Author: ruschein
Date: 2010-06-15 14:04:21 -0700 (Tue, 15 Jun 2010)
New Revision: 20546
Added:
cytoscape/trunk/src/cytoscape/util/AbstractScaler.java
cytoscape/trunk/src/cytoscape/util/LinearScaler.java
cytoscape/trunk/src/cytoscape/util/RankScaler.java
cytoscape/trunk/src/cytoscape/util/Scaler.java
cytoscape/trunk/src/cytoscape/util/ScalerFactory.java
cytoscape/trunk/tests/cytoscape/util/LinearScalerTest.java
cytoscape/trunk/tests/cytoscape/util/RankScalerTest.java
cytoscape/trunk/tests/cytoscape/util/ScalerFactoryTest.java
Removed:
cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java
cytoscape/trunk/tests/cytoscape/util/ProbabilityScalerTest.java
Modified:
cytoscape/trunk/src/cytoscape/util/MathUtil.java
Log:
Replaced ProbabilityScaler with a hopefully cleaner Scaler interface and a
ScalerFactory class.
Copied: cytoscape/trunk/src/cytoscape/util/AbstractScaler.java (from rev 20541,
cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java)
===================================================================
--- cytoscape/trunk/src/cytoscape/util/AbstractScaler.java
(rev 0)
+++ cytoscape/trunk/src/cytoscape/util/AbstractScaler.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -0,0 +1,67 @@
+/*
+ File: AbstractScaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.AbstractCollection;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+public abstract class AbstractScaler implements Scaler {
+ public abstract double[] scale(final double values[], final double a,
final double b) throws IllegalArgumentException;
+
+ public final double[] scale(final AbstractCollection<Double> values,
final double a,
+ final double b) throws
IllegalArgumentException
+ {
+ // Convert the collection to an array:
+ final double[] array = new double[values.size()];
+ int i = 0;
+ for (final Double d : values)
+ array[i++] = d;
+
+ return scale(array, a, b);
+ }
+
+ public abstract float[] scale(final float values[], final float a,
final float b) throws IllegalArgumentException;
+
+ public final float[] scale(final AbstractCollection<Float> values,
final float a,
+ final float b) throws
IllegalArgumentException
+ {
+ // Convert the collection to an array:
+ final float[] array = new float[values.size()];
+ int i = 0;
+ for (final Float f : values)
+ array[i++] = f;
+
+ return scale(array, a, b);
+ }
+}
Copied: cytoscape/trunk/src/cytoscape/util/LinearScaler.java (from rev 20541,
cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java)
===================================================================
--- cytoscape/trunk/src/cytoscape/util/LinearScaler.java
(rev 0)
+++ cytoscape/trunk/src/cytoscape/util/LinearScaler.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -0,0 +1,94 @@
+/*
+ File: LinearScaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+class LinearScaler extends AbstractScaler {
+ public double[] scale(final double values[], final double a, final
double b) throws IllegalArgumentException
+ {
+ if (values.length < 2)
+ throw new IllegalArgumentException("need at least 2
values for scaling!");
+ if (a >= b)
+ throw new IllegalArgumentException("bad bounds!");
+
