diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
index 65f47010f9653f9337b4cb0c1316454349b6bf33..6986d7a493070db902944d2bfefe2a2e33942e7e 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
@@ -40,6 +40,8 @@ public abstract class MDAbstractArray<T> implements Serializable
protected int hyperRowLength;
protected int capacityHyperRows;
+
+ protected int size;
protected MDAbstractArray(int[] dimensions, int arrayLength, int capacityHyperRows)
{
@@ -50,6 +52,7 @@ public abstract class MDAbstractArray<T> implements Serializable
if (hyperRowLength == 0)
{
this.capacityHyperRows = 0;
+ this.size = 0;
} else
{
if (arrayLength % hyperRowLength != 0)
@@ -60,6 +63,7 @@ public abstract class MDAbstractArray<T> implements Serializable
this.capacityHyperRows =
(capacityHyperRows > 0) ? capacityHyperRows : Math.max(dimensions[0], arrayLength
/ hyperRowLength);
+ this.size = dimensions[0] * hyperRowLength;
}
}
@@ -116,7 +120,10 @@ public abstract class MDAbstractArray<T> implements Serializable
/**
* Returns the number of elements in the array.
*/
- public abstract int size();
+ public int size()
+ {
+ return size;
+ }
/**
* Return an object which has the same value as the element of the array specified by
@@ -144,25 +151,38 @@ public abstract class MDAbstractArray<T> implements Serializable
protected abstract void adaptCapacityHyperRows();
+ /**
+ * Returns the capacity of elements in the array.
+ */
+ public abstract int capacity();
+
/**
* Increase the number of hyper-rows by <var>count</var>. Doubles the capacity if needed.
+ *
+ * @return The new number of rows.
*/
- public void incNumberOfHyperRows(int count)
+ public int incNumberOfHyperRows(int count)
{
dimensions[0] += count;
if (dimensions[0] > capacityHyperRows)
{
- capacityHyperRows *= 2;
+ capacityHyperRows = Math.max(capacityHyperRows * 2, dimensions[0]);
adaptCapacityHyperRows();
}
+ size += count * hyperRowLength;
+ return dimensions[0];
}
/**
* Decrease the number of hyper-rows by <var>count</var>.
+ *
+ * @return The new number of rows.
*/
- public void decNumberOfHyperRows(int count)
+ public int decNumberOfHyperRows(int count)
{
dimensions[0] -= count;
+ size -= count * hyperRowLength;
+ return dimensions[0];
}
/**
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java
index 5daa2fb8d91ebdfa2a2d89fd7c31da8b2276d240..861acd77b9d0fe8123e47db6545abb4c77d97a8b 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java
@@ -132,7 +132,7 @@ public class MDArray<T> extends MDAbstractArray<T>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -331,6 +331,10 @@ public class MDArray<T> extends MDAbstractArray<T>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
index 0a74be19af6573cafed024f71c22b62fb1e0c3e6..b724d6fce008588314ea47c575ac7284f6d26dc2 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
@@ -145,8 +145,8 @@ public final class MDByteArray extends MDAbstractArray<Byte>
final int sizeX = dimensions[0];
final int sizeY = dimensions[1];
- int size = getLength(dimensions, 0);
- this.flattenedArray = new byte[size];
+ int length = getLength(dimensions, 0);
+ this.flattenedArray = new byte[length];
for (int i = 0; i < sizeX; ++i)
{
System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
@@ -162,7 +162,7 @@ public final class MDByteArray extends MDAbstractArray<Byte>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -355,6 +355,10 @@ public final class MDByteArray extends MDAbstractArray<Byte>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
index 833f9eeb04a5e636bdba3bfd32dfcfd87d58e59d..40c60fef379f2fbcf967c1f9460c58ecf69813c2 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
@@ -145,8 +145,8 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
final int sizeX = dimensions[0];
final int sizeY = dimensions[1];
- int size = getLength(dimensions, 0);
- this.flattenedArray = new double[size];
+ int length = getLength(dimensions, 0);
+ this.flattenedArray = new double[length];
for (int i = 0; i < sizeX; ++i)
{
System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
@@ -162,7 +162,7 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -355,6 +355,10 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
index f7e28dbcf8fc572c0f41d45962901641ea72d684..69e7e076d2f19793ed2cb189b739c7610b6aebc2 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
