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From chen...@apache.org
Subject svn commit: r1388092 [22/22] - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-chunker/desc/ ctakes-chunker/scripts/groovy/data/chunk/ ctakes-chunker/scripts/java/data/chunk/ ctakes-chunker/scripts/java/data/chunk/genia/ ctakes-chunker/src/main/j...
Date Thu, 20 Sep 2012 16:07:33 GMT
Modified: incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/crtNominateAndTransform.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/crtNominateAndTransform.bat?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/crtNominateAndTransform.bat (original)
+++ incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/crtNominateAndTransform.bat Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+@REM
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM   http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM
+
 @ECHO OFF
 SETLOCAL ENABLEDELAYEDEXPANSION
 REM - The two required parameters are 1) fully qualified file containing file source and target files (e.g. R:\Dept\projects\Text\temporalRelations\docs\TemporalRelations_remapped_documents.txt)

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency Parser.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency%20Parser.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency Parser.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency Parser.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=Constituency Parser
 classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;
 datapath=$main_root/resources;$main_root/../core/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug NER.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug%20NER.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug NER.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug NER.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=Drug NER
 classpath=$main_root/bin;$main_root/resources;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/junit.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/trove.jar;$main_root/../core/bin;$main_root/../dictionary lookup/bin;$main_root/../NE contexts/bin;$main_root/../context dependent tokenizer/bin;$main_root/../document preprocessor/bin;$main_root/../LVG/bin;$main_root/../clinical documents pipeline/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;$main_root/../chunker/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../POS tagger/bin;$main_root/../document preprocessor/resources;
 datapath=$main_root/resources;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=LVG
 classpath=$main_root/bin;$main_root/resources;$main_root/../core/bin;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/resources;$main_root/lib/lvg2008dist.jar;$main_root/../core/lib/log4j-1.2.8.jar;
 datapath=$main_root/resources;$main_root/../core/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE contexts.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE%20contexts.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE contexts.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE contexts.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=NE contexts
 classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;
 datapath=$main_root/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD term spotter.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD%20term%20spotter.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD term spotter.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD term spotter.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=PAD term spotter
 classpath=$main_root/bin;$main_root/resources;$main_root/../core/bin;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/trove.jar;$main_root/../NE contexts/bin;$main_root/../dictionary lookup/bin;$main_root/../context dependent tokenizer/bin;$main_root/../chunker/bin;$main_root/../POS tagger/bin;$main_root/../clinical documents pipeline/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;
 datapath=$main_root/resources;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS tagger.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS%20tagger.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS tagger.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS tagger.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=POS tagger
 classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/trove.jar;$main_root/../core/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/SQLWrapper.jar;$main_root/resources;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;
 datapath=$main_root/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=SideEffect
 classpath=$main_root/bin;$main_root/../dictionary lookup/resources/lookup;$main_root/resources;$main_root/../Drug NER/bin;$main_root/../clinical documents pipeline/bin;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/lib/libsvm-2.91.jar;$main_root/../core/bin;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/trove.jar;$main_root/../NE contexts/bin;$main_root/../dictionary lookup/bin;$main_root/../chunker/bin;$main_root/../POS tagger/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../context dependent tokenizer/bin;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../chunker/resources;$main_root/../POS tagger/resources;$main_root/../LVG/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
 datapath=$main_root/../dictionary lookup/resources/lookup;$main_root/resources;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../chunker/resources;$main_root/../POS tagger/resources;$main_root/../LVG/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=chunker
 classpath=$main_root/bin;$main_root/../context dependent tokenizer/bin;$main_root/resources;$main_root/../LVG/bin;$main_root/../dictionary lookup/bin;$main_root/../NE contexts/bin;$main_root/../core/resources;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;
 aeDescriptor=desc/AggregateAE.xml
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical documents pipeline.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical%20documents%20pipeline.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical documents pipeline.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical documents pipeline.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=clinical documents pipeline
 classpath=$main_root/bin;$main_root/../context dependent tokenizer/bin;$main_root/resources;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
 aeDescriptor=desc/analysis_engine/AggregatePlaintextProcessor.xml
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context dependent tokenizer.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context%20dependent%20tokenizer.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context dependent tokenizer.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context dependent tokenizer.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=context dependent tokenizer
 classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;
 datapath=$main_root/resources;$main_root/../core/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.core.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.core.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.core.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.core.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=core
 classpath=$main_root/bin;$main_root/bin;$main_root/resources;$main_root/lib/opennlp-tools-1.4.3.jar;$main_root/lib/maxent-2.5.0.jar;$main_root/lib/jdom.jar;$main_root/lib/log4j-1.2.8.jar;$main_root/lib/lucene-core-3.0.2.jar;$main_root/lib/trove.jar;$main_root/lib/OpenAI_FSM.jar;$main_root/lib/SQLWrapper.jar;
 datapath=$main_root/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=coref-resolver
 classpath=$main_root/bin;$main_root/../Constituency Parser/bin;$main_root/lib/Jama-1.0.2.jar;$main_root/lib/libsvm.jar;$main_root/../core/bin;$main_root/../context dependent tokenizer/bin;$main_root/../clinical documents pipeline/bin;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
 datapath=$main_root/resources;$main_root/../core/resources;$main_root/../Constituency Parser/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency parser.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency%20parser.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency parser.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency parser.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=dependency parser
 classpath=$main_root/bin;$main_root/clinical documents pipeline/bin;$main_root/../context dependent tokenizer/bin;$main_root/resources;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
 aeDescriptor=desc/analysis_engine/ClearParserPlaintextAggregate.xml
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary lookup.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary%20lookup.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary lookup.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary lookup.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=dictionary lookup
 classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;
 datapath=$main_root/resources;$main_root/../core/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document preprocessor.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document%20preprocessor.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document preprocessor.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document preprocessor.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=document preprocessor
 classpath=$main_root/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/bin;$main_root/resources;$main_root/lib/xercesImpl.jar;$main_root/lib/xml-apis.jar;$main_root/lib/xmlParserAPIs.jar;
 aeDescriptor=desc/AggregateAE.xml
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java Thu Sep 20 16:07:04 2012
@@ -1,3 +1,21 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.build;
 
