Merge pull request #44 from PankratzLab/develop

DonorCheck v0.0.14

pom.xml

@@ -8,7 +8,7 @@
 	<groupId>org.pankratzlab</groupId>
 	<artifactId>donor-check</artifactId>
 	<!-- if version number changes, be sure to update in project.properties file also -->
-	<version>0.0.13</version>
+	<version>0.0.14</version>
 	<packaging>jar</packaging>
 
 	<description>A stand-alone tool for validating DonorNet typing entries.</description>
@@ -28,6 +28,11 @@
 			<name>Kaitlin Clarke</name>
 			<email>krclarke@umn.edu</email>
 		</developer>
+		<developer>
+			<id>rcoleb</id>
+			<name>Ben Cole</name>
+			<email>cole0482@umn.edu</email>
+		</developer>
 	</developers>
 
 

src/main/java/org/pankratzlab/unet/deprecated/hla/Antigen.java

@@ -45,7 +45,7 @@
 
 /** Abstract superclass for general antigen information. Allows comparison and sorting. */
 public abstract class Antigen<L extends Locus<L>, A extends Antigen<L, A>>
-                             implements Serializable, Comparable<A> {
+    implements Serializable, Comparable<A> {
 
   private static final long serialVersionUID = 5L;
 
@@ -56,8 +56,8 @@ public abstract class Antigen<L extends Locus<L>, A extends Antigen<L, A>>
   public static final String LOCUS_DELIM = "*";
 
   /** {@link Pattern} for matching antigen specificities. */
-  public static final Pattern SPEC_PATTERN = Pattern.compile("\\" + LOCUS_DELIM
-                                                             + "?([0-9]+[:[0-9]+]*)(?:\\(([0-9]+[:[0-9]+]*)\\))*");
+  public static final Pattern SPEC_PATTERN =
+      Pattern.compile("\\" + LOCUS_DELIM + "?([0-9]+[:[0-9]+]*)(?:\\(([0-9]+[:[0-9]+]*)\\))*");
 
   public static final int LATEST_REVISION = 1;
 
@@ -130,7 +130,7 @@ public String specString() {
       return String.format("%d", spec().get(0));
     }
     return spec().stream().map(i -> String.format("%02d", i))
-                 .collect(Collectors.joining(getSpecDelim()));
+        .collect(Collectors.joining(getSpecDelim()));
   }
 
   /**
@@ -196,12 +196,17 @@ public int hashCode() {
 
   @Override
   public boolean equals(Object obj) {
-    if (this == obj) return true;
-    if (obj == null) return false;
-    if (getClass() != obj.getClass()) return false;
+    if (this == obj)
+      return true;
+    if (obj == null)
+      return false;
+    if (getClass() != obj.getClass())
+      return false;
     Antigen<?, ?> other = (Antigen<?, ?>) obj;
-    if (locus != other.locus()) return false;
-    if (!Arrays.equals(specificity, other.specificity)) return false;
+    if (locus != other.locus())
+      return false;
+    if (!Arrays.equals(specificity, other.specificity))
+      return false;
     return true;
   }
 
@@ -277,9 +282,10 @@ public static boolean is(String text, Pattern typePattern) {
    * @param antigens Collection of antigens
    * @return Sorted string of antigen strings
    */
-  public static <L extends Locus<L>, T extends Antigen<L, T>> String toString(Collection<T> antigens) {
+  public static <L extends Locus<L>, T extends Antigen<L, T>> String toString(
+      Collection<T> antigens) {
     return antigens.stream().sorted().map(Antigen::toString).collect(Collectors.joining(", "))
-                   .toString();
+        .toString();
   }
 
   /**
@@ -313,12 +319,12 @@ public static String sanitize(String antigenString) {
    *     B*2} would translate to {@code A*21:03, A*15, B*02}
    * @param lociPattern A {@link Pattern} for parsing out the {@link Locus}
    * @param typeParser Method for converting individual locus + spec string combinations to a
-   *          particular type
+   *        particular type
    * @return A list of the <b>unique</b> and <b>non-null</b> antigens parsed from the text, in the
    *         order of their first appearance
    */
   public static <T extends Antigen<?, T>> List<T> parseTypes(String text, Pattern lociPattern,
-                                                             Function<String, T> typeParser) {
+      Function<String, T> typeParser) {
     if (text == null || text.isEmpty()) {
       return Collections.emptyList();
     }
@@ -349,8 +355,8 @@ public static <T extends Antigen<?, T>> List<T> parseTypes(String text, Pattern
       String locus = locusMap.get(locusStartPos);
       // The current locus has a range to the start pos of the next locus, or the end of the string
       // if this is the last locus.
-      int rangeEnd = locusIndex + 1 == locusStarts.size() ? text.length()
-                                                          : locusStarts.get(locusIndex + 1);
+      int rangeEnd =
+          locusIndex + 1 == locusStarts.size() ? text.length() : locusStarts.get(locusIndex + 1);
       // The search space substring is where we look for specs
       String searchSpace = text.substring(locusStartPos + locus.length(), rangeEnd);
       Matcher specMatcher = SPEC_PATTERN.matcher(searchSpace);

