initialise sequrnce storage, throwing IAE

otter606 · otter606 · commit cff87dd13969 · 2021-11-25T18:20:45.000Z
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
@@ -23,6 +23,7 @@
 package org.biojava.nbio.core.sequence;
 
 
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
@@ -46,8 +47,15 @@ public class CDSSequence extends DNASequence {
 	 * @param bioBegin
 	 * @param bioEnd
 	 * @param phase
+	 * @throws  IllegalArgumentException if  parentSequence is incompatible with DNACompoundSet
 	 */
 	public CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase) {
+		setCompoundSet(DNACompoundSet.getDNACompoundSet());
+		try {
+			initSequenceStorage(parentSequence.getSequenceAsString());
+		} catch (CompoundNotFoundException e) {
+			throw new IllegalArgumentException(e);
+		}
 		parentTranscriptSequence = parentSequence;
 		this.setParentSequence(parentTranscriptSequence);
 		setBioBegin(bioBegin);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonSequence.java
@@ -22,6 +22,9 @@
  */
 package org.biojava.nbio.core.sequence;
 
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
+
 /**
  * A gene contains a collection of Exon sequences
  * @author Scooter Willis
@@ -41,6 +44,12 @@ public class ExonSequence extends DNASequence {
 	 * @param bioEnd
 	 */
 	public ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) {
+		setCompoundSet(DNACompoundSet.getDNACompoundSet());
+		try {
+			initSequenceStorage(parentGeneSequence.getSequenceAsString());
+		} catch (CompoundNotFoundException e) {
+			throw new IllegalArgumentException(e);
+		}
 		this.setParentSequence(parentGeneSequence);
 		setBioBegin(bioBegin);
 		setBioEnd(bioEnd);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
@@ -65,13 +65,18 @@ public class GeneSequence extends DNASequence {
 	 * @param end inclusive of end
 	 * @param strand force a gene to have strand and transcription sequence will inherit
 	 */
-	public GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Strand strand) {
+	public GeneSequence(ChromosomeSequence parentSequence,  int begin, int end, Strand strand) {
+		setCompoundSet(DNACompoundSet.getDNACompoundSet());
+		try {
+			initSequenceStorage(parentSequence.getSequenceAsString());
+		} catch (CompoundNotFoundException e) {
+			throw new IllegalArgumentException(e);
+		}
 		chromosomeSequence = parentSequence;
 		setParentSequence(parentSequence);
 		setBioBegin(begin);
 		setBioEnd(end);
 		setStrand(strand);
-		this.setCompoundSet(DNACompoundSet.getDNACompoundSet());
 	}
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
@@ -52,13 +52,19 @@ public class TranscriptSequence extends DNASequence {
 	 * @param parentDNASequence
 	 * @param begin
 	 * @param end inclusive of end
+	 * @throws  IllegalArgumentException if the parentDNASequence is incompatible with DNACompoundSet
 	 */
 	public TranscriptSequence(GeneSequence parentDNASequence, int begin, int end) {
+		setCompoundSet(DNACompoundSet.getDNACompoundSet());
+		try {
+			initSequenceStorage(parentDNASequence.getSequenceAsString());
+		} catch (CompoundNotFoundException e) {
+			throw new IllegalArgumentException(e);
+		}
 		setParentSequence(parentDNASequence);
 		this.parentGeneSequence = parentDNASequence;
 		setBioBegin(begin);
 		setBioEnd(end);
-		this.setCompoundSet(DNACompoundSet.getDNACompoundSet());
 	}
 
 		@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -88,6 +88,11 @@ public AbstractSequence() {
 	 */
 	public AbstractSequence(String seqString, CompoundSet<C> compoundSet) throws CompoundNotFoundException {
 		setCompoundSet(compoundSet);
+		initSequenceStorage(seqString);
+	}
+
+	//  so it can be called from subclass constructors
+	protected void initSequenceStorage(String seqString) throws CompoundNotFoundException {
 		sequenceStorage = new ArrayListSequenceReader<C>();
 		sequenceStorage.setCompoundSet(this.getCompoundSet());
 		sequenceStorage.setContents(seqString);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/ExonSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/ExonSequenceTest.java
@@ -16,8 +16,7 @@ void createExon() throws CompoundNotFoundException {
     }
 
