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Copyright + minor pre-release pom corrections.

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dbolotin committed Jan 30, 2019
1 parent 28484a0 commit 06d5523f238d217f842e7fe42fe0dcfb6a672e5f
Showing with 1,508 additions and 172 deletions.
  1. +1 −1 milib
  2. +15 −18 pom.xml
  3. +1 −1 repseqio
  4. +29 −0 src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java
  5. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java
  6. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java
  7. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java
  8. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java
  9. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java
  10. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java
  11. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java
  12. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java
  13. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java
  14. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java
  15. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java
  16. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java
  17. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java
  18. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java
  19. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java
  20. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java
  21. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java
  22. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java
  23. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java
  24. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java
  25. +1 −1 src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java
  26. +29 −0 src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java
  27. +29 −0 src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java
  28. +29 −0 src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java
  29. +29 −0 src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java
  30. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java
  31. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java
  32. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java
  33. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java
  34. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java
  35. +29 −0 src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java
  36. +29 −0 src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java
  37. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java
  38. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java
  39. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/Clone.java
  40. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java
  41. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java
  42. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java
  43. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java
  44. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java
  45. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/IO.java
  46. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java
  47. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/Merger.java
  48. +29 −0 src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java
  49. +29 −0 src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java
  50. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java
  51. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java
  52. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
  53. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java
  54. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java
  55. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java
  56. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java
  57. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java
  58. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java
  59. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java
  60. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java
  61. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java
  62. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java
  63. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java
  64. +1 −1 src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java
  65. +1 −1 src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java
  66. +1 −1 src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java
  67. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java
  68. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java
  69. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java
  70. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java
  71. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java
  72. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java
  73. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java
  74. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java
  75. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java
  76. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandExport.java
  77. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java
  78. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java
  79. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java
  80. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java
  81. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java
  82. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java
  83. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java
  84. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java
  85. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandMain.java
  86. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java
  87. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java
  88. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandReport.java
  89. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java
  90. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java
  91. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java
  92. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java
  93. +29 −0 src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java
  94. +1 −1 src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java
  95. +29 −0 src/main/java/com/milaboratory/mixcr/cli/Main.java
  96. +29 −0 src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java
  97. +1 −1 src/main/java/com/milaboratory/mixcr/cli/Report.java
  98. +1 −1 src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java
  99. +1 −1 src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java
  100. +5 −4 src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java
  101. +1 −1 src/main/java/com/milaboratory/mixcr/cli/Util.java
  102. +1 −1 src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java
  103. +1 −1 src/main/java/com/milaboratory/mixcr/export/AbstractField.java
  104. +1 −1 src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java
  105. +1 −1 src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
  106. +1 −1 src/main/java/com/milaboratory/mixcr/export/Field.java
  107. +1 −1 src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java
  108. +1 −1 src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java
  109. +1 −1 src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java
  110. +1 −1 src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java
  111. +1 −1 src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java
  112. +1 −1 src/main/java/com/milaboratory/mixcr/export/InfoWriter.java
  113. +1 −1 src/main/java/com/milaboratory/mixcr/export/OutputMode.java
  114. +1 −1 src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java
  115. +1 −1 src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java
  116. +1 −1 src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java
  117. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java
  118. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java
  119. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java
  120. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java
  121. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java
  122. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java
  123. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java
  124. +1 −1 src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java
  125. +1 −1 src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java
  126. +1 −1 src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java
  127. +1 −1 src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java
  128. +1 −1 src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java
  129. +1 −1 src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java
  130. +1 −1 src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java
  131. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java
  132. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java
  133. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java
  134. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java
  135. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java
  136. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java
  137. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java
  138. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java
  139. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java
  140. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java
  141. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java
  142. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java
  143. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java
  144. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java
  145. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java
  146. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java
  147. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java
  148. +1 −1 src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java
  149. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java
  150. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java
  151. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java
  152. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java
  153. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java
  154. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java
  155. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java
  156. +1 −1 src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java
  157. +29 −0 src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java
  158. +29 −0 src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java
  159. +1 −1 src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java
  160. +1 −1 src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java
  161. +1 −1 src/test/java/com/milaboratory/mixcr/basictypes/MergerTest.java
  162. +4 −3 src/test/java/com/milaboratory/mixcr/basictypes/SequenceHistoryTest.java
  163. +4 −3 src/test/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatterTest.java
  164. +29 −0 src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java
  165. +1 −1 src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java
  166. +29 −0 src/test/java/com/milaboratory/mixcr/cli/CommandAnalyzeTest.java
  167. +1 −1 src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java
  168. +29 −0 src/test/java/com/milaboratory/mixcr/cli/MainTest.java
  169. +1 −1 src/test/java/com/milaboratory/mixcr/cli/UtilTest.java
  170. +1 −1 src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java
  171. +1 −1 src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java
  172. +1 −1 src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
  173. +1 −1 src/test/java/com/milaboratory/mixcr/partialassembler/RangeSetTest.java
  174. +1 −1 src/test/java/com/milaboratory/mixcr/partialassembler/TargetMergerTest.java
  175. +1 −1 src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java
  176. +1 −1 src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java
  177. +1 −1 src/test/java/com/milaboratory/mixcr/tests/TargetBuilder.java
  178. +1 −1 src/test/java/com/milaboratory/mixcr/tests/TargetBuilderTest.java
  179. +1 −1 src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java
  180. +29 −0 src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java
  181. +1 −1 src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java
  182. +1 −1 src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java
  183. +1 −1 src/test/java/com/milaboratory/mixcr/util/VDJCObjectExtenderTest.java
  184. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java
  185. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java
  186. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java
  187. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
  188. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java
  189. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java
  190. +1 −1 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java
33 pom.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<!--
~ Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
~ Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
~ (here and after addressed as Inventors)
~ All Rights Reserved
~
@@ -28,7 +28,8 @@
~ PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
~ PATENT, TRADEMARK OR OTHER RIGHTS.
-->
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>com.milaboratory</groupId>
@@ -37,22 +38,16 @@
<packaging>jar</packaging>
<name>MiXCR</name>