 import java.io.File;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking status.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking%20status.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking status.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking status.properties Thu Sep 20 16:07:04 2012
@@ -1,3 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
 project=smoking status
 classpath=$main_root/bin;$main_root/resources;$main_root/desc;$main_root/../context dependent tokenizer/bin;$main_root/../clinical documents pipeline/bin;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/lib/libsvm-2.91.jar;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;$main_root/../context dependent tokenizer/bin;
 datapath=$main_root/resources;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java Thu Sep 20 16:07:04 2012
@@ -1,3 +1,21 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.build;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java Thu Sep 20 16:07:04 2012
@@ -1,3 +1,21 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 /*
  * This class was based on parts of 
  * @see <code>org.apache.uima.tools.pear.install.InstallPear</code>

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java Thu Sep 20 16:07:04 2012
@@ -1,3 +1,21 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.build;
 
 import java.io.File;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Compare.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Compare.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Compare.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Compare.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 import java.io.*;
 

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Const.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Const.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Const.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/Const.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 
 import java.util.HashSet;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 import java.io.File;
 import java.io.FileWriter;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasAnnotation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasAnnotation.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasAnnotation.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasAnnotation.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 import java.util.Collection;
 import java.util.Vector;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasDiff.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasDiff.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasDiff.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasDiff.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 import java.util.LinkedList;
 import java.util.Collections;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasFile.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasFile.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasFile.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasFile.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 import java.util.Hashtable;
 import java.util.LinkedList;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasProcessor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasProcessor.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasProcessor.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/XcasProcessor.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
 package edu.mayo.bmi.utils.xcas_comparison;
 import java.util.Hashtable;
 import java.util.HashMap;

Modified: incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/attributes_to_ignore.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/attributes_to_ignore.properties?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/attributes_to_ignore.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/xcas_comparison/attributes_to_ignore.properties Thu Sep 20 16:07:04 2012
@@ -0,0 +1,19 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Thu Sep 20 16:07:04 2012
@@ -37,10 +37,10 @@
 		<module>ctakes-lvg</module>
 		<module>ctakes-ne-contexts</module>
 		<module>ctakes-constituency-parser</module>
-		<module>ctakes-coreference</module>		
+		<module>ctakes-coreference</module>
 		<module>ctakes-drug-ner</module>
 		<module>ctakes-side-effect</module>
-		<module>ctakes-smoking-status</module>		
+		<module>ctakes-smoking-status</module>
 		<module>ctakes-dependency-parser</module>
 		<module>ctakes-relation-extractor</module>
 		<module>ctakes-clinical-pipeline</module>
@@ -58,7 +58,7 @@
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>ctakes-utils</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>			
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>ctakes-core</artifactId>
@@ -88,7 +88,7 @@
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>ctakes-lvg</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>			
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
@@ -102,21 +102,21 @@
 					ctakes-ne-contexts
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>			
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
 					ctakes-constituency-parser
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>	
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
 					ctakes-coreference
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>						
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
@@ -137,14 +137,14 @@
 					ctakes-smoking-status
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>		
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
 					ctakes-relation-extractor
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>						
+			</dependency>
 			<!-- cTAKES third party dependency versions -->
 			<dependency>
 				<groupId>jdom</groupId>
@@ -286,8 +286,19 @@
 				<plugin>
 					<groupId>com.mycila.maven-license-plugin</groupId>
 					<artifactId>maven-license-plugin</artifactId>
+					<version>1.9.0</version>
 					<configuration>
 						<header>license_header.txt</header>
+						<excludes>
+							<!-- We're disabling .txt files for now because some Annotators may 
+								not be able to handle standard comments in text files. This may break name 
+								values pairs such as stopWords.txt -->
+							<exclude>to-be-deleted-icTAKES/**</exclude>
+							<exclude>**.txt</exclude>
+						</excludes>
+						<useDefaultMapping>false</useDefaultMapping>
+						<quiet>false</quiet>
+						<failIfMissing>false</failIfMissing>
 						<mapping>
 							<java>JAVADOC_STYLE</java>
 							<groovy>JAVADOC_STYLE</groovy>
@@ -303,10 +314,6 @@
 							<apt>DOUBLETILDE_STYLE</apt>
 							<properties>SCRIPT_STYLE</properties>
 							<sh>SCRIPT_STYLE</sh>
-							<!-- We're disabling .txt files for now because some 
-							Annotators may not be able to handle standard comments
-							in text files. This may break name values pairs such as stopWords.txt
-							-->
 							<!-- <txt>TEXT</txt> -->
 							<bat>BATCH</bat>
 							<cmd>BATCH</cmd>



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