title: using cTAKES to parse clinical documents
body: <p>I am trying to figure out how to run the Clinical Document Pipeline
  from Java.  I have a set of clinical documents as plain texts. I want to parse these documents and extract a list of  that is in document doc_ID, there is CUI with frequency of freq. I spent several days installing cTAKES and looking for a solution. I narrow it down to ClinicalPipelineWithUmls.java where gets a test and runs SimplePipeline with a AnaylisisEngineDescription. Here is a part of the code:</p>
  
  <pre><code>String documentText = "Text of document to test goes here, such as the following. No edema, some soreness, denies pain.";
  InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText);
  CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream);
  AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createAnalysisEngineDescription(
              "desc/analysis_engine/AggregatePlaintextUMLSProcessor");
  AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
              XWriter.class,
              XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
              AssertionConst.evalOutputDir,
              XWriter.PARAM_XML_SCHEME_NAME,
              XWriter.XMI,
              XWriter.PARAM_FILE_NAMER_CLASS_NAME,
              CtakesFileNamer.class.getName());
  SimplePipeline.runPipeline(collectionReader, pipelineIncludingUmlsDictionaries, xWriter);
  System.out.println("Done at " + new Date());
  </code></pre>
  
  <p>The problem is it can not find "InputStreamCollectionReader". I searched for it but no success so far! Would you please give me a hint or show some directions?
  thanks for any help!</p>