it is the end of a section - line 1010: // TODO move coref adjustment uphill ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java (7 lines): - line 114: // TODO what if a range has both subsections and templates within it? - line 115: // TODO maybe templates will be terminated differently than sections/subsections? - line 728: //TODO version of findTemplates for given sub-section of document - line 841: // TODO when dealing with subsections, perhaps we need to call this once for each section? - line 901: oneBeforeNextRange = sectionEndOffset; // TODO not always using entireContents - line 918: // TODO this is where it's breaking!!! Should find not just one - line 967: //TODO must actually call adjustRangeEnds once per parent range ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java (7 lines): - line 59: // TODO https://www.w3schools.com/howto/howto_css_switch.asp - line 60: // TODO https://www.w3schools.com/html/tryit.asp?filename=tryhtml_layout_flexbox - line 61: // TODO https://www.w3schools.com/html/html5_new_elements.asp - line 63: // TODO https://css-tricks.com/snippets/css/a-guide-to-flexbox/ - line 64: // TODO https://www.quackit.com/css/flexbox/tutorial/nested_flex_containers.cfm - line 130: // TODO at each paragraph end index add a newline unless it is the end of a section - line 961: // TODO move coref adjustment uphill ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java (6 lines): - line 6: // TODO Auto-generated method stub - line 11: // TODO Auto-generated method stub - line 16: // TODO Auto-generated method stub - line 21: // TODO Auto-generated method stub - line 26: // TODO Auto-generated method stub - line 31: // TODO Auto-generated method stub ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java (6 lines): - line 848: // TODO - Create a page for bin/runctakes - line 849: // TODO - Create a page for PiperFileRunner - line 877: // TODO - Python Components. Pages -exist- but should be aggregated. - line 878: // TODO - edit that intro page so that each "first setup API here" is replaced with - line 889: // TODO Notes, annotations (link for anafora), pipelines, readers, annotators, writers ... - line 953: // TODO Copy the PBJ python pages. Plus a whole bunch of others like the gui pages. Maybe put those in
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java (5 lines): - line 158: // TODO Auto-generated catch block - line 650: //TODO: review the executeFSMs method - line 708: //TODO: Does this need to be commented out? Created Strength - line 1066: //TODO: need to fix - use the list above - uniqueNEs and subset that list instead of getting new list of annotations - line 1068: //TODO: 10/28/2010 -- exception ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/cc/ConsumeNamedEntityRecordModel.java (5 lines): - line 127: // TODO: Move to Common Type System - line 139: // TODO: Move to Common Type System - line 173: // TODO: Move to Common Type System - line 323: // TODO Auto-generated catch block - line 440: // TODO Auto-generated catch block ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (5 lines): - line 205: // TODO: normalize dir to real domainId - line 410: // TODO extract context features for annotations that don't fall within a sentence - line 411: LOGGER.log(Level.WARN, "FIXME/TODO: generate context features for entities that don't fall within a sentence"); - line 528: // TODO: extend to the case where the extractors take a different argument besides entityOrEventMention - line 606: // TODO: real normalization ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/XmlLoader.java (5 lines): - line 117: // TODO Auto-generated catch block - line 122: // TODO Auto-generated catch block - line 125: // TODO Auto-generated catch block - line 128: // TODO Auto-generated catch block - line 136: // TODO Auto-generated catch block ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java (4 lines): - line 8: // TODO Auto-generated method stub - line 13: // TODO Auto-generated method stub - line 20: // TODO Auto-generated constructor stub - line 24: // TODO Auto-generated method stub ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTerm.java (4 lines): - line 17: // TODO : follow https://clear.colorado.edu/compsem/documents/treebank_guidelines.pdf or later/ - line 24: // TODO : add contractions: - line 104: // TODO - this requires all lower or all-upper case. That is not the correct way to deal with things. - line 169: // TODO should this be exactly the same as getTokens in TextTokenizer (dictionary gui code) ? probably ... ctakes-core/src/user/resources/org/apache/ctakes/core/scripts/groovy/run_cTAKES.groovy (4 lines): - line 44: // TODO improve handling of whether user enters a trailing slash for these two constants: - line 70: if (path.startsWith("C:")) { // TODO generalize - line 81: //println("TODO -- consider having script download and unzip ctakes-resources-4.0.0.zip to lib"); - line 82: //println("TODO -- download and unzip ctakes-resources-4.0.0.zip to lib"); ctakes-core/src/user/resources/org/apache/ctakes/core/scripts/groovy/cTAKES_clinical_pipeline.groovy (4 lines): - line 119: // "SegmentID", // TODO update SimpleSegmentAnnotator.java to have a constant for this - line 211: // TODO - this is