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refactored sequence distances
Moved utility classes used only by the sequence distances into the org.cicirello.sequences.distance package, and made them package-private.
1 parent d4d253a commit 1b29429

11 files changed

+37
-73
lines changed

‎src/org/cicirello/sequences/distance/AbstractSequenceDistanceMeasurer.java‎

Lines changed: 21 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -20,8 +20,7 @@
2020
*/
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package org.cicirello.sequences.distance;
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23-
import org.cicirello.sequences.Sequence;
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import org.cicirello.sequences.PrimitiveSequence;
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/**
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* <p>Extend this abstract class to define a distance metric for permutations where distance is an integer value. To extend this class,
@@ -38,7 +37,7 @@
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* @version 2.18.8.28
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* @since 1.1
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*/
41-
public abstract class AbstractSequenceDistanceMeasurer implements SequenceDistanceMeasurer, SequenceDistanceMeasurerDouble {
40+
abstract class AbstractSequenceDistanceMeasurer implements SequenceDistanceMeasurer, SequenceDistanceMeasurerDouble {
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/**
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* {@inheritDoc}
@@ -186,10 +185,26 @@ public final int distance(String s1, String s2) {
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}
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/**
189-
* {@inheritDoc}
188+
* Measures the distance between two Sequences.
189+
*
190+
* @param s1 First String.
191+
* @param s2 Second String.
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* @param <T> Type of element in sequence
193+
* @return distance between s1 and s2
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*/
191-
@Override
192-
public <T> double distancef(Sequence<T> s1, Sequence<T> s2) {
195+
<T> int distance(Sequence<T> s1, Sequence<T> s2) {
196+
return distance(s1,s2);
197+
}
198+
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/**
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* Measures the distance between two Sequences.
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*
202+
* @param s1 First String.
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* @param s2 Second String.
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* @param <T> Type of element in sequence
205+
* @return distance between s1 and s2
206+
*/
207+
<T> double distancef(Sequence<T> s1, Sequence<T> s2) {
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return distance(s1,s2);
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}
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‎src/org/cicirello/sequences/distance/EditDistance.java‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,6 @@
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package org.cicirello.sequences.distance;
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import org.cicirello.sequences.Sequence;
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/**
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* <p>EditDistance is an implementation of Wagner and Fischer's dynamic programming algorithm for computing string edit distance.</p>
@@ -110,8 +109,8 @@ public EditDistance(int insertCost, int deleteCost, int changeCost) {
110109
* {@inheritDoc}
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* @throws UnsupportedOperationException if costs were initialized with double values.
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*/
113-
@Override
114-
public <T> int distance(Sequence<T> s1, Sequence<T> s2) {
112+
@Override
113+
<T> int distance(Sequence<T> s1, Sequence<T> s2) {
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if (insert_i < 0) throw new UnsupportedOperationException("EditDistance.distance not supported for floating-point costs.");
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int L1 = s1.length();
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int L2 = s2.length();
@@ -140,7 +139,7 @@ public <T> int distance(Sequence<T> s1, Sequence<T> s2) {
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* {@inheritDoc}
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*/
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@Override
143-
public <T> double distancef(Sequence<T> s1, Sequence<T> s2) {
142+
<T> double distancef(Sequence<T> s1, Sequence<T> s2) {
144143
int L1 = s1.length();
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int L2 = s2.length();
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double[][] D = new double[L1 + 1][L2 + 1];

‎src/org/cicirello/sequences/distance/ExactMatchDistance.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,6 @@
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*/
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package org.cicirello.sequences.distance;
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import org.cicirello.sequences.Sequence;
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/**
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* <p>ExactMatch distance (or Hamming Distance) of a pair of non-binary strings (or more generally sequences) is the number of
@@ -52,7 +51,7 @@ public final class ExactMatchDistance extends AbstractSequenceDistanceMeasurer {
5251
* {@inheritDoc}
5352
*/
5453
@Override
55-
public <T> int distance(Sequence<T> s1, Sequence<T> s2) {
54+
<T> int distance(Sequence<T> s1, Sequence<T> s2) {
5655
int n = s1.length();
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int m = s2.length();
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if (m < n) {

