Sequence.getReverse() has been changed to getInverse() to avoid confusion.

andrewyatz · andrewyatz · commit 2f5015590d9b · 2010-11-03T20:18:45.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8393 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleAlignedSequence.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleAlignedSequence.java
@@ -372,7 +372,7 @@ private void setLocation(List<Step> steps) {
 
     @Override
     //TODO Needs to implements
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         throw new UnsupportedOperationException("Not supported yet.");
     }
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/DNASequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/DNASequence.java
@@ -29,8 +29,11 @@
 import org.biojava3.core.sequence.template.CompoundSet;
 import org.biojava3.core.sequence.template.ProxySequenceReader;
 import org.biojava3.core.sequence.template.SequenceMixin;
+import org.biojava3.core.sequence.template.SequenceView;
 import org.biojava3.core.sequence.transcription.Frame;
 import org.biojava3.core.sequence.transcription.TranscriptionEngine;
+import org.biojava3.core.sequence.views.ComplementSequenceView;
+import org.biojava3.core.sequence.views.ReversedSequenceView;
 
 /**
  *
@@ -83,6 +86,27 @@ public int getGCCount() {
         return SequenceMixin.countGC(this);
     }
 
+    /**
+     * Returns a Sequence which runs in the current reverse order
+     */
+    public SequenceView<NucleotideCompound> getReverse() {
+        return new ReversedSequenceView<NucleotideCompound>(this);
+    }
+
+    /**
+     * Returns a Sequence which will complement every base
+     */
+    public SequenceView<NucleotideCompound> getComplement() {
+        return new ComplementSequenceView<NucleotideCompound>(this);
+    }
+
+    /**
+     * Delegates to {@link #getInverse() } for the reverse complement
+     */
+    public SequenceView<NucleotideCompound> getReverseComplement() {
+        return getInverse();
+    }
+
     /**
      * @return the dnaType
      */
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java
@@ -56,10 +56,10 @@ public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader,
   }
 
   public SequenceView<NucleotideCompound> getReverseComplement() {
-    return new ComplementSequenceView<NucleotideCompound>(getReverse());
+    return new ComplementSequenceView<NucleotideCompound>(getInverse());
   }
 
-  public SequenceView<NucleotideCompound> getReverse() {
+  public SequenceView<NucleotideCompound> getInverse() {
     return new ReversedSequenceView<NucleotideCompound>(this);
   }
 
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java
@@ -198,7 +198,7 @@ public int countCompounds(C... compounds) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/StringProxySequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/StringProxySequenceReader.java
@@ -138,7 +138,7 @@ public int countCompounds(C... compounds) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java
@@ -134,7 +134,7 @@ public List<C> getAsList() {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java
@@ -157,7 +157,7 @@ public int countCompounds(C... compounds) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/BitSequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/BitSequenceReader.java
@@ -153,7 +153,7 @@ public SequenceView<C> getSubSequence(Integer start, Integer end) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/JoiningSequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/JoiningSequenceReader.java
@@ -296,7 +296,7 @@ public SequenceView<C> getSubSequence(Integer start, Integer end) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java
@@ -155,7 +155,7 @@ public Iterator<C> iterator() {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
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
@@ -537,7 +537,7 @@ public int countCompounds(C... compounds) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/template/Sequence.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/template/Sequence.java
@@ -27,25 +27,85 @@
 
 import java.util.List;
 
+/**
+ * Main interface for defining a collection of Compounds and accessing them
+ * using biological indexes
+ *
+ * @author Richard Holland
+ * @author Andy Yates
+ * @author Scooter Willis
+ * @param <C> Compound a Sequence holds
+ */
 public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 
+    /**
+     * Returns the length of the Sequence
+     */
     public int getLength();
 
+    /**
+     * Returns the Compound at the given biological index
+     *
+     * @param position Biological index (1 to n)
+     * @return Compound at the specified position
+     */
     public C getCompoundAt(int position);
 
