Examples of FilterHandler

Examples of filters.FilterHandler

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     *
     * @param settings
     */
    private void fastaReader() {

        FilterHandler filterHandler = new FilterHandler(this.settings);
        try {
            FileReader fr = new FileReader(this.settings.getInput());
            BufferedReader br = new BufferedReader(fr);

            String line = null;
            String header = "";
            StringBuilder seq = new StringBuilder();
            int counter = 0;

            while ((line = br.readLine()) != null) {

                if (line.startsWith(">")) {
                    if (!(header.equals(""))) {

                        counter++;
                        // write to CSV file per protein
                        if (settings.getOutput() != null) {this.writer.writeCSVFile(header, seq);}
                       
                        // filter per protein and show results
                        outputResults(filterHandler.preformFilters(header, seq), counter);
                        seq.delete(0, seq.length());
                    }
                    header = line;
                } else {seq.append(line);}
            }
            if (header.equals("")) {
                System.err.println("The file is empty or it is missing a header");
                System.exit(1);}
           
            // process last protein in the given file
            counter++;
            if (settings.getOutput() != null) {this.writer.writeCSVFile(header, seq);}
            outputResults(filterHandler.preformFilters(header, seq), counter);

        } catch (FileNotFoundException ex) {
            System.err.println("The given file is not found");
        } catch (IOException ex) {
            System.err.println("IOException: " + ex.getLocalizedMessage());
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Examples of io.undertow.servlet.handlers.FilterHandler

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                    initialHandler = servletChain(targetServlet, targetServlet.getManagedServlet());
                } else {
                    initialHandler = defaultHandler;
                }
            } else {
                FilterHandler handler;
                if (targetServlet != null) {
                    handler = new FilterHandler(noExtension, targetServlet);
                } else {
                    handler = new FilterHandler(noExtension, defaultServlet);
                }
                initialHandler = servletChain(handler, targetServlet == null ? defaultServlet.getManagedServlet() : targetServlet.getManagedServlet());
            }

            if (path.endsWith("/*")) {
                String prefix = path.substring(0, path.length() - 2);
                builder.addPrefixMatch(prefix, initialHandler);

                for (Map.Entry<String, Map<DispatcherType, List<ManagedFilter>>> entry : extension.entrySet()) {
                    ServletHandler pathServlet = targetServlet;
                    if (pathServlet == null) {
                        pathServlet = extensionServlets.get(entry.getKey());
                    }
                    if (pathServlet == null) {
                        pathServlet = defaultServlet;
                    }
                    HttpHandler handler = pathServlet;
                    if (!entry.getValue().isEmpty()) {
                        handler = new FilterHandler(entry.getValue(), handler);
                    }
                    builder.addExtensionMatch(prefix, entry.getKey(), servletChain(handler, pathServlet.getManagedServlet()));
                }
            } else if (path.isEmpty()) {
                builder.addExactMatch("/", initialHandler);
            } else {
                builder.addExactMatch(path, initialHandler);
            }
        }

        //now setup name based mappings
        //these are used for name based dispatch
        for (Map.Entry<String, ServletHandler> entry : allServlets.entrySet()) {
            final Map<DispatcherType, List<ManagedFilter>> filters = new HashMap<DispatcherType, List<ManagedFilter>>();
            for (final FilterMappingInfo filterMapping : deploymentInfo.getFilterMappings()) {
                ManagedFilter filter = managedFilterMap.get(filterMapping.getFilterName());
                if (filterMapping.getMappingType() == FilterMappingInfo.MappingType.SERVLET) {
                    if (filterMapping.getMapping().equals(entry.getKey())) {
                        addToListMap(filters, filterMapping.getDispatcher(), filter);
                    }
                }
            }
            if (filters.isEmpty()) {
                builder.addNameMatch(entry.getKey(), servletChain(entry.getValue(), entry.getValue().getManagedServlet()));
            } else {
                builder.addNameMatch(entry.getKey(), servletChain(new FilterHandler(filters, entry.getValue()), entry.getValue().getManagedServlet()));
            }
        }


        builder.setDefaultServlet(defaultHandler);
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Examples of io.undertow.servlet.handlers.FilterHandler