a longer range TODO item: it would be nice to be able to set values here that would be used instead of what's in the LookupDesc*.xml files - line 296: // TODO When generalize this script to run specific components instead of the whole pipeline, - line 389: // TODO handle LvgCmdApi here ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java (4 lines): - line 222: // TODO: Ambiguous constructor for AnalysisEngineDescription named as AnnotatorDescription. Consider refactor - line 224: // TODO: Create UTest for deprecated JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY - line 234: // TODO: Ambiguous constructor for AnalysisEngineDescription named as AnnotatorDescription. Consider refactor - line 236: // TODO: Create UTest for deprecated JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java (4 lines): - line 194: // TODO: normalize dir to real domainId - line 321: // TODO : Windowed Assertion: - line 463: // TODO: extend to the case where the extractors take a different argument besides entityOrEventMention - line 514: // TODO: real normalization ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java (4 lines): - line 101: // TODO Consider using a parameter for includeSectionMarkers - line 105: // TODO Consider using a parameter for hyphWindow/HyphenDetectionWindow - line 127: * TODO - move this to TextModifier and take a Logger - line 160: //TODO: A bit over engineered? Is this config really parsed very time??? ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java (4 lines): - line 184: // // TODO Auto-generated catch block - line 298: // // TODO Auto-generated catch block - line 301: // // TODO Auto-generated catch block - line 463: // TODO: how to remove if it is in a relation ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java (4 lines): - line 8: // TODO Auto-generated method stub - line 13: // TODO Auto-generated method stub - line 18: // TODO Auto-generated method stub - line 23: // TODO Auto-generated method stub ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/TreeKernelTrainer.java (3 lines): - line 82: // TODO Auto-generated catch block - line 96: // TODO Auto-generated catch block - line 129: // TODO Auto-generated catch block ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java (3 lines): - line 58: // TODO Only take perfect matches? - line 69: // TODO Only take perfect matches? - line 95: // TODO Auto-generated catch block ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java (3 lines): - line 47: // TODO Auto-generated constructor stub - line 55: // TODO Auto-generated constructor stub - line 67: // TODO Auto-generated method stub ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java (3 lines): - line 228: .splitAtLineBreaksAndTrim(NEWLINE)); // TODO Determine - line 321: // TODO: Actually import a Dictionary of abbreviations - line 326: // TODO: language should be generic (i.e. params.getLang() ) ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/SaxParser.java (3 lines): - line 60: // TODO Auto-generated catch block - line 63: // TODO Auto-generated catch block - line 66: // TODO Auto-generated catch block ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/ContiguousLookupEngine.java (3 lines): - line 135: // TODO - Do we really want lower-case candidates? - line 196: // TODO Add overlap logic ... - line 230: // TODO Add overlap logic ... ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/DrugMention.java (3 lines): - line 439: // TODO Auto-generated method stub - line 448: // TODO Auto-generated method stub - line 1031: // TODO double == float direct comparison is bad. ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/DefaultDictionarySpec.java (3 lines): - line 85: // TODO check for completion of pairings - line 113: // TODO log - line 129: // TODO log ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java (3 lines): - line 46: // TODO @ConfigurationParam - line 76: // TODO Auto-generated catch block - line 87: // TODO @ConfigurationParam ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/ae/CasedAnnotationFinder.java (3 lines): - line 42: // TODO : New Tables ... - line 48: // TODO: The above will make a much larger secondary table, with a larger cui index. - line 52: // TODO: There are some uppercase synonyms that should be lowercase. Check for synonym length > 10 and then force? ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java (3 lines): - line 33: // TODO - We don't seem to be returning relations (etc.) anywhere, so why does the war contain so many modules? - line 34: // TODO - consider having multiple return types available. see ctakes-tiny-rest service/response/* and - line 36: // TODO - consider an additional json such as UmlsJsonFormatter. ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/PropFile.java (3 lines): - line 48: // TODO Auto-generated catch block - line 51: // TODO Auto-generated catch block - line 68: // TODO Auto-generated catch block ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/RestDockerBuilder.java (3 lines): - line 70: // TODO Maybe the rest could output html if the css and js are specified in index.jsp ?? - line 72: // TODO Local src/bin Installation, Local Rest WAR, Installation Docker, Rest Docker. - line 74: // TODO set the Buildable boolean supplier in wizard controller ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java (3 lines): - line 130: // TODO Auto-generated catch block - line 139: // TODO Auto-generated catch block - line 142: // TODO Auto-generated catch block ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/DomParser.java (3 lines): - line 58: // TODO Auto-generated catch block - line 61: // TODO Auto-generated catch block - line 64: // TODO Auto-generated catch block ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (3 lines): - line 256: // TODO Auto-generated catch block - line 259: // TODO Auto-generated catch block - line 430: // TODO: Is this necessary? Doesn't the default view have the text populated in the xmis? ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima/co/ParserTreeWriterConsumer.java (3 lines): - line 53: // TODO Auto-generated catch block - line 61: // TODO Auto-generated method stub - line 66: // TODO Auto-generated catch block ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java (2 lines): - line 6: // TODO Auto-generated constructor stub - line 10: // TODO Auto-generated method stub ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Feature.java (2 lines): - line 30: // TODO Giant file Attributes ? Uses Windowed *** - line 31: // TODO Dictionary : Default, Custom. Allow Custom to either select existing or launch dictionary creator. ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java (2 lines): - line 57: // // TODO Progress Dialog. - line 73: // TODO : Make this a 3 option dialog: "Maven Not Found. Want to 1) Select existing 2) Install maven 3) cancel ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java (2 lines): - line 72: // TODO property validation could be done here - line 82: // TODO property validation could be done here ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__both_regular_and_mayo.xml (2 lines): - line 608: TODO: change this attribute because of name clash (UMLS/SNOMED) - line 3027: TODO: change this attribute because of name clash (UMLS/SNOMED) ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/KernelMatrixCompositor.java (2 lines): - line 28: // TODO - Think about how to combine kernels here because it affects how the program works, can they be read - line 79: // TODO Auto-generated catch block ctakes-core/src/main/java/org/apache/ctakes/core/sentence/SentenceDetectorCtakes.java (2 lines): - line 236: // TODO: Fix the EventStream to throw exceptions when training goes wrong - line 328: // TODO: add support for iterations and cutoff settings ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java (2 lines): - line 92: // FIXME do automatic parse? - line 121: // FIXME - do automatic parse here... ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/TreeFeatureConsumer.java (2 lines): - line 98: // TODO Auto-generated catch block - line 206: // TODO Auto-generated method stub ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java (2 lines): - line 55: // TODO Finish this refactor - line 186: * TODO Consider adding common words as possible performance improvement ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupEngine.java (2 lines): - line 204: // // TODO Add overlap logic ... - line 238: // // TODO Add overlap logic ... ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DictionaryLookupFactory.java (2 lines): - line 34: // TODO: Create UTest for deprecated JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY - line 51: // TODO: Create UTest for deprecated JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHelper.java (2 lines): - line 11: * // TODO: consider renaming it with something more suitable - line 25: // TODO: consider refactor using JOOQ ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/NonIndicator.java (2 lines): - line 22: * TODO To change the template for this generated file go to - line 32: * TODO To change the template for this generated type comment go to ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/pagerank/PageRankServiceImpl.java (2 lines): - line 521: // TODO Auto-generated method stub - line 527: // TODO Auto-generated method stub ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TLinkTypeArray2.java (2 lines): - line 187: // TODO What follows is just info - line 280: // TODO This needs to be changed so two before/after make a contained and begins/ends-on makes overlap ctakes-core/src/main/java/org/apache/ctakes/core/fsm/state/NonTerminalEndState.java (2 lines): - line 37: // TODO Auto-generated method stub - line 47: // TODO Auto-generated method stub ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/WsdTermConsumer.java (2 lines): - line 81: // // TODO At least four different exceptions are thrown here, and should be caught and handled individually - line 174: // // TODO Poor form - refactor ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java (2 lines): - line 66: // TODO @ConfigurationParameter all of these parameters. - line 413: // TODO Auto-generated catch block ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java (2 lines): - line 107: // TODO property validation could be done here - line 232: // TODO specify exceptions, get rid of the catch for "Exception" ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java (2 lines): - line 135: // TODO Local src/bin Installation, Local Rest WAR, Installation Docker, Rest Docker. - line 138: // TODO For local source installations, instead of doing svn etc., ask which ide. ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationCounter.java (2 lines): - line 29: //TODO: substitute hard-coded boundaries to flexible conditions - line 37: //TODO: substitute hard-coded boundaries to flexible conditions ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml (2 lines): - line 34: TODO: Add, Deprecate, migrate code, then get rid of -nonsense-. - line 203: TODO: change this attribute because of name clash (UMLS/SNOMED) ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java (2 lines): - line 46: // TODO This and TrainAllAssertionModels are the only classes in ctakes-assertion that uses commons-cli. It should be replaced. - line 65: // TODO Auto-generated method stub ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/types/TypeSystem.xml (2 lines): - line 34: TODO: Add, Deprecate, migrate code, then get rid of -nonsense-. - line 203: TODO: change this attribute because of name clash (UMLS/SNOMED) ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AttributeCalculator.java (2 lines): - line 66: if (t.getPartOfSpeech().startsWith("PRP")) // TODO: since only 3rd person pronouns are added as markables, no need to check - line 188: // TODO test this ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java (2 lines): - line 81: // TODO -- see if this applies to this relation: - line 120: // TODO - use if relevant. ctakes-core/src/main/java/org/apache/ctakes/core/fsm/state/NamedState.java (2 lines): - line 41: // TODO Auto-generated method stub - line 51: // TODO Auto-generated method stub ctakes-core/src/main/java/org/apache/ctakes/core/ci/HyphenTextModifierImpl.java (2 lines): - line 235: * TODO - move this to TextModifier and take a Logger - line 287: // TODO Auto-generated catch block ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java (2 lines): - line 218: // TODO Auto-generated catch block - line 301: // TODO Auto-generated catch block ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThymeCasOrderer.java (2 lines): - line 18: // TODO: Maybe this should just be done when we read them in? - line 30: // TODO: Resort this based on last item of name (e.g. ID001_clinic_003 use 003 as its index) ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java (2 lines): - line 96: // TODO Consider adding a parameter for the type of annotation to look for - line 121: // TODO Consider validating values in pattern to type system ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/SinglePackageFabricator.java (2 lines): - line 18: // TODO : Copy basic elements (name, packaging, war plugin) from entity pom to other poms. - line 36: // TODO - make save/load installation types? ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/LinearKernelMatrixWriter.java (2 lines): - line 84: // TODO Auto-generated catch block - line 120: // TODO Auto-generated catch block ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java (2 lines): - line 49: // TODO property validation could be done here - line 55: // TODO property validation could be done here ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/BaseMetaDataHitImpl.java (2 lines): - line 60: // TODO add types to MetaDataHit - line 75: // TODO As far as I have seen, instances of MetaDataHit are immutable (and should be so annotated) ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/XcasAnnotation.java (2 lines): - line 70: for (XcasAnnotation a : this) //TODO is the order guaranteed to be the same? - line 110: //TODO Check for loop in references ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java (2 lines): - line 58: // TODO - fix to use an xml collection reader instead of the hacky way it's done now... - line 122: // FIXME - not using this right now, just use default jcas ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java (2 lines): - line 70: // TODO property validation could be done here - line 181: // TODO specify exceptions, get rid of the catch for "Exception" ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/SchemaUtil.java (2 lines): - line 84: // TODO Auto-generated catch block - line 102: // TODO Auto-generated catch block ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilities.java (2 lines): - line 196: * TODO Consider adding common words as possible performance improvement - line 205: System.out.println("Adding exclude value["+s+"]"); // TODO - use logger ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java (2 lines): - line 6: // TODO Auto-generated method stub - line 11: // TODO Auto-generated method stub ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/states/util/IndentStartState.java (2 lines): - line 40: // TODO Auto-generated method stub - line 49: // TODO Auto-generated method stub ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java (1 line): - line 249: // TODO Auto-generated catch block ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ImportWekaResults.java (1 line): - line 109: // TODO Auto-generated method stub ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java (1 