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From chen...@apache.org
Subject svn commit: r1389618 [12/22] - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-chunker/desc/ ctakes-chunker/resources/launch/ ctakes-chunker/src/main/java/edu/ ctakes-chunker/src/main/java/org/ ctakes-chunker/src/main/java/org/apache/ ctakes-chun...
Date Mon, 24 Sep 2012 22:05:23 GMT
Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml Mon Sep 24 22:04:51 2012
@@ -23,16 +23,16 @@
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -72,7 +72,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -101,7 +101,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>LVG Annotator</name>
                     <description/>
@@ -209,7 +209,7 @@
                         <nameValuePair>
                             <name>CmdCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_norm.voc</string>
+                                <string>/ctakes-lvg/2005_norm.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -264,7 +264,7 @@
                         <nameValuePair>
                             <name>LemmaCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_lemma.voc</string>
+                                <string>/ctakes-lvg/2005_lemma.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -310,7 +310,7 @@
                     <externalResourceDependency>
                         <key>LvgCmdApi</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -322,7 +322,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -338,7 +338,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.TokenizerAnnotatorPTB</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.TokenizerAnnotatorPTB</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>TokenizerAnnotatorPTB</name>
                     <description>Discovers tokens in the given text, following Penn TreeBank tokenization rules.  These tokens consist of words, punctuation, etc...</description>
@@ -363,7 +363,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <typePriorities/>
@@ -392,7 +392,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SentenceDetector</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SentenceDetector</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>Sentence Detector annotator</name>
                     <description>Discovers sentence boundaries.</description>
@@ -438,7 +438,7 @@
                     <externalResourceDependency>
                         <key>MaxentModel</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.core.resource.MaxentModelResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.core.resource.MaxentModelResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -450,7 +450,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:sentdetect/sdmed.mod</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -466,7 +466,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>SimpleSegmentAnnotator</name>
                     <description>Creates a single Segment annotation, encompassing the entire document.  For use prior to annotators that require a Segment annotation, when the input document is not in CDA/does not have another annotator that creates Segment annotations.</description>
@@ -507,7 +507,7 @@
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.pos_tagger.POSTagger</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.postagger.POSTagger</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>POSTagger</name>
                     <description/>
@@ -591,7 +591,7 @@
                 <node>TokenizerAnnotatorPTB</node>
                 <node>LVG Annotator</node>
                 <node>POSTagger</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</node>
             </fixedFlow>
         </flowConstraints>
         <capabilities/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml Mon Sep 24 22:04:51 2012
@@ -23,16 +23,16 @@
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -72,7 +72,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -101,7 +101,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>LVG Annotator</name>
                     <description/>
@@ -209,7 +209,7 @@
                         <nameValuePair>
                             <name>CmdCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_norm.voc</string>
+                                <string>/ctakes-lvg/2005_norm.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -264,7 +264,7 @@
                         <nameValuePair>
                             <name>LemmaCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_lemma.voc</string>
+                                <string>/ctakes-lvg/2005_lemma.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -310,7 +310,7 @@
                     <externalResourceDependency>
                         <key>LvgCmdApi</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -322,7 +322,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -338,7 +338,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>SimpleSegmentAnnotator</name>
                     <description>Creates a single Segment annotation, encompassing the entire document.  For use prior to annotators that require a Segment annotation, when the input document is not in CDA/does not have another annotator that creates Segment annotations.</description>
@@ -384,7 +384,7 @@
             <fixedFlow>
                 <node>SimpleSegmentAnnotator</node>
                 <node>LVG Annotator</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</node>
             </fixedFlow>
         </flowConstraints>
         <capabilities/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml Mon Sep 24 22:04:51 2012
@@ -23,16 +23,16 @@
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -72,7 +72,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -101,7 +101,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>LVG Annotator</name>
                     <description/>
@@ -209,7 +209,7 @@
                         <nameValuePair>
                             <name>CmdCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_norm.voc</string>
