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| edu.uchsc.* |
|---|
| edu.uchsc.ccp.iaa.Annotation | ||
|---|---|---|
public static final int |
IGNORE_SPANS_COMPARISON |
3 |
public static final int |
SPANS_EXACT_COMPARISON |
2 |
public static final int |
SPANS_OVERLAP_COMPARISON |
1 |
| edu.uchsc.ccp.iaa.matcher.MatchResult | ||
|---|---|---|
public static final int |
MATCH_RESULT_UNASSIGNED |
-1 |
public static final int |
NONTRIVIAL_MATCH |
0 |
public static final int |
NONTRIVIAL_NONMATCH |
2 |
public static final int |
TRIVIAL_MATCH |
1 |
public static final int |
TRIVIAL_NONMATCH |
3 |
| edu.uchsc.ccp.knowtator.BrowserTextUtil | ||
|---|---|---|
public static final String |
ANNOTATION_TEXT |
"[text]" |
| edu.uchsc.ccp.knowtator.FilterUtil | ||
|---|---|---|
public static final int |
ANY_FILTER |
0 |
public static final int |
CONSENSUS_FILTER |
1 |
public static final int |
NONCONSENSUS_FILTER |
2 |
| edu.uchsc.ccp.knowtator.Knowtator | ||
|---|---|---|
public static final String |
CHANGE_SORT_METHOD |
"CHANGE_SORT_METHOD" |
public static final String |
KNOWTATOR_MANAGER |
"KNOWTATOR_MANAGER" |
public static final String |
SELECT_FILTER |
"SELECT_FILTER" |
public static final String |
SELECT_NEXT_ANNOTATION |
"SELECT_NEXT_ANNOTATION" |
public static final String |
SELECT_NEXT_ANNOTATION_FILTER |
"SELECT_NEXT_ANNOTATION_FILTER" |
public static final String |
SELECT_PREVIOUS_ANNOTATION |
"SELECT_PREVIOUS_ANNOTATION" |
public static final String |
SELECT_PREVIOUS_ANNOTATION_FILTER |
"SELECT_PREVIOUS_ANNOTATION_FILTER" |
| edu.uchsc.ccp.knowtator.KnowtatorProjectUtil | ||
|---|---|---|
public static final String |
ACTIVE_FILTERS_SLOT_NAME |
"knowtator_active_filters" |
public static final String |
ANNOTATED_MENTION_SLOT_NAME |
"knowtator_annotated_mention" |
public static final String |
ANNOTATION_ANNOTATOR_SLOT_NAME |
"knowtator_annotation_annotator" |
public static final String |
ANNOTATION_CLS_NAME |
"knowtator annotation" |
public static final String |
ANNOTATION_COMMENT_SLOT_NAME |
"knowtator_annotation_comment" |
public static final String |
ANNOTATION_CREATION_DATE_SLOT_NAME |
"knowtator_annotation_creation_date" |
public static final String |
ANNOTATION_SPAN_SLOT_NAME |
"knowtator_annotation_span" |
public static final String |
ANNOTATION_TEXT_SLOT_NAME |
"knowtator_annotation_text" |
public static final String |
ANNOTATION_TEXT_SOURCE_SLOT_NAME |
"knowtator_annotation_text_source" |
public static final String |
ANNOTATOR_AFFILIATION_SLOT_NAME |
"knowtator_annotation_annotator_affiliation" |
public static final String |
ANNOTATOR_CLS_NAME |
"knowtator annotator" |
public static final String |
ANNOTATOR_FIRST_NAME_SLOT_NAME |
"knowtator_annotation_annotator_firstname" |
public static final String |
ANNOTATOR_ID_SLOT_NAME |
"knowtator_annotator_id" |
public static final String |
ANNOTATOR_LAST_NAME_SLOT_NAME |
"knowtator_annotation_annotator_lastname" |
public static final String |
ANNOTATOR_TEAM_CLS_NAME |
"knowtator annotator team" |
public static final String |
ANNOTATOR_TEAM_MEMBERS_SLOT_NAME |
"knowtator_annotator_team_members" |
public static final String |
ANNOTATOR_TEAM_NAME_SLOT_NAME |
"knowtator_annotator_team_name" |
public static final String |
BOOLEAN_SLOT_MENTION_CLS_NAME |
"knowtator boolean slot mention" |
public static final String |
CLASS_MATCH_CRITERIA_SLOT_NAME |
"knowtator_class_match_criteria" |
public static final String |
CLASS_MENTION_CLS_NAME |
"knowtator class mention" |
public static final String |
COLOR_ASSIGNMENT_CLS_NAME |
"knowtator color assignment" |
public static final String |
COLOR_ASSIGNMENTS_SLOT_NAME |
"knowtator_color_assignments" |
public static final String |
COLOR_CLASS_SLOT_NAME |
"knowtator_color_class" |
public static final String |
