for the fix for biojava#91 to work I believe we need to be more careful with CompoundSets

andreasprlic · andreasprlic · commit 521092982584 · 2014-03-19T17:14:24.000-07:00
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java
@@ -23,6 +23,7 @@
 package org.biojava3.core.sequence;
 
 
+import org.biojava3.core.sequence.compound.DNACompoundSet;
 import org.biojava3.core.sequence.compound.NucleotideCompound;
 import org.biojava3.core.sequence.template.CompoundSet;
 
@@ -52,6 +53,7 @@ public CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd,
         setBioBegin(bioBegin);
         setBioEnd(bioEnd);
         this.phase = phase;
+        this.setCompoundSet(DNACompoundSet.getDNACompoundSet());
 
     }
 
@@ -86,6 +88,7 @@ public Strand getStrand() {
      */
     public String getCodingSequence() {
         String sequence = this.getSequenceAsString(getBioBegin(), getBioEnd(), getStrand());
+        
         if (getStrand() == Strand.NEGATIVE) {
             //need to take complement of sequence because it is negative and we are returning a coding sequence
             StringBuilder b = new StringBuilder(getLength());
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java
@@ -26,6 +26,8 @@
 import java.util.Collections;
 import java.util.LinkedHashMap;
 import java.util.logging.Logger;
+
+import org.biojava3.core.sequence.compound.DNACompoundSet;
 import org.biojava3.core.sequence.compound.NucleotideCompound;
 import org.biojava3.core.sequence.template.CompoundSet;
 
@@ -66,6 +68,7 @@ public GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Stran
         setBioBegin(begin);
         setBioEnd(end);
         setStrand(strand);
+        this.setCompoundSet(DNACompoundSet.getDNACompoundSet());
     }
 
     /**
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java
@@ -26,6 +26,7 @@
 import java.util.Collections;
 import java.util.LinkedHashMap;
 
+import org.biojava3.core.sequence.compound.DNACompoundSet;
 import org.biojava3.core.sequence.transcription.TranscriptionEngine;
 
 /**
@@ -52,6 +53,7 @@ public TranscriptSequence(GeneSequence parentDNASequence, int begin, int end) {
         this.parentGeneSequence = parentDNASequence;
         setBioBegin(begin);
         setBioEnd(end);
+        this.setCompoundSet(DNACompoundSet.getDNACompoundSet());
 
     }
 
@@ -188,8 +190,9 @@ public ArrayList<ProteinSequence> getProteinCDSSequences() {
     public DNASequence getDNACodingSequence() {
         StringBuilder sb = new StringBuilder();
         for (CDSSequence cdsSequence : cdsSequenceList) {
-            sb.append(cdsSequence.getCodingSequence());
+        	sb.append(cdsSequence.getCodingSequence());
         }
+        
         DNASequence dnaSequence = new DNASequence(sb.toString().toUpperCase());
         dnaSequence.setAccession(new AccessionID(this.getAccession().getID()));
         return dnaSequence;
@@ -213,6 +216,7 @@ public ProteinSequence getProteinSequence(TranscriptionEngine engine) {
         RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine);
         ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine);
         proteinSequence.setAccession(new AccessionID(this.getAccession().getID()));
+        
         return proteinSequence;
     }
 
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
@@ -499,11 +499,19 @@ private SequenceReader<C> getSequenceStorage() {
         if (sequenceStorage != null) {
             return sequenceStorage;
         }
-        /*
         if (parentSequence != null) {
-            return parentSequence.getSequenceStorage();
+        
+        	//return parentSequence.getSequenceStorage();
+        	        	
+            if ( this.compoundSet.equals(parentSequence.getCompoundSet())){
+            	sequenceStorage = new ArrayListSequenceReader<C>();
+                sequenceStorage.setCompoundSet(this.getCompoundSet());
+                sequenceStorage.setContents(parentSequence.getSequenceAsString());
+                return sequenceStorage;
+            }
+            
         }
-        */
+        
         return null;
     }
 
@@ -515,6 +523,7 @@ private SequenceReader<C> getSequenceStorage() {
      * @return
      */
     public String getSequenceAsString(Integer bioStart, Integer bioEnd, Strand strand) {
+    	    	
         Location loc = new SimpleLocation(bioStart, bioEnd, strand);
         return loc.getSubSequence(this).getSequenceAsString();
     }
@@ -542,6 +551,7 @@ public List<C> getAsList() {
      * @return
      */
     public C getCompoundAt(int position) {
+    	
         return getSequenceStorage().getCompoundAt(position);
     }
 
