From 29af6f3f7589200f562e0a25ab3af38d68487e95 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Sun, 21 Sep 2008 20:44:06 +0000
Subject: [PATCH] change: rename getValue() -> get(), setValue() -> set() add:
specific getters and setters for arrays of rank 1, 2 and 3
SVN: 8400
---
.../systemsx/cisd/common/array/MDArray.java | 21 +++++
.../cisd/common/array/MDByteArray.java | 77 +++++++++++++++++--
.../cisd/common/array/MDDoubleArray.java | 73 +++++++++++++++++-
.../cisd/common/array/MDFloatArray.java | 73 +++++++++++++++++-
.../cisd/common/array/MDIntArray.java | 73 +++++++++++++++++-
.../cisd/common/array/MDLongArray.java | 77 +++++++++++++++++--
.../cisd/common/array/MDShortArray.java | 73 +++++++++++++++++-
.../cisd/common/array/MDArraytest.java | 25 +++++-
8 files changed, 463 insertions(+), 29 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDArray.java
index 29eacad2110..b83c7e38462 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDArray.java
@@ -107,6 +107,27 @@ public abstract class MDArray<T>
return index;
}
+ /**
+ * Computes the linear index for the two-dimensional (<var>indexX, indexY</var>) provided.
+ */
+ protected int computeIndex(int indexX, int indexY)
+ {
+ assert 2 == shape.length;
+
+ return shape[1] * indexX + indexY;
+ }
+
+ /**
+ * Computes the linear index for the three-dimensional (<var>indexX, indexY, indexZ</var>)
+ * provided.
+ */
+ protected int computeIndex(int indexX, int indexY, int indexZ)
+ {
+ assert 3 == shape.length;
+
+ return shape[2] * (shape[1] * indexX + indexY) + indexZ;
+ }
+
/**
* Converts the <var>shape</var> from <code>long[]</code> to <code>int[]</code>.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java
index 10a3868aa8d..493bf33d79a 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java
@@ -78,13 +78,13 @@ public final class MDByteArray extends MDArray<Byte>
@Override
public Byte getAsObject(int[] indices)
{
- return getValue(indices);
+ return get(indices);
}
@Override
public void setToObject(int[] indices, Byte value)
{
- setValue(indices, value);
+ set(indices, value);
}
/**
@@ -99,23 +99,88 @@ public final class MDByteArray extends MDArray<Byte>
/**
* Returns the value of array at the position defined by <var>indices</var>.
*/
- public byte getValue(int[] indices)
+ public byte get(int[] indices)
{
return flattenedArray[computeIndex(indices)];
}
-
+
+ /**
+ * Returns the value of a one-dimensional array at the position defined by <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public byte get(int index)
+ {
+ return flattenedArray[index];
+ }
+
+ /**
+ * Returns the value of a two-dimensional array at the position defined by <var>indexX</var> and
+ * <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public byte get(int indexX, int indexY)
+ {
+ return flattenedArray[computeIndex(indexX, indexY)];
+ }
+
+ /**
+ * Returns the value of a three-dimensional array at the position defined by <var>indexX</var>,
+ * <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public byte get(int indexX, int indexY, int indexZ)
+ {
+ return flattenedArray[computeIndex(indexX, indexY, indexZ)];
+ }
+
/**
* Sets the <var>value</var> of array at the position defined by <var>indices</var>.
*/
- public void setValue(int[] indices, byte value)
+ public void set(int[] indices, byte value)
{
flattenedArray[computeIndex(indices)] = value;
}
+ /**
+ * Sets the <var>value</var> of a one-dimension array at the position defined by
+ * <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public void set(int index, byte value)
+ {
+ flattenedArray[index] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a two-dimensional array at the position defined by
+ * <var>indexX</var> and <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, byte value)
+ {
+ flattenedArray[computeIndex(indexX, indexY)] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a three-dimensional array at the position defined by
+ * <var>indexX</var>, <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int indexZ, byte value)
+ {
+ flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
+ }
+
//
// Object
//
-
+
@Override
public int hashCode()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java
index c8b826f0fa8..fb4bdd49c29 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java
@@ -78,13 +78,13 @@ public final class MDDoubleArray extends MDArray<Double>
@Override
public Double getAsObject(int[] indices)
{
- return getValue(indices);
+ return get(indices);
}
@Override
public void setToObject(int[] indices, Double value)
{
- setValue(indices, value);
+ set(indices, value);
}
/**
@@ -99,19 +99,84 @@ public final class MDDoubleArray extends MDArray<Double>
/**
* Returns the value of array at the position defined by <var>indices</var>.