     @Test
-    @Disabled("getAsList throws NPE in AbstractSequence#equals")
-    void equalsAndHaschcode() throws CompoundNotFoundException {
+    void equalsAndHashcode() throws CompoundNotFoundException {
         GeneSequence gene = anyGeneSequence();
         ExonSequence es = new ExonSequence(gene, 30, 40);
         ExonSequence es2 = new ExonSequence(gene, 30, 40);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/GeneSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/GeneSequenceTest.java
@@ -113,11 +113,9 @@ void addRemoveExon() throws Exception {
         assertEquals(2, geneSequence.getExonSequences().size());
         geneSequence.removeExon("unknown");
         assertEquals(2, geneSequence.getExonSequences().size());
-        // this causes NPE in equals() methods as sequence proxy loader isn't set.
-        // either call super constructor in GeneSequence (which will require adding exception)
-        // or alter equals()  in AbstractSequence not to use properties like sequenceStorage, that may be null.
-        // geneSequence.removeExon("b");
-        // assertEquals(1, geneSequence.getExonSequences().size());
+
+         geneSequence.removeExon("c");
+         assertEquals(1, geneSequence.getExonSequences().size());
     }
 
    @Test
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranscriptSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranscriptSequenceTest.java
@@ -42,15 +42,19 @@ void CDSListIsEmpty() {
         }
 
         @Test
-        @Disabled("NPE thrown from AbstractSequence 'getAsList'")
+        // whether it's -ve or +ve doesn't affect equals?
         void equals() {
-            assertFalse(transcriptSeq.equals(transcriptNegativeSeq));
+            assertTrue(transcriptSeq.equals(transcriptSeq));
+        }
+
+        // whether it's -ve or +ve doesn't affect equals?
+        void equalsDoesntDependOnStrand() {
+            assertTrue(transcriptSeq.equals(transcriptNegativeSeq));
         }
 
         @Test
-        @Disabled("NPE thrown from AbstractSequence 'getAsList'")
         void hashcode() {
-            assertFalse(transcriptSeq.hashCode() == (transcriptNegativeSeq.hashCode()));
+            assertTrue(transcriptSeq.hashCode() == (transcriptNegativeSeq.hashCode()));
         }
     }
 
@@ -89,7 +93,6 @@ void getCDNASeqNegativeStrand() throws Exception {
     }
 
     @Test
-    @Disabled("Can't  remove, as NPE thrown from equals()")
     void removeCDS() throws Exception {
         transcriptSeq.addCDS(new AccessionID("a"), 50, 60, 1);
         assertEquals(1, transcriptSeq.getCDSSequences().size());

Original file line number	Diff line number	Diff line change
`@@ -16,8 +16,7 @@ void createExon() throws CompoundNotFoundException {`
`16`	`16`	`}`
`17`	`17`
`18`	`18`	`@Test`
`19`		`- @Disabled("getAsList throws NPE in AbstractSequence#equals")`
`20`		`- void equalsAndHaschcode() throws CompoundNotFoundException {`
	`19`	`+ void equalsAndHashcode() throws CompoundNotFoundException {`
`21`	`20`	`GeneSequence gene = anyGeneSequence();`
`22`	`21`	`ExonSequence es = new ExonSequence(gene, 30, 40);`
`23`	`22`	`ExonSequence es2 = new ExonSequence(gene, 30, 40);`
Original file line number	Diff line number	Diff line change
`@@ -42,15 +42,19 @@ void CDSListIsEmpty() {`
`42`	`42`	`}`
`43`	`43`
`44`	`44`	`@Test`
`45`		`- @Disabled("NPE thrown from AbstractSequence 'getAsList'")`
	`45`	`+ // whether it's -ve or +ve doesn't affect equals?`
`46`	`46`	`void equals() {`
`47`		`- assertFalse(transcriptSeq.equals(transcriptNegativeSeq));`
	`47`	`+ assertTrue(transcriptSeq.equals(transcriptSeq));`
	`48`	`+ }`
	`49`	`+`
	`50`	`+ // whether it's -ve or +ve doesn't affect equals?`
	`51`	`+ void equalsDoesntDependOnStrand() {`
	`52`	`+ assertTrue(transcriptSeq.equals(transcriptNegativeSeq));`
`48`	`53`	`}`
`49`	`54`
`50`	`55`	`@Test`
`51`		`- @Disabled("NPE thrown from AbstractSequence 'getAsList'")`
`52`	`56`	`void hashcode() {`
`53`		`- assertFalse(transcriptSeq.hashCode() == (transcriptNegativeSeq.hashCode()));`
	`57`	`+ assertTrue(transcriptSeq.hashCode() == (transcriptNegativeSeq.hashCode()));`
`54`	`58`	`}`
`55`	`59`	`}`
`56`	`60`
`@@ -89,7 +93,6 @@ void getCDNASeqNegativeStrand() throws Exception {`
`89`	`93`	`}`
`90`	`94`
`91`	`95`	`@Test`
`92`		`- @Disabled("Can't remove, as NPE thrown from equals()")`
`93`	`96`	`void removeCDS() throws Exception {`
`94`	`97`	`transcriptSeq.addCDS(new AccessionID("a"), 50, 60, 1);`
`95`	`98`	`assertEquals(1, transcriptSeq.getCDSSequences().size());`