+ double min = Double.POSITIVE_INFINITY;
+ double max = Double.NEGATIVE_INFINITY;
+ for (final double d : values) {
+ if (d < min)
+ min = d;
+ if (d > max)
+ max = d;
+ }
+
+ if (min == max)
+ throw new IllegalArgumentException("input values are
all identical!");
+
+ final double c = (a - b) / (min - max);
+ final double d = a - c * min;
+
+ final double[] scaledValues = new double[values.length];
+ for (int i = 0; i < values.length; ++i)
+ scaledValues[i] = c * values[i] + d;
+
+ return scaledValues;
+ }
+
+ public float[] scale(final float values[], final float a, final float
b) throws IllegalArgumentException
+ {
+ if (values.length < 2)
+ throw new IllegalArgumentException("need at least 2
values for scaling!");
+ if (a >= b)
+ throw new IllegalArgumentException("bad bounds!");
+
+ float min = Float.POSITIVE_INFINITY;
+ float max = Float.NEGATIVE_INFINITY;
+ for (final float d : values) {
+ if (d < min)
+ min = d;
+ if (d > max)
+ max = d;
+ }
+
+ if (min == max)
+ throw new IllegalArgumentException("input values are
all identical!");
+
+ final float c = (a - b) / (min - max);
+ final float d = a - c * min;
+
+ final float[] scaledValues = new float[values.length];
+ for (int i = 0; i < values.length; ++i)
+ scaledValues[i] = c * values[i] + d;
+
+ return scaledValues;
+ }
+}
Modified: cytoscape/trunk/src/cytoscape/util/MathUtil.java
===================================================================
--- cytoscape/trunk/src/cytoscape/util/MathUtil.java 2010-06-15 20:15:40 UTC
(rev 20545)
+++ cytoscape/trunk/src/cytoscape/util/MathUtil.java 2010-06-15 21:04:21 UTC
(rev 20546)
@@ -12,6 +12,16 @@
final int BIT_OFFSET = 23;
return (bits >> BIT_OFFSET) - BIAS;
}
+ /**
+ * @returns the unbiased exponent of a double-precision IEEE floating
point number
+ */
+ static public long getExponent(final double f) {
+ final long EXPONENT_MASK = 0x7FFFF00000000000L;
+ final long bits = Double.doubleToLongBits(f) & EXPONENT_MASK;
+ final int BIAS = 1023;
+ final int BIT_OFFSET = 52;
+ return (bits >> BIT_OFFSET) - BIAS;
+ }
static public boolean almostEqual(final float x1, final float x2) {
if (x1 == x2)
@@ -31,4 +41,23 @@
else
return Math.abs(x1 - x2) / Math.abs(x2) < 1.0e-6f;
}
+
+ static public boolean almostEqual(final double x1, final double x2) {
+ if (x1 == x2)
+ return true;
+
+ if (Math.signum(x1) != Math.signum(x2))
+ return false;
+
+ if (MathUtil.getExponent(x1) != MathUtil.getExponent(x2))
+ return false;
+
+ final double absX1 = Math.abs(x1);
+ final double absX2 = Math.abs(x2);
+
+ if (x1 != 0.0)
+ return Math.abs(x1 - x2) / Math.abs(x1) < 1.0e-10;
+ else
+ return Math.abs(x1 - x2) / Math.abs(x2) < 1.0e-10;
+ }
}
\ No newline at end of file
Deleted: cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java
===================================================================
--- cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java 2010-06-15
20:15:40 UTC (rev 20545)
+++ cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -1,110 +0,0 @@
-package cytoscape.util;
-
-
-import java.util.Arrays;
-
-
-/**
- * This class exists to support scaling of numeric values to the range
(0.5,1.0).