COMPLEX_SLOT_MATCH_CRITERIA_CLS_NAME |
"knowtator complex slot match criteria" |
public static final String |
COMPLEX_SLOT_MENTION_CLS_NAME |
"knowtator complex slot mention" |
public static final String |
CONFIGURATION_CLS_NAME |
"knowtator configuration" |
public static final String |
CONSENSUS_FILTER_CLS_NAME |
"knowtator consensus filter" |
public static final String |
CONSENSUS_SET_CLS_NAME |
"knowtator consensus set" |
public static final String |
CONSENSUS_SET_CONSENSUS_FILTER_SLOT_NAME |
"knowtator_consensus_filter" |
public static final String |
CONSENSUS_SET_INDIVIDUAL_FILTER_SLOT_NAME |
"knowtator_individual_filter" |
public static final String |
CONSENSUS_SET_TEAM_ANNOTATOR_SLOT_NAME |
"knowtator_team_annotator" |
public static final String |
CURRENT_VERSION |
"V007" |
public static final String |
DISPLAY_COLOR_B_SLOT_NAME |
"knowtator_display_color_B" |
public static final String |
DISPLAY_COLOR_CLS_NAME |
"knowtator display color" |
public static final String |
DISPLAY_COLOR_G_SLOT_NAME |
"knowtator_display_color_G" |
public static final String |
DISPLAY_COLOR_NAME_SLOT_NAME |
"knowtator_display_color_name" |
public static final String |
DISPLAY_COLOR_R_SLOT_NAME |
"knowtator_display_color_R" |
public static final String |
DISPLAY_COLOR_SLOT_NAME |
"knowtator_display_color" |
public static final String |
FADE_UNSELECTED_ANNOTATIONS |
"knowtator_fade_unselected_annotations" |
public static final String |
FILTER_ANNOTATOR_SLOT_NAME |
"knowtator_filter_annotator" |
public static final String |
FILTER_CLS_NAME |
"knowtator filter" |
public static final String |
FILTER_NAME_SLOT_NAME |
"knowtator_filter_name" |
public static final String |
FILTER_SET_SLOT_NAME |
"knowtator_filter_set" |
public static final String |
FILTER_TYPE_SLOT_NAME |
"knowtator_filter_type" |
public static final String |
FILTER_TYPES_NOT_SELECTABLE_FROM_TEXT_VIEWER |
"knowtator_types_not_selectable_from_text_viewer" |
public static final String |
FLOAT_SLOT_MENTION_CLS_NAME |
"knowtator float slot mention" |
public static final String |
HUMAN_ANNOTATOR_CLS_NAME |
"knowtator human annotator" |
public static final String |
INSTANCE_MENTION_CLS_NAME |
"knowtator instance mention" |
public static final String |
INTEGER_SLOT_MENTION_CLS_NAME |
"knowtator integer slot mention" |
public static final String |
KNOWTATOR_SUPPORT_CLASSES_VERSION |
"KNOWTATOR_SUPPORT_CLASSES_VERSION" |
public static final String |
KNOWTATOR_SUPPORT_CLS_NAME |
"knowtator support class" |
public static final String |
KNOWTATOR_VERSION_CLS_NAME |
"knowtator version" |
public static final String |
MENTION_ANNOTATION_SLOT_NAME |
"knowtator_mention_annotation" |
public static final String |
MENTION_CLASS_SLOT_NAME |
"knowtator_mention_class" |
public static final String |
MENTION_CLS_NAME |
"knowtator mention" |
public static final String |
MENTION_INSTANCE_SLOT_NAME |
"knowtator_mention_instance" |
public static final String |
MENTION_SLOT_SLOT_NAME |
"knowtator_mention_slot" |
public static final String |
MENTION_SLOT_VALUE_SLOT_NAME |
"knowtator_mention_slot_value" |
public static final String |
MENTIONED_IN_SLOT_NAME |
"knowtator_mentioned_in" |
public static final String |
PROPOGATE_TRIVIAL_MATCH_SLOT_NAME |
"knowtator_propogate_trivial_match" |
public static final String |
ROOT_CLSES_SLOT_NAME |
"knowtator_root_clses" |
public static final String |
SELECTED_ANNOTATION_SET_SLOT_NAME |
"knowtator_selected_annotation_set" |
public static final String |
SELECTED_ANNOTATOR_SLOT_NAME |
"knowtator_selected_annotator" |
public static final String |
SELECTED_FILTER_SLOT_NAME |
"knowtator_selected_filter" |
public static final String |
SELECTED_FILTERS_CLS_NAME |
"knowtator selected filters" |
public static final String |