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                    initialHandler = servletChain(targetServlet, targetServlet.getManagedServlet());
                } else {
                    initialHandler = defaultHandler;
                }
            } else {
                FilterHandler handler;
                if (targetServlet != null) {
                    handler = new FilterHandler(noExtension, targetServlet);
                } else {
                    handler = new FilterHandler(noExtension, defaultServlet);
                }
                initialHandler = servletChain(handler, targetServlet == null ? defaultServlet.getManagedServlet() : targetServlet.getManagedServlet());
            }

            if (path.endsWith("/*")) {
                String prefix = path.substring(0, path.length() - 2);
                builder.addPrefixMatch(prefix, initialHandler);

                for (Map.Entry<String, Map<DispatcherType, List<ManagedFilter>>> entry : extension.entrySet()) {
                    ServletHandler pathServlet = targetServlet;
                    if (pathServlet == null) {
                        pathServlet = extensionServlets.get(entry.getKey());
                    }
                    if (pathServlet == null) {
                        pathServlet = defaultServlet;
                    }
                    HttpHandler handler = pathServlet;
                    if (!entry.getValue().isEmpty()) {
                        handler = new FilterHandler(entry.getValue(), handler);
                    }
                    builder.addExtensionMatch(prefix, entry.getKey(), servletChain(handler, pathServlet.getManagedServlet()));
                }
            } else if (path.isEmpty()) {
                builder.addExactMatch("/", initialHandler);
            } else {
                builder.addExactMatch(path, initialHandler);
            }
        }

        //now setup name based mappings
        //these are used for name based dispatch
        for (Map.Entry<String, ServletHandler> entry : allServlets.entrySet()) {
            final Map<DispatcherType, List<ManagedFilter>> filters = new HashMap<DispatcherType, List<ManagedFilter>>();
            for (final FilterMappingInfo filterMapping : deploymentInfo.getFilterMappings()) {
                ManagedFilter filter = managedFilterMap.get(filterMapping.getFilterName());
                if (filterMapping.getMappingType() == FilterMappingInfo.MappingType.SERVLET) {
                    if (filterMapping.getMapping().equals(entry.getKey())) {
                        addToListMap(filters, filterMapping.getDispatcher(), filter);
                    }
                }
            }
            if (filters.isEmpty()) {
                builder.addNameMatch(entry.getKey(), servletChain(entry.getValue(), entry.getValue().getManagedServlet()));
            } else {
                builder.addNameMatch(entry.getKey(), servletChain(new FilterHandler(filters, entry.getValue()), entry.getValue().getManagedServlet()));
            }
        }


        builder.setDefaultServlet(defaultHandler);
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Examples of io.undertow.servlet.handlers.FilterHandler

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                    initialHandler = servletChain(targetServlet, targetServlet.getManagedServlet());
                } else {
                    initialHandler = defaultHandler;
                }
            } else {
                FilterHandler handler;
                if (targetServlet != null) {
                    handler = new FilterHandler(noExtension, targetServlet);
                } else {
                    handler = new FilterHandler(noExtension, defaultServlet);
                }
                initialHandler = servletChain(handler, targetServlet == null ? defaultServlet.getManagedServlet() : targetServlet.getManagedServlet());
            }

            if (path.endsWith("/*")) {
                String prefix = path.substring(0, path.length() - 2);
                builder.addPrefixMatch(prefix, initialHandler);

                for (Map.Entry<String, Map<DispatcherType, List<ManagedFilter>>> entry : extension.entrySet()) {
                    ServletHandler pathServlet = targetServlet;
                    if (pathServlet == null) {
                        pathServlet = extensionServlets.get(entry.getKey());
                    }
                    if (pathServlet == null) {
                        pathServlet = defaultServlet;
                    }
                    HttpHandler handler = pathServlet;
                    if (!entry.getValue().isEmpty()) {
                        handler = new FilterHandler(entry.getValue(), handler);
                    }
                    builder.addExtensionMatch(prefix, entry.getKey(), servletChain(handler, pathServlet.getManagedServlet()));
                }
            } else if (path.isEmpty()) {
                builder.addExactMatch("/", initialHandler);
            } else {
                builder.addExactMatch(path, initialHandler);
            }
        }