src/main/java/org/pankratzlab/unet/deprecated/hla/AntigenDictionary.java

@@ -65,8 +65,8 @@ public final class AntigenDictionary implements Serializable {
   private final SetMultimap<SeroType, HLAType> seroDict;
   private final Set<HLAType> validTypes;
 
-  private AntigenDictionary(
-      SetMultimap<HLAType, SeroType> hla, SetMultimap<SeroType, HLAType> sero, Set<HLAType> valid) {
+  private AntigenDictionary(SetMultimap<HLAType, SeroType> hla, SetMultimap<SeroType, HLAType> sero,
+      Set<HLAType> valid) {
     hlaDict = hla;
     seroDict = sero;
     validTypes = valid;
@@ -164,12 +164,8 @@ private static void parseDictionaries() {
     // NB: what's considered a valid HLA type diverges from the HLA map keyset and thus must be
     // tracked separately
     Builder<HLAType> validHLATypes = ImmutableSet.builder();
-    try (BufferedReader reader =
-        new BufferedReader(
-            new InputStreamReader(
-                AntigenDictionary.class
-                    .getClassLoader()
-                    .getResourceAsStream(MASTER_MAP_RECORDS))); ) {
+    try (BufferedReader reader = new BufferedReader(new InputStreamReader(
+        AntigenDictionary.class.getClassLoader().getResourceAsStream(MASTER_MAP_RECORDS)));) {
       while (reader.ready()) {
         // Read one mapping at a time
         String line = reader.readLine();

src/main/java/org/pankratzlab/unet/deprecated/hla/HLALocus.java

@@ -25,18 +25,10 @@
 
 /** {@link Locus} implementation for HLA types */
 public enum HLALocus implements Locus<HLALocus> {
-  A(SeroLocus.A, TIER_1),
-  B(SeroLocus.B, TIER_1),
-  C(SeroLocus.C, TIER_1),
-  DRB1(SeroLocus.DRB, TIER_2),
-  DRB3(SeroLocus.DRB, TIER_2),
-  DRB4(SeroLocus.DRB, TIER_2),
-  DRB5(SeroLocus.DRB, TIER_2),
-  DQA1(SeroLocus.DQA, TIER_2),
-  DQB1(SeroLocus.DQB, TIER_2),
-  DPA1(SeroLocus.DPA, TIER_2),
-  DPB1(SeroLocus.DPB, TIER_2),
-  MICA(SeroLocus.MICA, TIER_2);
+  A(SeroLocus.A, TIER_1), B(SeroLocus.B, TIER_1), C(SeroLocus.C, TIER_1), DRB1(SeroLocus.DRB,
+      TIER_2), DRB3(SeroLocus.DRB, TIER_2), DRB4(SeroLocus.DRB, TIER_2), DRB5(SeroLocus.DRB,
+          TIER_2), DQA1(SeroLocus.DQA, TIER_2), DQB1(SeroLocus.DQB, TIER_2), DPA1(SeroLocus.DPA,
+              TIER_2), DPB1(SeroLocus.DPB, TIER_2), MICA(SeroLocus.MICA, TIER_2);
 
   private final SeroLocus sero;
   private final int tier;

src/main/java/org/pankratzlab/unet/deprecated/hla/HLAType.java

@@ -45,9 +45,10 @@ public class HLAType extends Antigen<HLALocus, HLAType> {
   /**
    * Matches string representations of {@link HLAType}s
    *
-   * <p>Group 1 is the {@link HLALocus}, group 2 is the {@link #SPEC_DELIM}ited specification, and
-   * group 3 is the parent specification e.g. 2(5) (NB: group 0 is the complete match in the {@link
-   * Matcher#group(int)} api)
+   * <p>
+   * Group 1 is the {@link HLALocus}, group 2 is the {@link #SPEC_DELIM}ited specification, and
+   * group 3 is the parent specification e.g. 2(5) (NB: group 0 is the complete match in the
+   * {@link Matcher#group(int)} api)
    */
   public static final Pattern TYPE_PATTERN;
 