line): - line 112: // TODO Auto-generated catch block ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java (1 line): - line 53: // TODO property validation ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableTreeUtils.java (1 line): - line 66: // TODO test this ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/TextMatch.java (1 line): - line 21: //TODO: Should be upgraded ctakes-utils/src/main/java/org/apache/ctakes/utils/env/EnvironmentVariable.java (1 line): - line 27: // TODO never return null unless there is a great reason. Refactor to non-null NOT_PRESENT ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java (1 line): - line 110: /*** DON'T CHANGE THESE ***/ /* TODO - please comment why these should not be changed */ ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/Loader.java (1 line): - line 42: // TODO Auto-generated catch block ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java (1 line): - line 116: // TODO get rid of these google commons collection creators. ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java (1 line): - line 70: // TODO: this is the correct implementatino, but it does not perform as well ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/lstm_classify.py (1 line): - line 39: # TODO: 'none' is not in vocabulary! ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java (1 line): - line 40: //TODO: currently status is an int in the old system. Let's update this to a constant string? ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/HobbsTreeNavigator.java (1 line): - line 207: // TODO : add code to work from p-1 backwards 3 sentences and add all those which have not been removed from allMarks yet? ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java (1 line): - line 69: // TODO: this is the correct implementatino, but it does not perform as well ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java (1 line): - line 35: // * TODO -- work in progress for use in WSD ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityServiceImpl.java (1 line): - line 754: * initialize information content caches TODO replace strings with concept ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java (1 line): - line 467: // TODO: use consistent naming convention (obj vs o vs object) in equals ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSectionFeaturesExtractor.java (1 line): - line 36: // FIXME - should be paragraphs that only cover one sentence ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java (1 line): - line 51: // TODO Auto-generated constructor stub ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java (1 line): - line 38: // TODO - make document aware for mention-cluster coreference? Not as easy as relation remover because this should work for ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java (1 line): - line 42: // TODO: use consistent variable names (_logger vs LOGGER vs logger) ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__normal.xml (1 line): - line 603: TODO: change this attribute because of name clash (UMLS/SNOMED) ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/VocabularyStore.java (1 line): - line 96: // TODO replace with getBestClassFuture when ctakes is upgraded to accept double and int ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/WizardController.java (1 line): - line 196: // TODO : Internal ActionListener class. Has boolean "firingAction". Is added to every AbstractWizardStep. ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java (1 line): - line 43: // TODO handle subjects ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java (1 line): - line 67: // TODO property validation could be done here ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/BaseLookupConsumerImpl.java (1 line): - line 31: // TODO rename this class properly: AbstractBaseLookupConsumer. Requires refactoring outside module ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEQAAnaforaXMLReader.java (1 line): - line 109: // TODO -- need mapping from id to relation ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java (1 line): - line 37: // TODO Auto-generated constructor stub ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java (1 line): - line 106: psf.setFeatures( feaArray ); // TODO ?? - could be no text in ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java (1 line): - line 176: // TODO too much tui confusion in non-rxnorm drugs ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java (1 line): - line 37: * TODO We may need to provide a way to specify some portion of the path of the file ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java (1 line): - line 12: // TODO Auto-generated method stub ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java (1 line): - line 49: // TODO replace pairs of 3 lists with 2 instances of a single class. Put a build() (sub) method in class? ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java (1 line): - line 82: private static final String dirWithGoldViews = AssertionConst.testDirectories.get("polarity");// TODO parameterize this ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java (1 line): - line 193: * TODO: using rules for now; switch to using a negation module ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java (1 line): - line 360: // TODO only needs to be done once ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/TokenizerPTB.java (1 line): - line 172: // TODO potential place to add some self-checking code ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeCNNAnnotator.java (1 line): - line 36: // TODO Auto-generated constructor stub ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java (1 line): - line 27: // TODO - put all exclusions in a data file, display for user, allow changes and save, etc. ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java (1 line): - line 51: // TODO Consolidate all of the duplicate code in the coref module ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java (1 line): - line 46: // TODO Auto-generated constructor stub ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java (1 line): - line 139: // TODO: fix data so that this is not necessary ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java (1 line): - line 276: // TODO - allow User to blacklist ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java (1 line): - line 31: // TODO Create and extend AbstractInputFileReader a'la the abstract writer ctakes-core/desc/analysis_engine/FilterAnnotator.xml (1 line): - line 30: TODO: ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java (1 line): - line 60: // TODO @ConfigurationParam ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java (1 line): - line 285: // TODO should this be exactly the same as getTokens in TextTokenizer (dictionary gui code) ? probably ... ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java (1 line): - line 51: // TODO: Uncomment below when good features are found: ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/JdbcUtil.java (1 line): - line 28: // TODO At least four different exceptions are thrown here, and should be caught and handled individually ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BaseSparseDataFormatter.java (1 line): - line 179: // TODO fix me! ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifier.java (1 line): - line 220: // TODO - The following code CONDITIONALLY turns tokenText to lowercase, ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java (1 line): - line 54: // TODO In a future release (2 from now = 3.2.5) these -correction- methods should be removed ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java (1 line): - line 224: // TODO fix this ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java (1 line): - line 210: // TODO: make it so you don't sort every time for same sentence. ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java (1 line): - line 154: // TODO handle MedicationAllergyModifier here when / if the value is set/disovered some day ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java (1 line): - line 28: // TODO make this an enum ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnaphoricityAttributeCalculator.java (1 line): - line 175: // FIXME use parser output instead of LWA ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/JustJudgeStep.java (1 line): - line 65: // if (true) /** TODO Should this be done here? **/ AssertionEvaluation.main(parmsAsArray); ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/XcasFile.java (1 line): - line 237: return null; //TODO implement clone? ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TlinkType.java (1 line): - line 42: // TODO refactor to use TlinkAttributeValue enum ctakes-core/desc/analysis_engine/SentenceDetectorAnnotatorBIO.xml (1 line): - line 606: TODO: change this attribute because of name clash (UMLS/SNOMED) ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java (1 line): - line 53: // TODO property validation ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java (1 line): - line 470: // TODO - hook "set" to the parameter selected in the parameter table. Can use Value from table. ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java (1 line): - line 814: // TODO - make document aware so it can run with mention-cluster as intended ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventEventTokenBasedAnnotator.java (1 line): - line 199: // TODO Auto-generated catch block ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java (1 line): - line 43: // TODO extend AbstractOutputFileWriter ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EmptyFeaturesExtractor.java (1 line): - line 15: // TODO Auto-generated method stub ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java (1 line): - line 43: * TODO: Parameterize this so that, e.g., multiple projects could use this feature if necessary. ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java (1 line): - line 45: // TODO Use a plain old java HashMap>. ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/WindowBasedAnnotator.java (1 line): - line 193: // // TODO Auto-generated catch block ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java (1 line): - line 92: }// TODO this should be IOException, but the command-line maven build was breaking ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocumentCreationTimeAnnotator.java (1 line): - line 42: // TODO Auto-generated constructor stub ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java (1 line): - line 167: // TODO: this is kinda redundant, but needed the sections in sorted ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/DeterministicMarkableAnnotator.java (1 line): - line 144: // TODO fix this godawful hack: ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java (1 line): - line 290: // TODO send stop as MULTICAST to stop all receivers on the queue. v6 ? ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java (1 line): - line 52: // TODO property validation ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java (1 line): - line 36: // TODO: This class hardcoded all the criteria, ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java (1 line): - line 157: // TODO make some sort of "enabled" list, so that a piper command is only added if previous piper commands exist. ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java (1 line): - line 163: // TODO handle MedicationAllergyModifier here when / if the value is set/disovered some day ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java (1 line): - line 943: // TODO Auto-generated catch block ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__mayo.xml (1 line): - line 603: TODO: change this attribute because of name clash (UMLS/SNOMED) ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/StatusIndicatorFSM.java (1 line): - line 405: // TODO resolve conflict between history & family history ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java (1 line): - line 52: // TODO property validation could be done here ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java (1 line): - line 38: // TODO Abstract common methods for PropertyTextWriter and PrettyTextWriter ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java (1 line): - line 36: // TODO If this is in use then it should be updated to modern jdk standards ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedDictionaryLookupAnnotator.java (1 line): - line 185: // TODO - last ditch memory reclamation, haven't tried yet - spf ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/AbstractBaseDictionary.java (1 line): - line 34: * TODO - get rid of the using class iterators and use Collection foreach ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/UncertaintyCleartkAnalysisEngineWindowed.java (1 line): - line 56: // TODO: Uncomment below when good features are found: ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java (1 line): - line 231: // TODO Auto-generated method stub ctakes-core/src/main/java/org/apache/ctakes/core/util/FSUtil.java (1 line): - line 65: // TODO uimafit ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetector.java (1 line): - line 355: .splitAtLineBreaksAndTrim(NEWLINE)); // TODO Determine ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/ZscoreNormalizationExtractor.java (1 line): - line 190: // TODO Auto-generated method stub ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java (1 line): - line 70: // TODO Should batchSize be an int ? Are we getting an exception from ConfigurationParameter? ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/TextTokenizer.java (1 line): - line 18: // TODO : add contractions: ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java (1 line): - line 38: // TODO Auto-generated constructor stub ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java (1 line): - line 45: * TODO: Parameterize & unstaticize this so that, e.g., multiple projects could use this feature if necessary. ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java (1 line): - line 32: * TODO: eventually replace the relation extraction version with this one. ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java (1 line): - line 207: // TODO Auto-generated catch block ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationDepRegex.java (1 line): - line 441: // FIXME - not sure this one works correctly -- this example parses weirdly in CVD. ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java (1 line): - line 206: //TODO: need to re-define this in TypeSystemConst.java and re-release core ctakes-ytex/src/main/java/org/apache/ctakes/jdl/AppMain.java (1 line): - line 79: // TODO refactor for jewel ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java (1 line): - line 50: // TODO: remove dependency of a hardcoded path ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java (1 line): - line 337: // TODO hardcoded max offset window is 10 char ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/impl/NegContextInitializerImpl.java (1 line): - line 124: // TODO Auto-generated method stub ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientScoringWriter.java (1 line): - line 242: // FIXME - this is never called by the parent ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java (1 line): - line 73: // TODO subject ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java (1 line): - line 71: * @TODO more doc ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java (1 line): - line 135: // TODO: don't just create Modifiers, create the XXXModifier subtypes ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/SubSectionIndicator.java (1 line): - line 22: * TODO To change