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Fixing issue #663 #665

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Fixing issue #663 #665

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9 changes: 4 additions & 5 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -122,8 +122,8 @@ public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundExc
* time before the first result is available.<br>
* <b>N.B.</b>
* <ul>
* <li>This method ca'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 can't be called after calling its NO-ARGUMENT twin.</li>
* <li>remember to close the underlying resource when you are done, by using {@link #close()}.</li>
* </ul>
* @see #process()
* @author Amr AL-Hossary
Expand All @@ -136,7 +136,7 @@ public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundExc
*/
public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotFoundException {
LinkedHashMap<String,S> sequences = new LinkedHashMap<String,S>();
@SuppressWarnings("unchecked")

int i=0;
BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
while(true) {
Expand All @@ -145,6 +145,7 @@ public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotF
String seqString = genbankParser.getSequence(br, 0);
//reached end of file?
if(seqString==null) break;
@SuppressWarnings("unchecked")
S sequence = (S) sequenceCreator.getSequence(seqString, 0);
genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);

Expand All @@ -165,8 +166,6 @@ public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotF

sequences.put(sequence.getAccession().getID(), sequence);
}
br.close();
close();
return sequences;
}

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