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Version information now is incorporated into output *.clns and *.vdjc…
…a files. Special action added to retrieve this information (versionInfo). This fixes #17
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89
src/main/java/com/milaboratory/mixcr/cli/VersionInfoAction.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| /* | ||
| * Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail | ||
| * (here and after addressed as Inventors) | ||
| * All Rights Reserved | ||
| * | ||
| * Permission to use, copy, modify and distribute any part of this program for | ||
| * educational, research and non-profit purposes, by non-profit institutions | ||
| * only, without fee, and without a written agreement is hereby granted, | ||
| * provided that the above copyright notice, this paragraph and the following | ||
| * three paragraphs appear in all copies. | ||
| * | ||
| * Those desiring to incorporate this work into commercial products or use for | ||
| * commercial purposes should contact the Inventors using one of the following | ||
| * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com | ||
| * | ||
| * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, | ||
| * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, | ||
| * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN | ||
| * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| * | ||
| * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS | ||
| * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR | ||
| * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO | ||
| * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT | ||
| * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A | ||
| * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY | ||
| * PATENT, TRADEMARK OR OTHER RIGHTS. | ||
| */ | ||
| package com.milaboratory.mixcr.cli; | ||
|
|
||
| import com.beust.jcommander.Parameter; | ||
| import com.beust.jcommander.ParameterException; | ||
| import com.beust.jcommander.Parameters; | ||
| import com.milaboratory.mitools.cli.Action; | ||
| import com.milaboratory.mitools.cli.ActionHelper; | ||
| import com.milaboratory.mitools.cli.ActionParameters; | ||
| import com.milaboratory.mixcr.basictypes.CloneSet; | ||
| import com.milaboratory.mixcr.basictypes.CloneSetIO; | ||
| import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; | ||
| import com.milaboratory.mixcr.reference.LociLibraryManager; | ||
|
|
||
| import java.util.List; | ||
|
|
||
| public class VersionInfoAction implements Action { | ||
| final AParameters parameters = new AParameters(); | ||
|
|
||
| @Override | ||
| public void go(ActionHelper helper) throws Exception { | ||
| String inputFile = parameters.getInputFile(); | ||
| String i = inputFile.toLowerCase(); | ||
| if (i.endsWith(".vdjca.gz") || i.endsWith(".vdjca")) { | ||
| try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(inputFile, LociLibraryManager.getDefault())) { | ||
| reader.init(); | ||
| System.out.println(reader.getVersionInfo()); | ||
| } | ||
| } else if (i.endsWith(".clns.gz") || i.endsWith(".clns")) { | ||
| CloneSet cs = CloneSetIO.read(inputFile, LociLibraryManager.getDefault()); | ||
| System.out.println(cs.getVersionInfo()); | ||
| } else | ||
| throw new ParameterException("Wrong file type."); | ||
| } | ||
|
|
||
| @Override | ||
| public String command() { | ||
| return "versionInfo"; | ||
| } | ||
|
|
||
| @Override | ||
| public ActionParameters params() { | ||
| return parameters; | ||
| } | ||
|
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| @Parameters(commandDescription = "Outputs information about MiXCR version which generated the file.", | ||
| optionPrefixes = "-") | ||
| private static class AParameters extends ActionParameters { | ||
| @Parameter(description = "binary_file{.vdjca|.clns}[.gz]") | ||
| public List<String> input; | ||
|
|
||
| public String getInputFile() { | ||
| return input.get(0); | ||
| } | ||
|
|
||
| @Override | ||
| public void validate() { | ||
| if (input.size() != 1) | ||
| throw new ParameterException("Wrong number of parameters."); | ||
| } | ||
| } | ||
| } |
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