SELECTED_FILTERS_SLOT_NAME |
"knowtator_selected_filters" |
public static final String |
SET_CLS_NAME |
"knowtator set" |
public static final String |
SET_DESCRIPTION_SLOT_NAME |
"knowtator_set_description" |
public static final String |
SET_NAME_SLOT_NAME |
"knowtator_set_name" |
public static final String |
SET_SLOT_NAME |
"knowtator_set" |
public static final String |
SIMPLE_SLOT_MATCH_CRITERIA_CLS_NAME |
"knowtator simple slot match criteria" |
public static final String |
SLOT_MATCH_CRITERIA_SLOT_NAME |
"knowtator_slot_match_criteria" |
public static final String |
SLOT_MATCHER_CONFIG_CLS_NAME |
"knowtator slot matcher config" |
public static final String |
SLOT_MATCHER_SIMPLE_SLOTS_SLOT_NAME |
"knowtator_slot_matcher_simple_slots" |
public static final String |
SLOT_MATCHER_SLOT_SLOT_NAME |
"knowtator_slot_matcher_slot" |
public static final String |
SLOT_MENTION_CLS_NAME |
"knowtator slot mention" |
public static final String |
SLOT_MENTION_SLOT_NAME |
"knowtator_slot_mention" |
public static final String |
SPAN_MATCH_CRITERIA_SLOT_NAME |
"knowtator_span_match_criteria" |
public static final String |
STRING_SLOT_MENTION_CLS_NAME |
"knowtator string slot mention" |
public static final String |
SUBTEXT_SLOT_SLOT_NAME |
"knowtator_subtext_slot" |
public static final String |
TEXT_SOURCE_CLS_NAME |
"knowtator text source" |
public static final String |
TOKEN_REGEX_SLOT_NAME |
"knowtator_token_regex" |
public static final String |
TSC_IMPLEMENTATION_SLOT_NAME |
"knowtator_tsc_implementation" |
public static final String |
TSC_IMPLEMENTATIONS_CLS_NAME |
"knowtator text source collection implementations" |
public static final String |
UNVERSIONED |
"UNVERSIONED" |
public static final String |
V001 |
"V001" |
public static final String |
V002 |
"V002" |
public static final String |
V003 |
"V003" |
public static final String |
V004 |
"V004" |
public static final String |
V005 |
"V005" |
public static final String |
V006 |
"V006" |
public static final String |
V007 |
"V007" |
public static final String |
VERSION_BEING_UPDATED |
"VERSION_BEING_UPDATED" |
| edu.uchsc.ccp.knowtator.SpanUtil | ||
|---|---|---|
public static final String |
GROW_ANNOTATION_LEFT |
"GROW_ANNOTATION_LEFT" |
public static final String |
GROW_ANNOTATION_LEFT_WORD |
"GROW_ANNOTATION_LEFT_WORD" |
public static final String |
GROW_ANNOTATION_RIGHT |
"GROW_ANNOTATION_RIGHT" |
public static final String |
GROW_ANNOTATION_RIGHT_WORD |
"GROW_ANNOTATION_RIGHT_WORD" |
public static final String |
SHRINK_ANNOTATION_LEFT |
"SHRINK_ANNOTATION_LEFT" |
public static final String |
SHRINK_ANNOTATION_LEFT_WORD |
"SHRINK_ANNOTATION_LEFT_WORD" |
public static final String |
SHRINK_ANNOTATION_RIGHT |
"SHRINK_ANNOTATION_RIGHT" |
public static final String |
SHRINK_ANNOTATION_RIGHT_WORD |
"SHRINK_ANNOTATION_RIGHT_WORD" |
| edu.uchsc.ccp.knowtator.textsource.DefaultTextSource | ||
|---|---|---|
public static final String |
CLS_NAME |
"knowtator text source" |
| edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection | ||
|---|---|---|
public static final String |
CLS_NAME |
"file line text source" |
public static final String |
DISPLAY_NAME |
"Lines from file" |
| edu.uchsc.ccp.knowtator.textsource.filelines.FileLineTextSource | ||
|---|---|---|
public static final String |
CLS_NAME |
"file line text source" |
| edu.uchsc.ccp.knowtator.textsource.files.FileTextSource | ||
|---|---|---|
public static final String |
CLS_NAME |
"file text source" |
| edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection | ||
|---|---|---|
public static final String |
DISPLAY_NAME |
"Local Files" |
| edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource | ||
|---|---|---|
public static final String |
CLS_NAME |
"generifs text source" |