+                                <string>/ctakes-lvg/2005_norm.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -264,7 +264,7 @@
                         <nameValuePair>
                             <name>LemmaCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_lemma.voc</string>
+                                <string>/ctakes-lvg/2005_lemma.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -310,7 +310,7 @@
                     <externalResourceDependency>
                         <key>LvgCmdApi</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -322,7 +322,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -338,7 +338,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>SimpleSegmentAnnotator</name>
                     <description>Creates a single Segment annotation, encompassing the entire document.  For use prior to annotators that require a Segment annotation, when the input document is not in CDA/does not have another annotator that creates Segment annotations.</description>
@@ -379,7 +379,7 @@
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.pos_tagger.POSTagger</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.postagger.POSTagger</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>POSTagger</name>
                     <description/>
@@ -461,7 +461,7 @@
                 <node>SimpleSegmentAnnotator</node>
                 <node>LVG Annotator</node>
                 <node>POSTagger</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</node>
             </fixedFlow>
         </flowConstraints>
         <capabilities/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml Mon Sep 24 22:04:51 2012
@@ -23,16 +23,16 @@
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -72,7 +72,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -101,7 +101,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>LVG Annotator</name>
                     <description/>
@@ -209,7 +209,7 @@
                         <nameValuePair>
                             <name>CmdCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_norm.voc</string>
+                                <string>/ctakes-lvg/2005_norm.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -264,7 +264,7 @@
                         <nameValuePair>
                             <name>LemmaCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_lemma.voc</string>
+                                <string>/ctakes-lvg/2005_lemma.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -310,7 +310,7 @@
                     <externalResourceDependency>
                         <key>LvgCmdApi</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -322,7 +322,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -338,7 +338,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.TokenizerAnnotatorPTB</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.TokenizerAnnotatorPTB</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>TokenizerAnnotatorPTB</name>
                     <description>Discovers tokens in the given text, following Penn TreeBank tokenization rules.  These tokens consist of words, punctuation, etc...</description>
@@ -363,7 +363,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <typePriorities/>
@@ -388,16 +388,16 @@
                 <resourceManagerConfiguration/>
             </taeDescription>
         </delegateAnalysisEngine>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -424,7 +424,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -453,7 +453,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SentenceDetector</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SentenceDetector</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>Sentence Detector annotator</name>
                     <description>Discovers sentence boundaries.</description>
@@ -499,7 +499,7 @@
                     <externalResourceDependency>
                         <key>MaxentModel</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.core.resource.MaxentModelResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.core.resource.MaxentModelResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -511,7 +511,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:sentdetect/sdmed.mod</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -527,7 +527,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>SimpleSegmentAnnotator</name>
                     <description>Creates a single Segment annotation, encompassing the entire document.  For use prior to annotators that require a Segment annotation, when the input document is not in CDA/does not have another annotator that creates Segment annotations.</description>
@@ -568,7 +568,7 @@
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.pos_tagger.POSTagger</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.postagger.POSTagger</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>POSTagger</name>
                     <description/>
@@ -652,8 +652,8 @@
                 <node>TokenizerAnnotatorPTB</node>
                 <node>LVG Annotator</node>
                 <node>POSTagger</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</node>
             </fixedFlow>
         </flowConstraints>
         <capabilities/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml Mon Sep 24 22:04:51 2012
@@ -23,16 +23,16 @@
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -72,7 +72,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -101,7 +101,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>LVG Annotator</name>
                     <description/>
@@ -209,7 +209,7 @@
                         <nameValuePair>
                             <name>CmdCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_norm.voc</string>
+                                <string>/ctakes-lvg/2005_norm.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -264,7 +264,7 @@
                         <nameValuePair>
                             <name>LemmaCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_lemma.voc</string>
+                                <string>/ctakes-lvg/2005_lemma.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -310,7 +310,7 @@