<parent>
<groupId>org.sonatype.oss</groupId>
<artifactId>oss-parent</artifactId>
<version>7</version>
</parent>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<milib.version>1.10-SNAPSHOT</milib.version>
<milib.version>1.10</milib.version>
</properties>

<dependencies>
<dependency>
<groupId>io.repseq</groupId>
<artifactId>repseqio</artifactId>
<version>1.3</version>
<version>1.3.1</version>
<exclusions>
<exclusion>
<groupId>com.milaboratory</groupId>
@@ -189,13 +184,13 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.17</version>
<version>2.22.1</version>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.2</version>
<version>3.1.1</version>
<executions>
<execution>
<goals>
@@ -208,11 +203,10 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<verbose>true</verbose>
</configuration>
</plugin>

@@ -228,7 +222,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4</version>
<version>3.2.1</version>
<executions>
<execution>
<phase>pre-integration-test</phase>
@@ -271,12 +265,15 @@
</filter>
</filters>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer">
<transformer
implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer">
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
<transformer
implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
<addHeader>false</addHeader>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>com.milaboratory.mixcr.cli.Main</mainClass>
</transformer>
</transformers>
Submodule repseqio updated 157 files
@@ -1,3 +1,32 @@
/*
* Copyright (c) 2014-2019, 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 MiLaboratory LLC, which owns exclusive
* rights for distribution of this program for commercial purposes, using the
* following email address: licensing@milaboratory.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.assembler;

import cc.redberry.pipe.OutputPort;
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
* (here and after addressed as Inventors)
* All Rights Reserved
*
@@ -1,3 +1,32 @@
/*
* Copyright (c) 2014-2019, 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 MiLaboratory LLC, which owns exclusive
* rights for distribution of this program for commercial purposes, using the
* following email address: licensing@milaboratory.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.assembler.fullseq;

import cc.redberry.pipe.CUtils;
@@ -1,3 +1,32 @@
/*
* Copyright (c) 2014-2019, 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 MiLaboratory LLC, which owns exclusive
* rights for distribution of this program for commercial purposes, using the
* following email address: licensing@milaboratory.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.assembler.fullseq;

import com.fasterxml.jackson.annotation.JsonAutoDetect;
@@ -1,3 +1,32 @@
/*
* Copyright (c) 2014-2019, 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 MiLaboratory LLC, which owns exclusive
* rights for distribution of this program for commercial purposes, using the
* following email address: licensing@milaboratory.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.assembler.fullseq;

import com.fasterxml.jackson.annotation.JsonProperty;
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