Add Gff3 Writer (#1486)

* Adds a Gff3Writer to write out Gff3 files. 
* Also adjusts the attributes field to account for the fact that attributes map a key to a list of strings, which are separated by commas. As previously written, the comma separated list was left as a single string, which could later be processed into a list by the user. This was vulnerable to situations where one of the entries in the list contained an encoded comma (ie %2C), so that after decoding the decoded comma could not be differentiated from the list separating commas.
* This required breaking changes to the existing Gff3 api's but the changes should be simple for downstream users to adapt.

src/main/java/htsjdk/tribble/gff/Gff3BaseData.java

@@ -2,8 +2,10 @@
 
 import htsjdk.tribble.annotation.Strand;
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 
 public class Gff3BaseData {
@@ -18,15 +20,15 @@ public class Gff3BaseData {
     private final double score;
     private final Strand strand;
     private final int phase;
-    private final Map<String, String> attributes;
+    private final Map<String, List<String>> attributes;
     private final String id;
     private final String name;
-    private final String alias;
+    private final List<String> aliases;
     private final int hashCode;
 
     public Gff3BaseData(final String contig, final String source, final String type,
                  final int start, final int end, final Double score, final Strand strand, final int phase,
-                 final Map<String, String> attributes) {
+                 final Map<String, List<String>> attributes) {
         this.contig = contig;
         this.source = source;
         this.type = type;
@@ -35,13 +37,24 @@ public Gff3BaseData(final String contig, final String source, final String type,
         this.score = score;
         this.phase = phase;
         this.strand = strand;
-        this.attributes = Collections.unmodifiableMap(new LinkedHashMap<>(attributes));
-        this.id = attributes.get(ID_ATTRIBUTE_KEY);
-        this.name = attributes.get(NAME_ATTRIBUTE_KEY);
-        this.alias = attributes.get(ALIAS_ATTRIBUTE_KEY);
+        this.attributes = copyAttributesSafely(attributes);
+        this.id = Gff3Codec.extractSingleAttribute(attributes.get(ID_ATTRIBUTE_KEY));
+        this.name = Gff3Codec.extractSingleAttribute(attributes.get(NAME_ATTRIBUTE_KEY));
+        this.aliases = attributes.getOrDefault(ALIAS_ATTRIBUTE_KEY, Collections.emptyList());
         this.hashCode = computeHashCode();
     }
 
+    private static Map<String, List<String>> copyAttributesSafely(final Map<String, List<String>> attributes) {
+        final Map<String, List<String>> modifiableDeepMap = new LinkedHashMap<>();
+
+        for (final Map.Entry<String, List<String>> entry : attributes.entrySet()) {
+            final List<String> unmodifiableDeepList = Collections.unmodifiableList(new ArrayList<>(entry.getValue()));
+            modifiableDeepMap.put(entry.getKey(), unmodifiableDeepList);
+        }
+
+        return Collections.unmodifiableMap(modifiableDeepMap);
+    }
+
     @Override
     public boolean equals(Object other) {
         if (other == this) {
@@ -73,11 +86,7 @@ public boolean equals(Object other) {
             ret = ret && otherBaseData.getName() != null && otherBaseData.getName().equals(getName());
         }
 
-        if (getAlias() == null) {
-            ret = ret && otherBaseData.getAlias() == null;
-        } else {
-            ret = ret && otherBaseData.getAlias() != null && otherBaseData.getAlias().equals(getAlias());
-        }
+        ret = ret && otherBaseData.getAliases().equals(getAliases());
 
         return ret;
     }
@@ -105,9 +114,7 @@ private int computeHashCode() {
             hash = 31 * hash + getName().hashCode();
         }
 
-        if (getAlias() != null) {
-            hash = 31 * hash + getAlias().hashCode();
-        }
+        hash = 31 * hash + aliases.hashCode();
 
         return hash;
     }
@@ -144,10 +151,14 @@ public int getPhase() {
         return phase;
     }
 
-    public Map<String, String> getAttributes() {
+    public Map<String, List<String>> getAttributes() {
         return attributes;
     }
 
+    public List<String> getAttribute(final String key) {
+        return attributes.getOrDefault(key, Collections.emptyList());
+    }
+
     public String getId() {
         return id;
     }
@@ -156,7 +167,7 @@ public String getName() {
         return name;
     }
 
-    public String getAlias() {
-        return alias;
+    public List<String> getAliases() {
+        return aliases;
     }
 }