        //now setup name based mappings
        //these are used for name based dispatch
        for (Map.Entry<String, ServletHandler> entry : allServlets.entrySet()) {
            final Map<DispatcherType, List<ManagedFilter>> filters = new HashMap<DispatcherType, List<ManagedFilter>>();
            for (final FilterMappingInfo filterMapping : deploymentInfo.getFilterMappings()) {
                ManagedFilter filter = managedFilterMap.get(filterMapping.getFilterName());
                if (filterMapping.getMappingType() == FilterMappingInfo.MappingType.SERVLET) {
                    if (filterMapping.getMapping().equals(entry.getKey())) {
                        addToListMap(filters, filterMapping.getDispatcher(), filter);
                    }
                }
            }
            if (filters.isEmpty()) {
                builder.addNameMatch(entry.getKey(), servletChain(entry.getValue(), entry.getValue().getManagedServlet()));
            } else {
                builder.addNameMatch(entry.getKey(), servletChain(new FilterHandler(filters, entry.getValue()), entry.getValue().getManagedServlet()));
            }
        }


        builder.setDefaultServlet(defaultHandler);
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Examples of nexj.core.util.XMLUtil.FilterHandler

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      private final List m_bindings; //of type Element
     
      public WSDLBindingsManager(Element wsdlDocElement)
      {
         m_bindings = XMLUtil.forEachElementRecur(wsdlDocElement, null, new FilterHandler()
         {
            public Object filterElement(Element element)
            {
               if (NAMESPACE_WSDL.equals(element.getNamespaceURI()))
               {
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Examples of org.apache.felix.http.base.internal.handler.FilterHandler

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        if (filter == null)
        {
            throw new IllegalArgumentException("Filter must not be null");
        }
        String filterName = null; // XXX
        FilterHandler handler = new FilterHandler(getServletContext(context), filter, pattern, ranking, filterName);
        handler.setInitParams(initParams);
        this.handlerRegistry.addFilter(handler);
        this.localFilters.add(filter);
    }
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Examples of org.apache.felix.http.base.internal.handler.FilterHandler

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        if (filter == null)
        {
            throw new IllegalArgumentException("Filter must not be null");
        }
        String filterName = null; // XXX
        FilterHandler handler = new FilterHandler(getServletContext(context), filter, pattern, ranking, filterName);
        handler.setInitParams(initParams);
        this.handlerRegistry.addFilter(handler);
        this.localFilters.add(filter);
    }
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Examples of org.eclipse.help.internal.dynamic.FilterHandler

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            ModelUtil.insertStyle(dom, styles[i]);
        }

        // filter the content
        if (domProcessor == null) {
          domProcessor = new DocumentProcessor(new ProcessorHandler[] { new FilterHandler(IntroEvaluationContext.getContext()) });
        }
        UAElement element = UAElementFactory.newElement(dom.getDocumentElement());
        domProcessor.process(element, null);
       
        // and resolve includes.
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Examples of org.eclipse.help.internal.dynamic.FilterHandler

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    // process dynamic content, normalize paths
    if (processor == null) {
      DocumentReader reader = new DocumentReader();
      processor = new DocumentProcessor(new ProcessorHandler[] {
        new FilterHandler(CheatSheetEvaluationContext.getContext()),
        new NormalizeHandler(),
        new IncludeHandler(reader, Platform.getNL()),
        new ExtensionHandler(reader, Platform.getNL())
      });
    }
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