Examples of HelpFormatter

Examples of org.apache.commons.cli.HelpFormatter

180
181
182
183
184
185
186
187
188
189
190
            }
            queryFile = args[0];
           
        } catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(120, "ClassifierCmd [options] <samplefile>\nNote this is the legacy command for one sample classification ", "", options, "");

            return;
        }

        if (propFile == null && gene == null) {
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

238
239
240
241
242
243
244
245
246
247
248
            if (samples.size() < 1) {
                throw new IllegalArgumentException("Require at least one sample files");
            }
        }catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
            return;
        }
       
        MultiClassifier multiClassifier = new MultiClassifier(propFile, gene, biomFile, metadataFile);
        MultiClassifierResult result = multiClassifier.multiCompare(samples, conf, assign_out, format, min_bootstrap_words);
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

161
162
163
164
165
166
167
168
169
170
171
                modification = line.getOptionValue("m");
            }
           
        } catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(120, "train", "", options, "", true);
            return;
        }
       
        ClassifierTraineeMaker maker = new ClassifierTraineeMaker(taxFile, seqFile, cnFile, trainset_no, version, modification, outdir);
    }
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

263
264
265
266
267
268
269
270
271
272
273
      CommandLineParser parser = new GnuParser();
      CommandLine commandLine = parser.parse(options, args);

      if (commandLine.hasOption('h')) {
        new HelpFormatter().printHelp("flume-ng agent", options, true);
        return;
      }

      String agentName = commandLine.getOptionValue('n');
      boolean reload = !commandLine.hasOption("no-reload-conf");
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
      .addOption("h", "help", false, "Display help");

    CommandLineParser parser = new GnuParser();
    CommandLine commandLine = parser.parse(options, args);
    if(commandLine.hasOption("help")) {
      new HelpFormatter().printHelp("java -jar fcintegritytool ",
        options, true);
      return false;
    }
    if(!commandLine.hasOption("dataDirs")) {
      new HelpFormatter().printHelp("java -jar fcintegritytool ", "",
        options, "dataDirs is required.", true);
      return false;
    } else {
      String dataDirStr[] = commandLine.getOptionValue("dataDirs").split(",");
      for(String dataDir : dataDirStr) {
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

176
177
178
179
180
181
182
183
184
185
186
                }
                GoodWordIterator.setWordSize(kmer);
            }*/
        } catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(120, "LeaveOneOutTesterMain", "", options, "", true);
            return;
        }


        LeaveOneOutTesterMain tester = new LeaveOneOutTesterMain(trainTaxonFile, trainSeqFile,
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

109
110
111
112
113
114
115
116
117
118
119
                    throw new IllegalArgumentException(min_bootstrap_words + " must be at least " + NBClassifier.MIN_BOOTSTRSP_WORDS);
                }               
            }
           
        } catch (ParseException ex) {
            new HelpFormatter().printHelp(120, "CrossValidateMain", "", options, "", true);
            return;
        }
       
        boolean useSeed = true;  // use seed for random number generator
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

396
397
398
399
400
401
402
403
404
405
406
407
      System.err.println("Error parsing command line: " + exp.getMessage());
      System.exit(-1);
    }

    if (!cmdline.hasOption(DATA_OPTION) || !cmdline.hasOption(OUTPUT_OPTION)) {
      HelpFormatter formatter = new HelpFormatter();
      formatter.printHelp(AsyncHTMLStatusBlockCrawler.class.getName(), options);
      System.exit(-1);
    }

    String data = cmdline.getOptionValue(DATA_OPTION);
    String output = cmdline.getOptionValue(OUTPUT_OPTION);
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

201
202
203
204
205
206
207
208
209
210
211
            trainseqFile = args[0];
            taxFile = args[1];
            outStream = new PrintStream(new File(args[2]));
         }catch (Exception e) {
            System.err.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(80, " [options] trainseqFile taxonFile outFile", "", options, "");
            return;
        }
                       
        PairwiseSeqDistance theObj = new PairwiseSeqDistance(trainseqFile,taxFile, mode, show_alignment);
       
View Full Code Here

Examples of org.apache.commons.cli.HelpFormatter

60
61
62
63
64
65
66
67
68
        System.out.println("total size of files in "+dir+" containing "+name+": "+SizeWhere.totalSize(dir, name));
      } catch( ParseException exp ) {
          // oops, something went wrong
          System.err.println( "Parsing failed.  Reason: " + exp.getMessage() );
         
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp( "sizewhere", options );
      }       
    }
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.