                     <externalResourceDependency>
                         <key>LvgCmdApi</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -322,7 +322,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -334,16 +334,16 @@
                 </resourceManagerConfiguration>
             </taeDescription>
         </delegateAnalysisEngine>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -370,7 +370,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -399,7 +399,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>SimpleSegmentAnnotator</name>
                     <description>Creates a single Segment annotation, encompassing the entire document.  For use prior to annotators that require a Segment annotation, when the input document is not in CDA/does not have another annotator that creates Segment annotations.</description>
@@ -445,8 +445,8 @@
             <fixedFlow>
                 <node>SimpleSegmentAnnotator</node>
                 <node>LVG Annotator</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</node>
             </fixedFlow>
         </flowConstraints>
         <capabilities/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml Mon Sep 24 22:04:51 2012
@@ -23,16 +23,16 @@
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -72,7 +72,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -101,7 +101,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>LVG Annotator</name>
                     <description/>
@@ -209,7 +209,7 @@
                         <nameValuePair>
                             <name>CmdCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_norm.voc</string>
+                                <string>/ctakes-lvg/2005_norm.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -264,7 +264,7 @@
                         <nameValuePair>
                             <name>LemmaCacheFileLocation</name>
                             <value>
-                                <string>/lvg/2005_lemma.voc</string>
+                                <string>/ctakes-lvg/2005_lemma.voc</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
@@ -310,7 +310,7 @@
                     <externalResourceDependency>
                         <key>LvgCmdApi</key>
                         <description/>
-                        <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+                        <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
                         <optional>false</optional>
                     </externalResourceDependency>
                 </externalResourceDependencies>
@@ -322,7 +322,7 @@
                             <fileResourceSpecifier>
                                 <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
                             </fileResourceSpecifier>
-                            <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+                            <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
                         </externalResource>
                     </externalResources>
                     <externalResourceBindings>
@@ -334,16 +334,16 @@
                 </resourceManagerConfiguration>
             </taeDescription>
         </delegateAnalysisEngine>
-        <delegateAnalysisEngine key="edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE">
+        <delegateAnalysisEngine key="org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE">
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
                 <analysisEngineMetaData>
-                    <name>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</name>
+                    <name>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</name>
                     <description>Descriptor automatically generated by uimaFIT</description>
                     <version>unknown</version>
-                    <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+                    <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
                             <name>ParserModelFileName</name>
@@ -370,7 +370,7 @@
                     </configurationParameterSettings>
                     <typeSystemDescription>
                         <imports>
-                            <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                            <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
                         </imports>
                     </typeSystemDescription>
                     <fsIndexCollection/>
@@ -399,7 +399,7 @@
             <taeDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>SimpleSegmentAnnotator</name>
                     <description>Creates a single Segment annotation, encompassing the entire document.  For use prior to annotators that require a Segment annotation, when the input document is not in CDA/does not have another annotator that creates Segment annotations.</description>
@@ -440,7 +440,7 @@
             <analysisEngineDescription>
                 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
                 <primitive>true</primitive>
-                <annotatorImplementationName>edu.mayo.bmi.uima.pos_tagger.POSTagger</annotatorImplementationName>
+                <annotatorImplementationName>org.apache.ctakes.postagger.POSTagger</annotatorImplementationName>
                 <analysisEngineMetaData>
                     <name>POSTagger</name>
                     <description/>
@@ -522,8 +522,8 @@
                 <node>SimpleSegmentAnnotator</node>
                 <node>LVG Annotator</node>
                 <node>POSTagger</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</node>
-                <node>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</node>
+                <node>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</node>
             </fixedFlow>
         </flowConstraints>
         <capabilities/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml Mon Sep 24 22:04:51 2012
@@ -22,12 +22,12 @@
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>true</primitive>
-    <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