@@ -145,8 +145,8 @@ public final class MDFloatArray extends MDAbstractArray<Float>
final int sizeX = dimensions[0];
final int sizeY = dimensions[1];
- int size = getLength(dimensions, 0);
- this.flattenedArray = new float[size];
+ int length = getLength(dimensions, 0);
+ this.flattenedArray = new float[length];
for (int i = 0; i < sizeX; ++i)
{
System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
@@ -162,7 +162,7 @@ public final class MDFloatArray extends MDAbstractArray<Float>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -355,6 +355,10 @@ public final class MDFloatArray extends MDAbstractArray<Float>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
index 77cb172a3702bbe74cb7d9780e9f767e4ba5cfce..7fea30fdd8bf69db3a64be1f3ed8ff126aaad8c6 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
@@ -145,8 +145,8 @@ public final class MDIntArray extends MDAbstractArray<Integer>
final int sizeX = dimensions[0];
final int sizeY = dimensions[1];
- int size = getLength(dimensions, 0);
- this.flattenedArray = new int[size];
+ int length = getLength(dimensions, 0);
+ this.flattenedArray = new int[length];
for (int i = 0; i < sizeX; ++i)
{
System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
@@ -162,7 +162,7 @@ public final class MDIntArray extends MDAbstractArray<Integer>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -355,6 +355,10 @@ public final class MDIntArray extends MDAbstractArray<Integer>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
index 0f100293eafc79e6eb59d26a9d076105f5caa625..085caffb57dc345ffbe1f6b966126b6efa52bd36 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
@@ -145,8 +145,8 @@ public final class MDLongArray extends MDAbstractArray<Long>
final int sizeX = dimensions[0];
final int sizeY = dimensions[1];
- int size = getLength(dimensions, 0);
- this.flattenedArray = new long[size];
+ int length = getLength(dimensions, 0);
+ this.flattenedArray = new long[length];
for (int i = 0; i < sizeX; ++i)
{
System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
@@ -162,7 +162,7 @@ public final class MDLongArray extends MDAbstractArray<Long>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -355,6 +355,10 @@ public final class MDLongArray extends MDAbstractArray<Long>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
index d9d36eea28c4d7ec7937015f86021d1a7b615486..122213b07fbfbde952571232a3b9ebc9c1e1b4a1 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
@@ -145,8 +145,8 @@ public final class MDShortArray extends MDAbstractArray<Short>
final int sizeX = dimensions[0];
final int sizeY = dimensions[1];
- int size = getLength(dimensions, 0);
- this.flattenedArray = new short[size];
+ int length = getLength(dimensions, 0);
+ this.flattenedArray = new short[length];
for (int i = 0; i < sizeX; ++i)
{
System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
@@ -162,7 +162,7 @@ public final class MDShortArray extends MDAbstractArray<Short>
}
@Override
- public int size()
+ public int capacity()
{
return flattenedArray.length;
}
@@ -355,6 +355,10 @@ public final class MDShortArray extends MDAbstractArray<Short>
{
this.capacityHyperRows = dimensions[0];
}
+ if (size == 0)
+ {
+ this.size = hyperRowLength * dimensions[0];
+ }
}
}
diff --git a/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java b/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
index 6bc4d870959e6288bc25f46e9b6432a5645ba02d..a20b743dd87687bab4aed3c1eca05818f058b3cf 100644
--- a/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
+++ b/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
@@ -61,6 +61,12 @@ public class MDArrayTests
return 0;
}
+ @Override
+ public int capacity()
+ {
+ return 0;
+ }
+
@Override
public Object getAsFlatArray()
{
@@ -229,6 +235,20 @@ public class MDArrayTests
assertEquals(8, arr.get(3, 1));
}
+ @Test
+ public void testChangeHyperRowCountIntArrayFromZero()
+ {
+ final MDIntArray arr = new MDIntArray(new int[] { 0 });
+ assertEquals(0, arr.size(0));
+ arr.incNumberOfHyperRows(1);
+ assertEquals(1, arr.size(0));
+ arr.set(17, 0);
+ assertEquals(17, arr.get(0));
+ arr.incNumberOfHyperRows(1);
+ arr.incNumberOfHyperRows(1);
+ assertEquals(3, arr.size());
+ }
+
@Test
public void testChangeHyperRowCountTArray()
{