+    /**
+     * Scans through the Sequence looking for the first occurrence of the given
+     * compound
+     *
+     * @param compound Compounds to look for
+     * @return Index of the first position of the compound in the sequence
+     */
     public int getIndexOf(C compound);
 
+/**
+     * Scans through the Sequence looking for the last occurrence of the given
+     * compound
+     *
+     * @param compound Compounds to look for
+     * @return Index of the last position of the compound in the sequence
+     */
     public int getLastIndexOf(C compound);
 
+    /**
+     * Returns the String representation of the Sequence
+     */
     public String getSequenceAsString();
 
+    /**
+     * Returns the Sequence as a List of compounds
+     */
     public List<C> getAsList();
 
+    /**
+     * Returns a portion of the sequence from the different positions. This is
+     * indexed from 1
+     *
+     * @param start Biological index start; must be greater than 0
+     * @param end Biological end; must be less than length + 1
+     * @return A SequenceView of the offset
+     */
     public SequenceView<C> getSubSequence(Integer start, Integer end);
 
+    /**
+     * Gets the compound set used to back this Sequence
+     */
     public CompoundSet<C> getCompoundSet();
 
+    /**
+     * Returns the number of times we found a compound in the Sequence
+     *
+     * @param compounds Vargs of the compounds to count
+     * @return Number of times a compound was found
+     */
     public int countCompounds(C... compounds);
 
-    public SequenceView<C> getReverse();
+    /**
+     * Does the <em>right thing</em> to get the inverse of the current
+     * Sequence. This means either reversing the Sequence and optionally
+     * complementing the Sequence.
+     */
+    public SequenceView<C> getInverse();
 }
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceProxyView.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceProxyView.java
@@ -144,7 +144,7 @@ public int countCompounds(C... compounds) {
     }
 
     @Override
-    public SequenceView<C> getReverse() {
+    public SequenceView<C> getInverse() {
         return SequenceMixin.reverse(this);
     }
 }
diff --git a/biojava3-core/src/test/java/org/biojava3/core/sequence/DNATest.java b/biojava3-core/src/test/java/org/biojava3/core/sequence/DNATest.java
@@ -33,7 +33,7 @@ public class DNATest {
 
     @Test
     public void reverseComplement() {
-        String s = getSeq().getReverse().getSequenceAsString();
+        String s = getSeq().getInverse().getSequenceAsString();
         assertThat("Reversed Complemented sequence not as expected", s, is("GCAT"));
     }
 
@@ -84,7 +84,7 @@ public void respectCase() {
         DNASequence dna = getSeq(s);
         assertThat("Sequence does not remember casing", dna.getSequenceAsString(), is(s));
         assertThat("Reversed complement sequence forgets case",
-                dna.getReverse().getSequenceAsString(), is("gcAT"));
+                dna.getInverse().getSequenceAsString(), is("gcAT"));
     }
 
     @Test(expected = CompoundNotFoundError.class)
diff --git a/biojava3-core/src/test/java/org/biojava3/core/sequence/SequenceViewTest.java b/biojava3-core/src/test/java/org/biojava3/core/sequence/SequenceViewTest.java
@@ -31,8 +31,8 @@ public void testLastIndexOf() {
   }
 
   @Test
-  public void testReverse() {
-    SequenceView<NucleotideCompound> s = new DNASequence("ATGC").getSubSequence(2, 3).getReverse();
+  public void testInverse() {
+    SequenceView<NucleotideCompound> s = new DNASequence("ATGC").getSubSequence(2, 3).getInverse();
     assertEquals("Reversed complementing view", s.getSequenceAsString(), "CA");
   }
 }