+    <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</annotatorImplementationName>
     <analysisEngineMetaData>
-        <name>edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE</name>
+        <name>org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE</name>
         <description>Descriptor automatically generated by uimaFIT</description>
         <version>unknown</version>
-        <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+        <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
         <configurationParameters>
             <configurationParameter>
                 <name>ParserModelFileName</name>
@@ -54,7 +54,7 @@
         </configurationParameterSettings>
         <typeSystemDescription>
             <imports>
-                <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
             </imports>
         </typeSystemDescription>
         <fsIndexCollection/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LemAssigner.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LemAssigner.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LemAssigner.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LemAssigner.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.nlp.parser.LemAssigner</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.dependency.parser.LemAssigner</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>LemAssigner</name>
     <description/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>LVG Annotator</name>
     <description/>
@@ -130,7 +130,7 @@
       <nameValuePair>
         <name>CmdCacheFileLocation</name>
         <value>
-          <string>/lvg/2005_norm.voc</string>
+          <string>/ctakes-lvg/2005_norm.voc</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -185,7 +185,7 @@
       <nameValuePair>
         <name>LemmaCacheFileLocation</name>
         <value>
-          <string>/lvg/2005_lemma.voc</string>
+          <string>/ctakes-lvg/2005_lemma.voc</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -234,7 +234,7 @@
     <externalResourceDependency>
       <key>LvgCmdApi</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource</interfaceName>
+      <interfaceName>org.apache.ctakes.lvg.resource.LvgCmdApiResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -246,7 +246,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:lvg/data/config/lvg.properties</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/PosAssigner.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/PosAssigner.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/PosAssigner.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/PosAssigner.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.nlp.parser.PosAssigner</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.dependency.parser.PosAssigner</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>PosAssigner</name>
     <description/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml Mon Sep 24 22:04:51 2012
@@ -21,7 +21,7 @@
 -->
 <casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-  <implementationName>edu.mayo.bmi.nlp.parser.DependencyNodeWriter</implementationName>
+  <implementationName>org.apache.ctakes.dependency.parser.DependencyNodeWriter</implementationName>
   <processingResourceMetaData>
     <name>DependencyNodeWriter</name>
     <description>Write Dependency Nodes from CAS to tab-delimited file</description>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml Mon Sep 24 22:04:51 2012
@@ -96,7 +96,7 @@
         </casProcessor>
         <casProcessor deployment="integrated" name="Write CAS to XML file">
             <descriptor>
-                <import location="../../../core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+                <import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
             </descriptor>
             <deploymentParameters/>
             <errorHandling>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerLemTestCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerLemTestCPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerLemTestCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerLemTestCPE.xml Mon Sep 24 22:04:51 2012
@@ -70,7 +70,7 @@
         </casProcessor>
         <casProcessor deployment="integrated" name="Write CAS to XML file">
             <descriptor>
-                <import location="../../../core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+                <import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
             </descriptor>
             <deploymentParameters/>
             <errorHandling>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerPosTestCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerPosTestCPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerPosTestCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerPosTestCPE.xml Mon Sep 24 22:04:51 2012
@@ -82,7 +82,7 @@
         </casProcessor>
         <casProcessor deployment="integrated" name="Write CAS to XML file">
             <descriptor>
-                <import location="../../../core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+                <import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
             </descriptor>
             <deploymentParameters/>
             <errorHandling>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_reader/DependencyFileCollectionReader.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_reader/DependencyFileCollectionReader.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_reader/DependencyFileCollectionReader.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/collection_reader/DependencyFileCollectionReader.xml Mon Sep 24 22:04:51 2012
@@ -21,7 +21,7 @@
 -->
 <collectionReaderDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-  <implementationName>edu.mayo.bmi.nlp.parser.DependencyFileCollectionReader</implementationName>
+  <implementationName>org.apache.ctakes.dependency.parser.DependencyFileCollectionReader</implementationName>
   <processingResourceMetaData>
     <name>DependencyCollectionReader</name>
     <description>For training dependency parsers.