*/
- public double getValue(int[] indices)
+ public double get(int[] indices)
{
return flattenedArray[computeIndex(indices)];
}
+ /**
+ * Returns the value of a one-dimensional array at the position defined by <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public double get(int index)
+ {
+ return flattenedArray[index];
+ }
+
+ /**
+ * Returns the value of a two-dimensional array at the position defined by <var>indexX</var> and
+ * <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public double get(int indexX, int indexY)
+ {
+ return flattenedArray[computeIndex(indexX, indexY)];
+ }
+
+ /**
+ * Returns the value of a three-dimensional array at the position defined by <var>indexX</var>,
+ * <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public double get(int indexX, int indexY, int indexZ)
+ {
+ return flattenedArray[computeIndex(indexX, indexY, indexZ)];
+ }
+
/**
* Sets the <var>value</var> of array at the position defined by <var>indices</var>.
*/
- public void setValue(int[] indices, double value)
+ public void set(int[] indices, double value)
{
flattenedArray[computeIndex(indices)] = value;
}
+ /**
+ * Sets the <var>value</var> of a one-dimension array at the position defined by
+ * <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public void set(int index, double value)
+ {
+ flattenedArray[index] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a two-dimensional array at the position defined by
+ * <var>indexX</var> and <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, double value)
+ {
+ flattenedArray[computeIndex(indexX, indexY)] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a three-dimensional array at the position defined by
+ * <var>indexX</var>, <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int indexZ, double value)
+ {
+ flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java
index 4bf9c845197..a6f310fc8dd 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java
@@ -78,13 +78,13 @@ public final class MDFloatArray extends MDArray<Float>
@Override
public Float getAsObject(int[] indices)
{
- return getValue(indices);
+ return get(indices);
}
@Override
public void setToObject(int[] indices, Float value)
{
- setValue(indices, value);
+ set(indices, value);
}
/**
@@ -99,19 +99,84 @@ public final class MDFloatArray extends MDArray<Float>
/**
* Returns the value of array at the position defined by <var>indices</var>.
*/
- public float getValue(int[] indices)
+ public float get(int[] indices)
{
return flattenedArray[computeIndex(indices)];
}
+ /**
+ * Returns the value of a one-dimensional array at the position defined by <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public float get(int index)
+ {
+ return flattenedArray[index];
+ }
+
+ /**
+ * Returns the value of a two-dimensional array at the position defined by <var>indexX</var> and
+ * <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public float get(int indexX, int indexY)
+ {
+ return flattenedArray[computeIndex(indexX, indexY)];
+ }
+
+ /**
+ * Returns the value of a three-dimensional array at the position defined by <var>indexX</var>,
+ * <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public float get(int indexX, int indexY, int indexZ)
+ {
+ return flattenedArray[computeIndex(indexX, indexY, indexZ)];
+ }
+
/**
* Sets the <var>value</var> of array at the position defined by <var>indices</var>.
*/
- public void setValue(int[] indices, float value)
+ public void set(int[] indices, float value)
{
flattenedArray[computeIndex(indices)] = value;
}
+ /**
+ * Sets the <var>value</var> of a one-dimension array at the position defined by
+ * <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public void set(int index, float value)
+ {
+ flattenedArray[index] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a two-dimensional array at the position defined by
+ * <var>indexX</var> and <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, float value)
+ {
+ flattenedArray[computeIndex(indexX, indexY)] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a three-dimensional array at the position defined by
+ * <var>indexX</var>, <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int indexZ, float value)
+ {
+ flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java
index 21fcc658284..802355a671c 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java
@@ -78,13 +78,13 @@ public final class MDIntArray extends MDArray<Integer>
@Override
public Integer getAsObject(int[] indices)
{
- return getValue(indices);
+ return get(indices);
}
@Override
public void setToObject(int[] indices, Integer value)
{
- setValue(indices, value);
+ set(indices, value);
}
/**
@@ -99,19 +99,84 @@ public final class MDIntArray extends MDArray<Integer>
/**
* Returns the value of array at the position defined by <var>indices</var>.
