Merge pull request #91 from emckee2006/master

andreasprlic · andreasprlic · commit 75ff1ab9d2fc · 2014-03-19T15:49:19.000-07:00
Remove Compile warning in a case where we are subverting the type system
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/ProteinSequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/ProteinSequence.java
@@ -24,6 +24,7 @@
 
 import org.biojava3.core.sequence.compound.AminoAcidCompound;
 import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava3.core.sequence.compound.NucleotideCompound;
 import org.biojava3.core.sequence.loader.StringProxySequenceReader;
 import org.biojava3.core.sequence.template.AbstractSequence;
 import org.biojava3.core.sequence.template.CompoundSet;
@@ -83,7 +84,9 @@ public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, Compo
      * @param begin
      * @param end
      */
-    public void setParentDNASequence(AbstractSequence parentDNASequence, Integer begin, Integer end) {
+    //TODO - Someone needs to check if this is a bug.  Shouldn't a parentDNASequence be something other then AminoAcid?
+    //However, due to the derivation of this class, this is the only possible type argument for this parameter...
+    public void setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence, Integer begin, Integer end) {
         this.setParentSequence(parentDNASequence);
         setBioBegin(begin);
         setBioEnd(end);
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java
@@ -62,7 +62,7 @@ public abstract class AbstractSequence<C extends Compound> implements Sequence<C
     private Collection<Object> userCollection;
     private Integer bioBegin = null;
     private Integer bioEnd = null;
-    private AbstractSequence<C> parentSequence = null;
+    private AbstractSequence<?> parentSequence = null;
     private String source = null;
     private ArrayList<String> notesList = new ArrayList<String>();
     private Double sequenceScore = null;
@@ -226,14 +226,14 @@ public void setOriginalHeader(String originalHeader) {
     /**
      * @return the parentSequence
      */
-    public AbstractSequence<C> getParentSequence() {
+    public AbstractSequence<?> getParentSequence() {
         return parentSequence;
     }
 
     /**
      * @param parentSequence the parentSequence to set
      */
-    public void setParentSequence(AbstractSequence<C> parentSequence) {
+    public void setParentSequence(AbstractSequence<?> parentSequence) {
         this.parentSequence = parentSequence;
     }
 
@@ -474,9 +474,13 @@ public CompoundSet<C> getCompoundSet() {
         if (compoundSet != null) {
             return compoundSet;
         }
+        // This is invalid since the parentSequence isn't guaranteed to have the same compound set as this sequence,
+        // e.g., the case where the parent sequence for a protein is a CDS.
+        /*
         if (parentSequence != null) {
             return parentSequence.getCompoundSet();
         }
+        */
         return null;
 
 
@@ -495,9 +499,11 @@ private SequenceReader<C> getSequenceStorage() {
         if (sequenceStorage != null) {
             return sequenceStorage;
         }
+        /*
         if (parentSequence != null) {
             return parentSequence.getSequenceStorage();
         }
+        */
         return null;
     }
 