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.uimafit/types.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.uimafit/types.txt?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.uimafit/types.txt (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.uimafit/types.txt Mon Sep 24 22:04:51 2012
@@ -1 +1 @@
-classpath*:edu/mayo/bmi/uima/core/type/**/*.xml
\ No newline at end of file
+classpath*:edu/mayo/bmi/uima/ctakes-core/type/**/*.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser;
+package org.apache.ctakes.dependency.parser;
 /*
  * Copyright: (c) 2010   Mayo Foundation for Medical Education and 
  * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
@@ -55,9 +55,9 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
 
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 
 /**

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserDependencyParserAE.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserDependencyParserAE.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserDependencyParserAE.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserDependencyParserAE.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae;
+package org.apache.ctakes.dependency.parser.ae;
 
 import java.io.File;
 import java.io.IOException;
@@ -39,7 +39,8 @@ import clear.dep.DepNode;
 import clear.dep.DepTree;
 import clear.morph.MorphEnAnalyzer;
 import clear.parse.AbstractDepParser;
-import edu.mayo.bmi.nlp.parser.util.ClearDependencyUtility;
+
+import org.apache.ctakes.dependency.parser.util.ClearDependencyUtility;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserSemanticRoleLabelerAE.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserSemanticRoleLabelerAE.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserSemanticRoleLabelerAE.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserSemanticRoleLabelerAE.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae;
+package org.apache.ctakes.dependency.parser.ae;
 
 import java.io.File;
 import java.io.IOException;
@@ -46,13 +46,14 @@ import clear.dep.srl.SRLHead;
 import clear.morph.MorphEnAnalyzer;
 import clear.parse.AbstractSRLParser;
 import clear.reader.AbstractReader;
+
+import org.apache.ctakes.core.util.ListFactory;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textsem.Predicate;
 import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
 import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.util.ListFactory;
 
 /**
  *This class provides a UIMA wrapper for the ClearParser Semantic Role Labeler, which is

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserUtil.java (from r1388092, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserUtil.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserUtil.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserUtil.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserUtil.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserUtil.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearParserUtil.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae;
+package org.apache.ctakes.dependency.parser.ae;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/LemAssigner.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/LemAssigner.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/LemAssigner.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/LemAssigner.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae;
+package org.apache.ctakes.dependency.parser.ae;
 /*
  * Copyright: (c) 2010   Mayo Foundation for Medical Education and 
  * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/PosAssigner.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/PosAssigner.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/PosAssigner.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/PosAssigner.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae;
+package org.apache.ctakes.dependency.parser.ae;
 /*
  * Copyright: (c) 2010   Mayo Foundation for Medical Education and 
  * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/TestClearParserAnalysisEngines.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/TestClearParserAnalysisEngines.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/TestClearParserAnalysisEngines.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/TestClearParserAnalysisEngines.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae.util;
+package org.apache.ctakes.dependency.parser.ae.util;
 
 import java.io.File;
 import java.io.IOException;
@@ -38,10 +38,10 @@ import org.uimafit.pipeline.SimplePipeli
 import org.uimafit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
-import edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE;
-import edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE;
-import edu.mayo.bmi.nlp.parser.util.DependencyUtility;
-import edu.mayo.bmi.nlp.parser.util.SRLUtility;
+import org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE;
+import org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE;
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.dependency.parser.util.SRLUtility;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
@@ -55,7 +55,7 @@ import org.apache.ctakes.typesystem.type
 public class TestClearParserAnalysisEngines {
 	public static String DEP_DUMMY_MODEL_FILE = "src/resources/dependency/dummy.dep.mod.jar";
 	public static String SRL_DUMMY_MODEL_FILE = "src/resources/srl/dummy.srl.mod.jar";
-	public static String INPUT_FILE = "../clinical documents pipeline/test/data/plaintext/testpatient_plaintext_1.txt";
+	public static String INPUT_FILE = "../ctakes-clinical-pipeline/test/data/plaintext/testpatient_plaintext_1.txt";
 
 
 	public static class Options extends Options_ImplBase {
@@ -116,7 +116,7 @@ public class TestClearParserAnalysisEngi
 		File srlModelFile = options.srlModelFile;
 		File inputFile = options.inputFile;
 		
-		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../common-type-system/desc/common_type_system.xml");
+		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../ctakes-type-system/desc/common_type_system.xml");
 				
