Now align will print library-level citation notice and warnings.

This fixes #285

CHANGELOG_CURRENT

@@ -1,2 +1,3 @@
 Now export fields like `-nMutationsRelative` supports alignment-attached gene features (e.g. this allows to export all mutations of V gene inside CDR3 region: `-nMutationsRelative VCDR3Part VRegionWithP`)
+Now `align` action prints library-level warnings and citation notice
 minor: `--noMerge` option renamed to `--no-merge` in assemble action

src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java

@@ -64,14 +64,10 @@
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult;
 import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets;
 import com.milaboratory.util.CanReportProgress;
-import com.milaboratory.util.GlobalObjectMappers;
 import com.milaboratory.util.SmartProgressReporter;
 import io.repseq.core.*;
 
 import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.nio.file.StandardOpenOption;
 import java.util.*;
 
 import static cc.redberry.pipe.CUtils.chunked;
@@ -121,6 +117,20 @@ public void go(ActionHelper helper) throws Exception {
 
         System.out.println("Reference library: " + library.getLibraryId());
 
+        // Printing library level warnings, if specified for the library
+        if (!library.getWarnings().isEmpty()) {
+            System.out.println("Library warnings:");
+            for (String l : library.getWarnings())
+                System.out.println(l);
+        }
+
+        // Printing citation notice, if specified for the library
+        if (!library.getCitations().isEmpty()) {
+            System.out.println("Please cite:");
+            for (String l : library.getCitations())
+                System.out.println(l);
+        }
+
         for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
             if (gene.getGeneType() == GeneType.Variable) {
                 totalV++;