Original file line number	Diff line number	Diff line change
`@@ -372,7 +372,7 @@ private void setLocation(List<Step> steps) {`
`372`	`372`
`373`	`373`	`@Override`
`374`	`374`	`//TODO Needs to implements`
`375`		`- public SequenceView<C> getReverse() {`
	`375`	`+ public SequenceView<C> getInverse() {`
`376`	`376`	`throw new UnsupportedOperationException("Not supported yet.");`
`377`	`377`	`}`
`378`	`378`	`}`
Original file line number	Diff line number	Diff line change
`@@ -56,10 +56,10 @@ public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader,`
`56`	`56`	`}`
`57`	`57`
`58`	`58`	`public SequenceView<NucleotideCompound> getReverseComplement() {`
`59`		`- return new ComplementSequenceView<NucleotideCompound>(getReverse());`
	`59`	`+ return new ComplementSequenceView<NucleotideCompound>(getInverse());`
`60`	`60`	`}`
`61`	`61`
`62`		`- public SequenceView<NucleotideCompound> getReverse() {`
	`62`	`+ public SequenceView<NucleotideCompound> getInverse() {`
`63`	`63`	`return new ReversedSequenceView<NucleotideCompound>(this);`
`64`	`64`	`}`
`65`	`65`
Original file line number	Diff line number	Diff line change
`@@ -198,7 +198,7 @@ public int countCompounds(C... compounds) {`
`198`	`198`	`}`
`199`	`199`
`200`	`200`	`@Override`
`201`		`- public SequenceView<C> getReverse() {`
	`201`	`+ public SequenceView<C> getInverse() {`
`202`	`202`	`return SequenceMixin.reverse(this);`
`203`	`203`	`}`
`204`	`204`	`}`
Original file line number	Diff line number	Diff line change
`@@ -138,7 +138,7 @@ public int countCompounds(C... compounds) {`
`138`	`138`	`}`
`139`	`139`
`140`	`140`	`@Override`
`141`		`- public SequenceView<C> getReverse() {`
	`141`	`+ public SequenceView<C> getInverse() {`
`142`	`142`	`return SequenceMixin.reverse(this);`
`143`	`143`	`}`
`144`	`144`	`}`
Original file line number	Diff line number	Diff line change
`@@ -134,7 +134,7 @@ public List<C> getAsList() {`
`134`	`134`	`}`
`135`	`135`
`136`	`136`	`@Override`
`137`		`- public SequenceView<C> getReverse() {`
	`137`	`+ public SequenceView<C> getInverse() {`
`138`	`138`	`return SequenceMixin.reverse(this);`
`139`	`139`	`}`
`140`	`140`
Original file line number	Diff line number	Diff line change
`@@ -157,7 +157,7 @@ public int countCompounds(C... compounds) {`
`157`	`157`	`}`
`158`	`158`
`159`	`159`	`@Override`
`160`		`- public SequenceView<C> getReverse() {`
	`160`	`+ public SequenceView<C> getInverse() {`
`161`	`161`	`return SequenceMixin.reverse(this);`
`162`	`162`	`}`
`163`	`163`	`}`
Original file line number	Diff line number	Diff line change
`@@ -153,7 +153,7 @@ public SequenceView<C> getSubSequence(Integer start, Integer end) {`
`153`	`153`	`}`
`154`	`154`
`155`	`155`	`@Override`
`156`		`- public SequenceView<C> getReverse() {`
	`156`	`+ public SequenceView<C> getInverse() {`
`157`	`157`	`return SequenceMixin.reverse(this);`
`158`	`158`	`}`
`159`	`159`
Original file line number	Diff line number	Diff line change
`@@ -296,7 +296,7 @@ public SequenceView<C> getSubSequence(Integer start, Integer end) {`
`296`	`296`	`}`
`297`	`297`
`298`	`298`	`@Override`
`299`		`- public SequenceView<C> getReverse() {`
	`299`	`+ public SequenceView<C> getInverse() {`
`300`	`300`	`return SequenceMixin.reverse(this);`
`301`	`301`	`}`
`302`	`302`	`}`
Original file line number	Diff line number	Diff line change
`@@ -155,7 +155,7 @@ public Iterator<C> iterator() {`
`155`	`155`	`}`
`156`	`156`
`157`	`157`	`@Override`
`158`		`- public SequenceView<C> getReverse() {`
	`158`	`+ public SequenceView<C> getInverse() {`
`159`	`159`	`return SequenceMixin.reverse(this);`
`160`	`160`	`}`
`161`	`161`	`}`