‎src/org/cicirello/sequences/distance/KendallTauDistance.java‎

Lines changed: 2 additions & 2 deletions
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@@ -20,7 +20,7 @@
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*/
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package org.cicirello.sequences.distance;
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import org.cicirello.sequences.Sequence;
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import java.util.Arrays;
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@@ -93,7 +93,7 @@ public final class KendallTauDistance extends AbstractSequenceDistanceMeasurer {
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* @throws IllegalArgumentException if sequences are of different lengths, or contain different elements
9494
*/
9595
@Override
96-
public <T> int distance(Sequence<T> s1, Sequence<T> s2) {
96+
<T> int distance(Sequence<T> s1, Sequence<T> s2) {
9797
if (s1.length() != s2.length()) throw new IllegalArgumentException("Sequences must be same length for Kendall Tau distance.");
9898
if (s1.length() == 0) return 0;
9999

src/org/cicirello/sequences/ObjectSequence.java renamed to src/org/cicirello/sequences/distance/ObjectSequence.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
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*
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*/
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package org.cicirello.sequences;
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package org.cicirello.sequences.distance;
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import java.util.Arrays;
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@@ -35,7 +35,7 @@
3535
* @version 2.18.8.29
3636
* @since 1.1
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*/
38-
public final class ObjectSequence<E extends Comparable<E>> implements Sequence<E> {
38+
final class ObjectSequence<E extends Comparable<E>> implements Sequence<E> {
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private final E[] a;
4141

src/org/cicirello/sequences/PrimitiveSequence.java renamed to src/org/cicirello/sequences/distance/PrimitiveSequence.java

Lines changed: 2 additions & 2 deletions
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@@ -20,7 +20,7 @@
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*
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*/
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package org.cicirello.sequences;
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package org.cicirello.sequences.distance;
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import java.util.Arrays;
2626

@@ -38,7 +38,7 @@
3838
* @version 2.18.8.29
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* @since 1.1
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*/
41-
public final class PrimitiveSequence implements Sequence<PrimitiveValue> {
41+
final class PrimitiveSequence implements Sequence<PrimitiveValue> {
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4343
private final AbstractPrimitiveSequence a;
4444

src/org/cicirello/sequences/PrimitiveValue.java renamed to src/org/cicirello/sequences/distance/PrimitiveValue.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
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*
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*/
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23-
package org.cicirello.sequences;
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package org.cicirello.sequences.distance;
2424

2525
/**
2626
* The PrimitiveValue class is a wrapper class for all eight of Java's primitive types.
@@ -39,7 +39,7 @@
3939
* @version 2.18.8.27
4040
* @since 1.1
4141
*/
42-
public final class PrimitiveValue {
42+
final class PrimitiveValue {
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4444
private final AbstractPrimitiveValue v;
4545

src/org/cicirello/sequences/Sequence.java renamed to src/org/cicirello/sequences/distance/Sequence.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
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*
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*/
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package org.cicirello.sequences;
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package org.cicirello.sequences.distance;
2424

2525
/**
2626
* A Sequence is an ordered sequence of values, similar to an array or a list, except a Sequence has a more limited, and specific set of
@@ -34,7 +34,7 @@
3434
* @version 2.18.8.29
3535
* @since 1.1
3636
*/
37-
public interface Sequence<E> {
37+
interface Sequence<E> {
3838

3939
/**
4040
* Returns the length of the sequence.

‎src/org/cicirello/sequences/distance/SequenceDistanceMeasurer.java‎

Lines changed: 1 addition & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
2020
*/
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package org.cicirello.sequences.distance;
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23-
import org.cicirello.sequences.Sequence;
23+
2424

2525
/**
2626
* <p>Implement this interface, SequenceDistanceMeasurer, to define a distance metric for sequences. A sequence may have duplicate elements, unlike
@@ -111,15 +111,4 @@ public interface SequenceDistanceMeasurer {
111111
* @return distance between s1 and s2
112112
*/
113113
int distance(String s1, String s2);
114-
115-
/**
116-
* Measures the distance between two Sequences.
117-
*
118-
* @param s1 First String.
119-
* @param s2 Second String.
120-
* @param <T> Type of element in sequence
121-
* @return distance between s1 and s2
122-
*/
123-
<T> int distance(Sequence<T> s1, Sequence<T> s2);
124-
125114
}

‎src/org/cicirello/sequences/distance/SequenceDistanceMeasurerDouble.java‎

Lines changed: 1 addition & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
2020
*/
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package org.cicirello.sequences.distance;
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23-
import org.cicirello.sequences.Sequence;
23+
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/**
2626
* <p>Implement this interface, SequenceDistanceMeasurerDouble, to define a distance metric for sequences. A sequence may have duplicate elements, unlike
@@ -112,14 +112,4 @@ public interface SequenceDistanceMeasurerDouble {
112112
*/
113113
double distancef(String s1, String s2);
114114

115-
/**
116-
* Measures the distance between two Sequences.
117-
*
118-
* @param s1 First String.
119-
* @param s2 Second String.
120-
* @param <T> Type of element in sequence
121-
* @return distance between s1 and s2
122-
*/
123-
<T> double distancef(Sequence<T> s1, Sequence<T> s2);
124-
125115
}

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