- * @author ruschein
- */
-public class ProbabilityScaler {
- private static float min, max;
-
- public static float[] scale(final float[] values,
- final ScalingMethod scalingMethod,
- final StringBuilder errorMessage)
- {
- errorMessage.setLength(0);
-
- // Sanity check:
- if (values.length < 2) {
- errorMessage.append("the values cannot be scaled since
there are/is only "
- + values.length + " of them!");
- return null;
- }
-
- if (scalingMethod == ScalingMethod.NONE)
- return values;
-
- findMinAndMax(values);
- if (min == max) {
- errorMessage.append("cannot scale any values because
they are all identical!");
- return null;
- }
-
-
- switch (scalingMethod) {
- case LINEAR_LOWER:
- return scaleLinearLower(values, errorMessage);
- case LINEAR_UPPER:
- return scaleLinearUpper(values, errorMessage);
- case RANK_LOWER:
- return scaleRankLower(values, errorMessage);
- case RANK_UPPER:
- return scaleRankUpper(values, errorMessage);
- default:
- throw new IllegalStateException("unknown scaling
method: " + scalingMethod);
- }
- }
-
- private static float[] scaleLinearLower(final float[] values, final
StringBuilder errorMessage)
- {
- final float eps = 0.5f / (values.length + 1);
-
- // We map the values from (max,min) to (0.5+eps,1.0-eps)
- final float x0 = max;
- final float x1 = min;
- final float a = (0.5f - 2.0f * eps) / (x1 - x0);
- final float b = 1.0f -eps - (0.5f - 2.0f * eps) * x1 / (x1 -
x0);
-
- for (int i = 0; i < values.length; ++i)
- values[i] = a * values[i] + b;
-
- return values;
- }
-
- private static float[] scaleLinearUpper(final float[] values, final
StringBuilder errorMessage)
- {
- final float eps = 0.5f / (values.length + 1);
-
- // We map the values from (min,max) to (0.5+eps,1.0-eps)
- final float x0 = min;
- final float x1 = max;
- final float a = (0.5f - 2.0f * eps) / (x1 - x0);
- final float b = 1.0f - eps - (0.5f - 2.0f * eps) * x1 / (x1 -
x0);
-
- for (int i = 0; i < values.length; ++i)
- values[i] = a * values[i] + b;
-
- return values;
- }
-
- private static float[] scaleRankLower(final float[] values, final
StringBuilder errorMessage)
- {
- float[] scaledValues = QuantileNorm.quantileNorm(values);
- for (int i = 0; i < scaledValues.length; ++i)
- scaledValues[i] = 0.5f + scaledValues[i] / 2.0f;
- return scaledValues;
- }
-
- private static float[] scaleRankUpper(final float[] values, final
StringBuilder errorMessage)
- {
- for (int i = 0; i < values.length; ++i)
- values[i] = -values[i];
- float[] scaledValues = QuantileNorm.quantileNorm(values);
- for (int i = 0; i < scaledValues.length; ++i)
- scaledValues[i] = 0.5f + scaledValues[i] / 2.0f;
- return scaledValues;
- }
-
- private static void findMinAndMax(final float[] values) {
- min = max = values[0];
- for (final float f : values) {
- if (f < min)
- min = f;
- else if (f > max)
- max = f;
- }
- }
-}
\ No newline at end of file
Copied: cytoscape/trunk/src/cytoscape/util/RankScaler.java (from rev 20541,
cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java)
===================================================================
--- cytoscape/trunk/src/cytoscape/util/RankScaler.java
(rev 0)
+++ cytoscape/trunk/src/cytoscape/util/RankScaler.java 2010-06-15 21:04:21 UTC
(rev 20546)
@@ -0,0 +1,112 @@
+/*
+ File: RankScaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Arrays;
+import java.util.HashMap;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+class RankScaler extends AbstractScaler {
+ public double[] scale(final double values[], final double a, final
double b) throws IllegalArgumentException
+ {
+ if (values.length < 2)
+ throw new IllegalArgumentException("need at least 2
values for scaling!");
+ if (a >= b)
+ throw new IllegalArgumentException("bad bounds!");
+
+ final double sortedValues[] = values.clone();
+ Arrays.sort(sortedValues);
+
+ final HashMap<Double, Double> origValueToRankValueMap = new
HashMap<Double, Double>();
+ final double stepSize = (b - a) / values.length;
+ double currentValue = sortedValues[0];
+ double sum = stepSize / 2.0;
+ double count = 1.0;
