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Remove Compile warning in a case where we are subverting the type system #91

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Merged
andreasprlic merged 3 commits into from
Mar 19, 2014
Merged

Remove Compile warning in a case where we are subverting the type system #91

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c2a4ad5
ProteinSequence was using parentSequence as a DNA Sequence. However,
emckee2006 Feb 10, 2014
9824913
Merge pull request #16 from biojava/master
emckee2006 Mar 18, 2014
d193131
Merge pull request #17 from biojava/master
emckee2006 Mar 19, 2014
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5 changes: 4 additions & 1 deletion biojava3-core/src/main/java/org/biojava3/core/sequence/ProteinSequence.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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);
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12 changes: 9 additions & 3 deletions biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
}

Expand Down Expand Up @@ -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;


Expand All @@ -495,9 +499,11 @@ private SequenceReader<C> getSequenceStorage() {
if (sequenceStorage != null) {
return sequenceStorage;
}
/*
if (parentSequence != null) {
return parentSequence.getSequenceStorage();
}
*/
return null;
}

Expand Down