@@ -84,9 +85,9 @@ public HLAType(HLALocus l, List<Integer> p) {
    * Note: this method is similar to {@link AntigenDictionary#lookup(HLAType)}, with two exceptions:
    *
    * <ul>
-   *   <li>In the case of multiple {@link SeroType} mappings, only the first will be returned
-   *   <li>If there is no explicit mapping for this type, a {@code SeroType} will be created using
-   *       the equivalent {@link SeroLocus} and the first value in this type's {@link #spec()}
+   * <li>In the case of multiple {@link SeroType} mappings, only the first will be returned
+   * <li>If there is no explicit mapping for this type, a {@code SeroType} will be created using the
+   * equivalent {@link SeroLocus} and the first value in this type's {@link #spec()}
    * </ul>
    *
    * @return {@link SeroType} equivalent of this antigen
@@ -124,7 +125,7 @@ public SeroType equivSafe() {
 
   /**
    * @return The {@link SeroType} equivalent of this allele without a lookup in antigen equivalences
-   *     table.
+   *         table.
    */
   public SeroType lowResEquiv() {
     return new SeroType(locus().sero(), spec().get(0));
@@ -188,18 +189,17 @@ public static List<HLAType> parseTypes(String text) {
   }
 
   /** @see Antigen#parseTypes(String, java.util.regex.Pattern, Function) */
-  public static <T extends Antigen<?, T>> List<T> parseTypes(
-      String text, Function<String, T> typeFunction) {
+  public static <T extends Antigen<?, T>> List<T> parseTypes(String text,
+      Function<String, T> typeFunction) {
     return Antigen.parseTypes(text, LOCI_PATTERN, typeFunction);
   }
 
   static {
     // Static initializer to create patterns
     // See also SeroType
 
-    LOCI_PATTERN =
-        makePattern(
-            Arrays.stream(HLALocus.values()).map(HLALocus::name).collect(Collectors.toList()));
+    LOCI_PATTERN = makePattern(
+        Arrays.stream(HLALocus.values()).map(HLALocus::name).collect(Collectors.toList()));
 
     TYPE_PATTERN = Pattern.compile(LOCI_PATTERN.pattern() + SPEC_PATTERN.pattern());
     PARTIAL_PATTERN =

src/main/java/org/pankratzlab/unet/deprecated/hla/LabelledType.java

@@ -52,8 +52,8 @@ public LabelledType(HLALocus parsedLocus, List<Integer> spec, char charAt) {
   /** @return A {@link HLAType} representation of the given string */
   public static LabelledType valueOf(String typeString) {
     RawType rt = new RawType(typeString, TYPE_PATTERN);
-    return new LabelledType(
-        new HLAType(rt.locus(), rt.spec()), typeString.charAt(typeString.length() - 1));
+    return new LabelledType(new HLAType(rt.locus(), rt.spec()),
+        typeString.charAt(typeString.length() - 1));
   }
 
   @Override

src/main/java/org/pankratzlab/unet/deprecated/hla/LoggingPlaceholder.java

@@ -61,12 +61,11 @@ public static void reportError(String error) {
   }
 
   public static void report(String error, AlertType alertType) {
-    Platform.runLater(
-        () -> {
-          Alert alert = new Alert(alertType);
-          alert.setHeaderText(error);
-          alert.showAndWait();
-        });
+    Platform.runLater(() -> {
+      Alert alert = new Alert(alertType);
+      alert.setHeaderText(error);
+      alert.showAndWait();
+    });
   }
 
