Revert to old behavior where process(int) return null on end-of-file.

arojnuckarin · josemduarte · commit 9f6ed0392ebc · 2017-12-11T16:02:24.000-08:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
@@ -122,8 +122,6 @@ public LinkedHashMap<String,S> process() throws IOException {
 	 * <ul>
 	 * <li>This method can't be called after calling its NO-ARGUMENT twin.</li>
 	 * <li>remember to close the underlying resource when you are done.</li>
-	 * <li>This method always return non-null hash map. When end-of-file is reached,
-	 * the number of sequences returned will be smaller than the number requested.</li>
 	 * </ul>
 	 * @see #process()
 	 * @author Amr AL-Hossary
@@ -219,7 +217,7 @@ public LinkedHashMap<String,S> process(int max) throws IOException {
 		this.line  = line;
 		this.header= header;
 
-		return sequences;
+		return max > -1 && sequences.isEmpty() ? null :  sequences;
 	}
 
 	public void close() throws IOException {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
@@ -72,8 +72,7 @@ private void testProcess1(String path) throws Exception {
             assertThat(out1.containsKey("P02768"),is(true));
             assertThat(out1.get("P02768").getLength(),is(609));
             LinkedHashMap<String,ProteinSequence> out2 = fastaReader.process(1);
-            assertThat(out2,is(notNullValue()));
-            assertThat(out2.size(),is(0));
+            assertThat(out2,is(nullValue()));
         } finally {
             if(fastaReader != null) fastaReader.close();
         }
@@ -120,8 +119,7 @@ private void testProcess2(String path) throws Exception {
             assertThat(out2.containsKey("P00698"),is(true));
             assertThat(out2.get("P00698").getLength(),is(147));
             LinkedHashMap<String,ProteinSequence> out3 = fastaReader.process(1);
-            assertThat(out3,is(notNullValue()));
-            assertThat(out3.size(),is(0));
+            assertThat(out3,is(nullValue()));
         } finally {
             if(fastaReader != null) fastaReader.close();
         }