 		CollectionReader reader1 = CollectionReaderFactory.createCollectionReader(
 				FilesCollectionReader.class,

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearParserDescriptors.java (from r1388092, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/WriteClearParserDescriptors.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearParserDescriptors.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearParserDescriptors.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/WriteClearParserDescriptors.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/WriteClearParserDescriptors.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearParserDescriptors.java Mon Sep 24 22:04:51 2012
@@ -16,13 +16,15 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae.util;
+package org.apache.ctakes.dependency.parser.ae.util;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 
+import org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE;
+import org.apache.ctakes.dependency.parser.ae.ClearParserSemanticRoleLabelerAE;
 import org.apache.uima.UIMAException;
 import org.apache.uima.UIMAFramework;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -38,8 +40,6 @@ import org.uimafit.factory.AnalysisEngin
 import org.uimafit.factory.TypeSystemDescriptionFactory;
 import org.xml.sax.SAXException;
 
-import edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE;
-import edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE;
 
 
 /**
@@ -47,11 +47,11 @@ import edu.mayo.bmi.nlp.parser.ae.ClearP
  *
  */
 public class WriteClearParserDescriptors {
-	public static final String SIMPLE_SEGMENTER_PATH = "../clinical documents pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml";
-	public static final String SENTENCE_DETECTOR_PATH="../core/desc/analysis_engine/SentenceDetectorAnnotator.xml";
-	public static final String TOKENIZER_PATH="../core/desc/analysis_engine/TokenizerAnnotator.xml";
+	public static final String SIMPLE_SEGMENTER_PATH = "../ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml";
+	public static final String SENTENCE_DETECTOR_PATH="../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml";
+	public static final String TOKENIZER_PATH="../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml";
 	public static final String LVG_BASE_TOKEN_ANNOTATOR_PATH="desc/analysis_engine/LvgBaseTokenAnnotator.xml";
-	public static final String POS_TAGGER_PATH="../POS tagger/desc/POSTagger.xml";
+	public static final String POS_TAGGER_PATH="../ctakes-pos-tagger/desc/POSTagger.xml";
 	public static final String DEP_NAME="ClearParserDependencyParser";
 	public static final String SRL_NAME="ClearParserSRL";
 
@@ -80,7 +80,7 @@ public class WriteClearParserDescriptors
 		Options options = new Options();
 		options.parseOptions(args);
 
-		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../../../common-type-system/desc/common_type_system.xml");
+		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../../../ctakes-type-system/desc/common_type_system.xml");
 
 		AnalysisEngineDescription clearparserSRLDesc = AnalysisEngineFactory.createPrimitiveDescription(
 				ClearParserSemanticRoleLabelerAE.class,

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java (from r1388092, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/XMIReader.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/XMIReader.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/XMIReader.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.ae.util;
+package org.apache.ctakes.dependency.parser.ae.util;
 
 import java.io.BufferedInputStream;
 import java.io.File;

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/cr/DependencyFileCollectionReader.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/cr/DependencyFileCollectionReader.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/cr/DependencyFileCollectionReader.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/cr/DependencyFileCollectionReader.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.cr;
+package org.apache.ctakes.dependency.parser.cr;
 /*
  * Copyright: (c) 2010   Mayo Foundation for Medical Education and 
  * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.util;
+package org.apache.ctakes.dependency.parser.util;
 
 import java.util.ArrayList;
 import java.util.List;

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/Delim.java (from r1388092, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/Delim.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/Delim.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/Delim.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/Delim.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/Delim.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/Delim.java Mon Sep 24 22:04:51 2012
@@ -41,7 +41,7 @@
  * limitations under the License. 
  */
 
-package edu.mayo.bmi.nlp.parser.util;
+package org.apache.ctakes.dependency.parser.util;
 
 
 public class Delim {

Copied: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyPath.java (from r1388196, incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyPath.java?p2=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyPath.java&p1=incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyPath.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.nlp.parser.util;
+package org.apache.ctakes.dependency.parser.util;
 
 import java.util.LinkedList;
 



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