*/
- public int getValue(int[] indices)
+ public int get(int[] indices)
{
return flattenedArray[computeIndex(indices)];
}
+ /**
+ * Returns the value of a one-dimensional array at the position defined by <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public int get(int index)
+ {
+ return flattenedArray[index];
+ }
+
+ /**
+ * Returns the value of a two-dimensional array at the position defined by <var>indexX</var> and
+ * <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public int get(int indexX, int indexY)
+ {
+ return flattenedArray[computeIndex(indexX, indexY)];
+ }
+
+ /**
+ * Returns the value of a three-dimensional array at the position defined by <var>indexX</var>,
+ * <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public int get(int indexX, int indexY, int indexZ)
+ {
+ return flattenedArray[computeIndex(indexX, indexY, indexZ)];
+ }
+
/**
* Sets the <var>value</var> of array at the position defined by <var>indices</var>.
*/
- public void setValue(int[] indices, int value)
+ public void set(int[] indices, int value)
{
flattenedArray[computeIndex(indices)] = value;
}
+ /**
+ * Sets the <var>value</var> of a one-dimension array at the position defined by
+ * <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public void set(int index, int value)
+ {
+ flattenedArray[index] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a two-dimensional array at the position defined by
+ * <var>indexX</var> and <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int value)
+ {
+ flattenedArray[computeIndex(indexX, indexY)] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a three-dimensional array at the position defined by
+ * <var>indexX</var>, <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int indexZ, int value)
+ {
+ flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java
index 7ac5c777294..35b6f8b5cb5 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java
@@ -78,13 +78,13 @@ public final class MDLongArray extends MDArray<Long>
@Override
public Long getAsObject(int[] indices)
{
- return getValue(indices);
+ return get(indices);
}
@Override
public void setToObject(int[] indices, Long value)
{
- setValue(indices, value);
+ set(indices, value);
}
/**
@@ -99,23 +99,88 @@ public final class MDLongArray extends MDArray<Long>
/**
* Returns the value of array at the position defined by <var>indices</var>.
*/
- public long getValue(int[] indices)
+ public long get(int[] indices)
{
return flattenedArray[computeIndex(indices)];
}
-
+
+ /**
+ * Returns the value of a one-dimensional array at the position defined by <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public long get(int index)
+ {
+ return flattenedArray[index];
+ }
+
+ /**
+ * Returns the value of a two-dimensional array at the position defined by <var>indexX</var> and
+ * <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public long get(int indexX, int indexY)
+ {
+ return flattenedArray[computeIndex(indexX, indexY)];
+ }
+
+ /**
+ * Returns the value of a three-dimensional array at the position defined by <var>indexX</var>,
+ * <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public long get(int indexX, int indexY, int indexZ)
+ {
+ return flattenedArray[computeIndex(indexX, indexY, indexZ)];
+ }
+
/**
* Sets the <var>value</var> of array at the position defined by <var>indices</var>.
*/
- public void setValue(int[] indices, long value)
+ public void set(int[] indices, long value)
{
flattenedArray[computeIndex(indices)] = value;
}
+ /**
+ * Sets the <var>value</var> of a one-dimension array at the position defined by
+ * <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public void set(int index, long value)
+ {
+ flattenedArray[index] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a two-dimensional array at the position defined by
+ * <var>indexX</var> and <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, long value)
+ {
+ flattenedArray[computeIndex(indexX, indexY)] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a three-dimensional array at the position defined by
+ * <var>indexX</var>, <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int indexZ, long value)
+ {
+ flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
+ }
+
//
// Object
//
-
+
@Override
public int hashCode()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java
index 6504bf9ce12..852b0c89992 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java
@@ -78,13 +78,13 @@ public final class MDShortArray extends MDArray<Short>
@Override
public Short getAsObject(int[] indices)
{
- return getValue(indices);
+ return get(indices);
}
@Override
public void setToObject(int[] indices, Short value)
{
- setValue(indices, value);
+ set(indices, value);
}
/**
@@ -99,19 +99,84 @@ public final class MDShortArray extends MDArray<Short>
/**
* Returns the value of array at the position defined by <var>indices</var>.