public static final String |
ENTREZ_GENE_SLOT_NAME |
"generif_entrez_gene" |
public static final String |
PMID_SLOT_NAME |
"generif_pmid" |
| edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection | ||
|---|---|---|
public static final String |
CLS_NAME |
"generifs text source" |
public static final String |
DISPLAY_NAME |
"GeneRIFs" |
| edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory | ||
|---|---|---|
public static final int |
SELECTION_ITEMS_COUNT_THRESHOLD |
20 |
| edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane | ||
|---|---|---|
public static final int |
DASHED_LINES |
2 |
public static final int |
NO_LINES |
0 |
public static final int |
SOLID_LINES |
1 |
public static final int |
VERTICAL_LINES |
3 |
| edu.uchsc.ccp.knowtator.ui.ModalDialog | ||
|---|---|---|
public static final int |
MODE_CLOSE |
14 |
public static final int |
MODE_OK_CANCEL |
11 |
public static final int |
MODE_YES_NO |
13 |
public static final int |
MODE_YES_NO_CANCEL |
12 |
public static final int |
OPTION_CANCEL |
4 |
public static final int |
OPTION_CLOSE |
5 |
public static final int |
OPTION_NO |
3 |
public static final int |
OPTION_OK |
1 |
public static final int |
OPTION_YES |
2 |
public static final int |
RESULT_ERROR |
6 |
| edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard | ||
|---|---|---|
public static final String |
CREATE_BUTTON_CLICKED |
"CREATE_BUTTON_CLICKED" |
public static final String |
FILTER_INSTRUCTIONS |
"Please select a filter that describes the set of annotations that you want to create a consensus set for. The selected filter must have either two annotators or two annotation sets specified. If you have not yet defined an appropriate filter, then please exit out of this wizard and create one. Please seehttp://knowtator.sourceforge.net//filters.shtml for information about filters." |
public static final String |
NAME_INSTRUCTIONS |
"Please enter a descriptive name for your consensus set. If you plan to have only one consensus set in your annotation project, then selecting the default name should be fine." |
public static final String |
TEXT_SOURCES_INSTRUCTIONS |
"Please select the text sources that you want included in the consensus set creation." |
public static final String |
TO_FILTER_FRAME |
"TO_FILTER_FRAME" |
public static final String |
TO_NAME_FRAME |
"TO_NAME_FRAME" |
public static final String |
TO_TEXTSOURCES_FRAME |
"TO_TEXTSOURCES_FRAME" |
public static final String |
TO_WELCOME_FRAME |
"TO_WELCOME_FRAME" |
public static final String |
WELCOME_MESSAGE |
"This wizard allows you to create a consensus set from existing, merged annotations. Typically, text sources will be individually annotated in separate projects and then merged together into a single project at which point consensus mode is used. This action will not delete or modify existing annotations. A consensus set consists of annotations that have been copied from the set of annotations defined by the filter that you will choose in this wizard. Consensus mode will then act on these copied annotations. For more information about how consensus mode works please consult the online documentation. http://knowtator.sourceforge.net//consensus.shtml" |
| edu.uchsc.ccp.knowtator.wizards.IAAWizard | ||
|---|---|---|
public static final String |
ADD_SLOT_MATCHER_CLICKED |
"ADD_SLOT_MATCHER_CLICKED" |
public static final String |
GO_CLICKED |
"GO_CLICKED" |
public static final String |
IAA_CONFIG |
"IAA_CONFIG" |
public static final String |
IAA_CONFIG_DISPLAY |
"IAA_CONFIG_DISPLAY" |
public static final String |
IAA_DIRECTORY |
"IAA_DIRECTORY" |
public static final String |
IAA_FILTER |
"IAA_FILTER" |
public static final String |
IAA_TEXTSOURCES |
"IAA_TEXTSOURCES" |
public static final String |