   /**
@@ -77,24 +76,19 @@ public static void report(String error, AlertType alertType) {
    * @param title Title to use on the dialog shown to the user
    */
   public static void reportError(Throwable exc, String title) {
-    Platform.runLater(
-        () -> {
-          StringBuilder sb =
-              new StringBuilder(
-                  "Please send the following to the developers:\n"
-                      + "- A screenshot of this error\n"
-                      + "- The input files (or MRN) that caused this error\n\n");
-          sb.append(exc.getClass());
-          sb.append(": ");
-          sb.append(exc.getMessage());
-          sb.append("\n");
-          sb.append(
-              Arrays.stream(exc.getStackTrace())
-                  .map(StackTraceElement::toString)
-                  .collect(Collectors.joining("\n")));
-          TextArea errorText = new TextArea(sb.toString());
-          errorText.setWrapText(true);
-          JFXUtilHelper.makeContentOnlyAlert(AlertType.ERROR, title, errorText).showAndWait();
-        });
+    Platform.runLater(() -> {
+      StringBuilder sb = new StringBuilder(
+          "Please send the following to the developers:\n" + "- A screenshot of this error\n"
+              + "- The input files (or MRN) that caused this error\n\n");
+      sb.append(exc.getClass());
+      sb.append(": ");
+      sb.append(exc.getMessage());
+      sb.append("\n");
+      sb.append(Arrays.stream(exc.getStackTrace()).map(StackTraceElement::toString)
+          .collect(Collectors.joining("\n")));
+      TextArea errorText = new TextArea(sb.toString());
+      errorText.setWrapText(true);
+      JFXUtilHelper.makeContentOnlyAlert(AlertType.ERROR, title, errorText).showAndWait();
+    });
   }
 }

src/main/java/org/pankratzlab/unet/deprecated/hla/SeroLocus.java

@@ -29,15 +29,8 @@
 
 /** {@link Locus} implementation for serological types */
 public enum SeroLocus implements Locus<SeroLocus> {
-  A(2, TIER_1),
-  B(2, TIER_1),
-  C(3, TIER_1),
-  DRB(1, TIER_2, "DR"),
-  DQB(1, TIER_2, "DQ"),
-  DQA(1, TIER_2),
-  DPB(1, TIER_2, "DP"),
-  DPA(1, TIER_2),
-  MICA(1, -1);
+  A(2, TIER_1), B(2, TIER_1), C(3, TIER_1), DRB(1, TIER_2, "DR"), DQB(1, TIER_2, "DQ"), DQA(1,
+      TIER_2), DPB(1, TIER_2, "DP"), DPA(1, TIER_2), MICA(1, -1);
 
   private final int severity;
   private final int tier;
@@ -51,7 +44,7 @@ private SeroLocus(int severity, int tier, String... alias) {
 
   /**
    * @return Numeric priority indicating whether antigens on this locus should be preferred as
-   *     unacceptable
+   *         unacceptable
    */
   public int priority() {
     return severity;

src/main/java/org/pankratzlab/unet/deprecated/hla/SeroType.java

@@ -41,9 +41,10 @@ public class SeroType extends Antigen<SeroLocus, SeroType> {
   /**
    * Matches string representations of {@link SeroType}s
    *
-   * <p>Group 1 is the {@link SeroLocus}, group 2 is the {@link #SPEC_DELIM}ited specification, and
-   * group 3 is the parent specification e.g. 2(5) (NB: group 0 is the complete match in the {@link
-   * Matcher#group(int)} api)
+   * <p>
+   * Group 1 is the {@link SeroLocus}, group 2 is the {@link #SPEC_DELIM}ited specification, and
+   * group 3 is the parent specification e.g. 2(5) (NB: group 0 is the complete match in the
+   * {@link Matcher#group(int)} api)
    */
   public static final Pattern TYPE_PATTERN;
 

src/main/java/org/pankratzlab/unet/deprecated/jfx/JFXPropertyHelper.java

@@ -38,18 +38,18 @@ private JFXPropertyHelper() {
    * Helper method to handle null checking when ORing two {@link ObservableBooleanValue}s.
    *
    * @return If {@code optional} is null, {@code reference} is returned. Otherwise a boolean OR
-   *     binding combining the two individual booleans is created and returned.
+   *         binding combining the two individual booleans is created and returned.
    */
-  public static ObservableBooleanValue orHelper(
-      @Nullable ObservableBooleanValue optional, ObservableBooleanValue reference) {
+  public static ObservableBooleanValue orHelper(@Nullable ObservableBooleanValue optional,
+      ObservableBooleanValue reference) {
     if (optional == null) {
       return reference;
     }
     return Bindings.or(optional, reference);
   }
 
-  public static ObservableBooleanValue andHelper(
-      @Nullable ObservableBooleanValue optional, ObservableBooleanValue reference) {
+  public static ObservableBooleanValue andHelper(@Nullable ObservableBooleanValue optional,
+      ObservableBooleanValue reference) {
     if (optional == null) {
       return reference;
     }