*/
- public short getValue(int[] indices)
+ public short get(int[] indices)
{
return flattenedArray[computeIndex(indices)];
}
+ /**
+ * Returns the value of a one-dimensional array at the position defined by <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public short get(int index)
+ {
+ return flattenedArray[index];
+ }
+
+ /**
+ * Returns the value of a two-dimensional array at the position defined by <var>indexX</var> and
+ * <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public short get(int indexX, int indexY)
+ {
+ return flattenedArray[computeIndex(indexX, indexY)];
+ }
+
+ /**
+ * Returns the value of a three-dimensional array at the position defined by <var>indexX</var>,
+ * <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public short get(int indexX, int indexY, int indexZ)
+ {
+ return flattenedArray[computeIndex(indexX, indexY, indexZ)];
+ }
+
/**
* Sets the <var>value</var> of array at the position defined by <var>indices</var>.
*/
- public void setValue(int[] indices, short value)
+ public void set(int[] indices, short value)
{
flattenedArray[computeIndex(indices)] = value;
}
+ /**
+ * Sets the <var>value</var> of a one-dimension array at the position defined by
+ * <var>index</var>.
+ * <p>
+ * <b>Do not call for arrays other than one-dimensional!</b>
+ */
+ public void set(int index, short value)
+ {
+ flattenedArray[index] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a two-dimensional array at the position defined by
+ * <var>indexX</var> and <var>indexY</var>.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, short value)
+ {
+ flattenedArray[computeIndex(indexX, indexY)] = value;
+ }
+
+ /**
+ * Sets the <var>value</var> of a three-dimensional array at the position defined by
+ * <var>indexX</var>, <var>indexY</var> and <var>indexZ</var>.
+ * <p>
+ * <b>Do not call for arrays other than three-dimensional!</b>
+ */
+ public void set(int indexX, int indexY, int indexZ, short value)
+ {
+ flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
+ }
+
//
// Object
//
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java b/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java
index bf4d685fec8..663d51c9b66 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java
@@ -35,7 +35,6 @@ public class MDArraytest
protected TestMDArray(int[] shape)
{
super(shape);
- // TODO Auto-generated constructor stub
}
@Override
@@ -89,4 +88,28 @@ public class MDArraytest
array = new TestMDArray(new int[] { 2, 7, 3 });
assertEquals(3 * 7 * 1 + 3 * 2 + 3, array.computeIndex(new int[] { 1, 2, 3 }));
}
+
+ @Test
+ public void testComputeIndex2D()
+ {
+ TestMDArray array;
+ array = new TestMDArray(new int[] { 100, 10 });
+ assertEquals(array.computeIndex(new int[] { 5, 8, }), array.computeIndex(5, 8));
+ assertEquals(array.computeIndex(new int[] { 9, 1, }), array.computeIndex(9, 1));
+ array = new TestMDArray(new int[] { 101, 11 });
+ assertEquals(array.computeIndex(new int[] { 5, 8, }), array.computeIndex(5, 8));
+ assertEquals(array.computeIndex(new int[] { 9, 1, }), array.computeIndex(9, 1));
+ }
+
+ @Test
+ public void testComputeIndex3()
+ {
+ TestMDArray array;
+ array = new TestMDArray(new int[] { 100, 10, 17 });
+ assertEquals(array.computeIndex(new int[] { 5, 8, 16 }), array.computeIndex(5, 8, 16));
+ assertEquals(array.computeIndex(new int[] { 9, 1, 5 }), array.computeIndex(9, 1, 5));
+ array = new TestMDArray(new int[] { 101, 11, 3 });
+ assertEquals(array.computeIndex(new int[] { 5, 8, 0 }), array.computeIndex(5, 8, 0));
+ assertEquals(array.computeIndex(new int[] { 9, 1, 2 }), array.computeIndex(9, 1, 2));
+ }
}
--
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