IAA_WELCOME_MESSAGE |
"This wizard allows you to configure how inter-annotator agreement (IAA) metrics will be calculated. All IAA results are written to local html files that are veiwable using a web browser. Please consult available documentation for details on how IAA is calculated and what the results mean. Calculating the IAA may take some time depending on how many matchers are used and how many annotations are in your project. Please be patient!" |
public static final String |
REMOVE_SLOT_MATCHER_CLICKED |
"REMOVE_SLOT_MATCHER_CLICKED" |
public static final String |
TO_CONFIG_FRAME |
"TO_CONFIG_FRAME" |
public static final String |
TO_FILTER_FRAME |
"TO_FILTER_FRAME" |
public static final String |
TO_OUTPUT_FRAME |
"TO_OUTPUT_FRAME" |
public static final String |
TO_TEXTSOURCES_FRAME |
"TO_TEXTSOURCES_FRAME" |
public static final String |
TO_WELCOME_FRAME |
"TO_WELCOME_FRAME" |
| edu.uchsc.ccp.knowtator.wizards.WizardFrame | ||
|---|---|---|
public static final String |
CANCEL |
"CANCEL" |
public static final String |
NEXT |
"NEXT" |
public static final String |
PREVIOUS |
"PREVIOUS" |
| edu.uchsc.ccp.knowtator.xml.XMLConstants | ||
|---|---|---|
public static final String |
ANNOTATION_ELEMENT_NAME |
"annotation" |
public static final String |
ANNOTATIONS_ELEMENT_NAME |
"annotations" |
public static final String |
ANNOTATOR_ELEMENT_NAME |
"annotator" |
public static final String |
BOOLEAN_SLOT_MENTION_ELEMENT_NAME |
"booleanSlotMention" |
public static final String |
BOOLEAN_SLOT_MENTION_VALUE_ELEMENT_NAME |
"booleanSlotMentionValue" |
public static final String |
CLASS_MENTION_ELEMENT_NAME |
"classMention" |
public static final String |
COMMENT_ELEMENT_NAME |
"annotationComment" |
public static final String |
COMPLEX_SLOT_MENTION_ELEMENT_NAME |
"complexSlotMention" |
public static final String |
COMPLEX_SLOT_MENTION_VALUE_ELEMENT_NAME |
"complexSlotMentionValue" |
public static final String |
CREATION_DATE_ELEMENT_NAME |
"creationDate" |
public static final String |
FLOAT_SLOT_MENTION_ELEMENT_NAME |
"floatSlotMention" |
public static final String |
FLOAT_SLOT_MENTION_VALUE_ELEMENT_NAME |
"floatSlotMentionValue" |
public static final String |
HAS_SLOT_MENTION_ELEMENT_NAME |
"hasSlotMention" |
public static final String |
ID_ATTRIBUTE_NAME |
"id" |
public static final String |
INSTANCE_MENTION_ELEMENT_NAME |
"instanceMention" |
public static final String |
INTEGER_SLOT_MENTION_ELEMENT_NAME |
"integerSlotMention" |
public static final String |
INTEGER_SLOT_MENTION_VALUE_ELEMENT_NAME |
"integerSlotMentionValue" |
public static final String |
MENTION_CLASS_ELEMENT_NAME |
"mentionClass" |
public static final String |
MENTION_ELEMENT_NAME |
"mention" |
public static final String |
MENTION_INSTANCE_ELEMENT_NAME |
"mentionInstance" |
public static final String |
MENTION_SLOT_ELEMENT_NAME |
"mentionSlot" |
public static final String |
SPAN_ELEMENT_NAME |
"span" |
public static final String |
SPAN_END_ATTRIBUTE_NAME |
"end" |
public static final String |
SPAN_START_ATTRIBUTE_NAME |
"start" |
public static final String |
SPANNED_TEXT_ELEMENT_NAME |
"spannedText" |
public static final String |
STRING_SLOT_MENTION_ELEMENT_NAME |
"stringSlotMention" |
public static final String |
STRING_SLOT_MENTION_VALUE_ELEMENT_NAME |
"stringSlotMentionValue" |
public static final String |
TEXT_SOURCE_ATTRIBUTE_NAME |
"textSource" |
public static final String |
VALUE_ATTRIBUTE_NAME |
"value" |
| edu.uchsc.ccp.knowtator.xml.XMLExport | ||
|---|---|---|
public static final String |
XML_EXPORT_DIRECTORY |
"XML_EXPORT_FILE" |
| edu.uchsc.ccp.knowtator.xml.XMLImport | ||
|---|---|---|
public static final String |
XML_IMPORT_DIRECTORY |
"XML_IMPORT_FILE" |
|
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