the template for this generated file go to ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java (1 line): - line 41: * TODO We may need to provide a way to specify some portion of the path of the file ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java (1 line): - line 47: // TODO Auto-generated constructor stub ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java (1 line): - line 6: // TODO Auto-generated constructor stub ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java (1 line): - line 122: // TODO test this ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java (1 line): - line 237: // @TODO: this is very inefficient. implement feedback arc algo ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/AnnotationIdCollection.java (1 line): - line 127: // // TODO necessary? ctakes-constituency-parser/src/user/resources/org/apache/ctakes/constituency/parser/scripts/groovy/parser.groovy (1 line): - line 73: //TODO: Separate downloads from URL here is a hack. ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java (1 line): - line 37: // TODO Rename. Also, extend AbstractTableFileWriter. ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java (1 line): - line 37: // TODO Auto-generated constructor stub ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java (1 line): - line 46: // TODO Make a similar abstract builder for BinaryTextRelation. abstract createRelation( JCas ) called by build() ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java (1 line): - line 41: * TODO Authentication before download would be nice, or perhaps an encrypted ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java (1 line): - line 76: * FIXME - Does not handle the case where a sentence is only numbers. This can happen at the end of a note ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/term/SpannedRareWordTerm.java (1 line): - line 32: // TODO No longer used - remove ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java (1 line): - line 95: // TODO build tree for multi-word phrases. ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java (1 line): - line 47: // TODO parameterize retainAttrTypeId = DISORDER_ANNOTATIONS = 2 ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java (1 line): - line 38: // TODO Auto-generated constructor stub ctakes-utils/src/main/java/org/apache/ctakes/utils/kernel/RBFKernel.java (1 line): - line 35: // TODO implement! ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java (1 line): - line 54: // TODO CodeableConcept applicable to the note type ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/table/TextTypeModel.java (1 line): - line 19: // TODO make a separate panel for examples. ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/CopyFileSpec.java (1 line): - line 12: */ // TODO pass vararg of TargetFileSpec to BaseInstaller. Call its copyToDisk method. ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java (1 line): - line 82: } else if (!s.equals("U") && !s.equals("N") && !s.equals("no") && !s.equals("I")){ //TODO: cleanup ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java (1 line): - line 551: // TODO Auto-generated method stub ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PersonChainAnnotator.java (1 line): - line 62: // TODO - smarter logic for Dr. Firstname Lastname ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java (1 line): - line 42: // TODO: turn these into configuration parameters ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java (1 line): - line 6: // TODO Auto-generated constructor stub ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java (1 line): - line 238: // TODO Auto-generated catch block ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java (1 line): - line 26: * TODO this interface is completely graphical and needs a lot of attention to be done well ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleParser.java (1 line): - line 76: // TODO build Map> with coref chain index to annotations that belong from the Basic Extensions ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/KerasStringOutcomeDataWriter.java (1 line): - line 34: // TODO Auto-generated method stub ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java (1 line): - line 88: // FIXME why is there a minus one here? ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml (1 line): - line 31: (TODO substitute ytex ctakes-core/src/main/java/org/apache/ctakes/core/sentence/EndOfSentenceScannerImpl.java (1 line): - line 79: positions.add( i ); // TODO - don't always create new, use a pool ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java (1 line): - line 383: // TODO look at scores in classifier and try best-pair rather than first-pair? ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_classify.py (1 line): - line 39: # TODO: 'none' is not in vocabulary! ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAttributeVectorExtractor.java (1 line): - line 18: // TODO Auto-generated method stub ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java (1 line): - line 66: // TODO property validation could be done here ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/CsvLoader.java (1 line): - line 266: // // TODO Auto-generated catch block