+ for (int i = 1; i < values.length; ++i) {
+ final double currentRankValue = stepSize * (0.5 + i);
+ if (sortedValues[i] == currentValue) {
+ ++count;
+ sum += currentRankValue;
+ } else {
+ origValueToRankValueMap.put(currentValue, sum /
count);
+ currentValue = sortedValues[i];
+ sum = currentRankValue;
+ count = 1.0;
+ }
+ }
+ origValueToRankValueMap.put(sortedValues[values.length - 1],
sum / count);
+
+ final double[] scaledValues = new double[values.length];
+ for (int i = 0; i < values.length; ++i)
+ scaledValues[i] =
origValueToRankValueMap.get(values[i]);
+
+ return scaledValues;
+ }
+
+ public float[] scale(final float values[], final float a, final float
b) throws IllegalArgumentException
+ {
+ if (values.length < 2)
+ throw new IllegalArgumentException("need at least 2
values for scaling!");
+ if (a >= b)
+ throw new IllegalArgumentException("bad bounds!");
+
+ final float sortedValues[] = values.clone();
+ Arrays.sort(sortedValues);
+
+ final HashMap<Float, Float> origValueToRankValueMap = new
HashMap<Float, Float>();
+ final float stepSize = (b - a) / values.length;
+ float currentValue = sortedValues[0];
+ float sum = stepSize / 2.0f;
+ float count = 1.0f;
+ for (int i = 1; i < values.length; ++i) {
+ final float currentRankValue = stepSize * (0.5f + i);
+ if (sortedValues[i] == currentValue) {
+ ++count;
+ sum += currentRankValue;
+ } else {
+ origValueToRankValueMap.put(currentValue, sum /
count);
+ currentValue = sortedValues[i];
+ sum = currentRankValue;
+ count = 1.0f;
+ }
+ }
+ origValueToRankValueMap.put(sortedValues[values.length - 1],
sum / count);
+
+ final float[] scaledValues = new float[values.length];
+ for (int i = 0; i < values.length; ++i)
+ scaledValues[i] =
origValueToRankValueMap.get(values[i]);
+
+ return scaledValues;
+ }
+}
Copied: cytoscape/trunk/src/cytoscape/util/Scaler.java (from rev 20541,
cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java)
===================================================================
--- cytoscape/trunk/src/cytoscape/util/Scaler.java
(rev 0)
+++ cytoscape/trunk/src/cytoscape/util/Scaler.java 2010-06-15 21:04:21 UTC
(rev 20546)
@@ -0,0 +1,48 @@
+/*
+ File: Scaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.AbstractCollection;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+interface Scaler {
+ double[] scale(final double values[], final double a, final double b)
throws IllegalArgumentException;
+ double[] scale(final AbstractCollection<Double> values, final double a,
final double b) throws IllegalArgumentException;
+
+ float[] scale(final float values[], final float a, final float b)
throws IllegalArgumentException;
+ float[] scale(final AbstractCollection<Float> values, final float a,
final float b) throws IllegalArgumentException;
+}
+
+
+
Copied: cytoscape/trunk/src/cytoscape/util/ScalerFactory.java (from rev 20541,
cytoscape/trunk/src/cytoscape/util/ProbabilityScaler.java)
===================================================================
--- cytoscape/trunk/src/cytoscape/util/ScalerFactory.java
(rev 0)
+++ cytoscape/trunk/src/cytoscape/util/ScalerFactory.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -0,0 +1,72 @@
+/*
+ File: ScalerFactory.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Map;
+import java.util.TreeMap;
+
+
+public class ScalerFactory {
+ private static Map<String, Scaler> typeToScalerMap = null;
+
+ /**
+ * @return one of the registered Scaler types. Preregistered are
"linear" and "rank".
+ */
+ public static synchronized Scaler getScaler(final String type) throws
IllegalArgumentException {
+ if (typeToScalerMap == null)
+ init();
+
+ final Scaler scaler = typeToScalerMap.get(type);
+ if (scaler == null)
+ throw new IllegalArgumentException("unknown type \"" +
type + "\"!");
+
+ return scaler;
+ }
+
+ public static synchronized void registerScaler(final String type, final
Scaler newScaler) {
+ if (typeToScalerMap == null)
+ init();
+
+ if (typeToScalerMap.containsKey(type))
+ throw new IllegalArgumentException("trying to register
a duplicate type \"" + type + "\"!");
+
+ typeToScalerMap.put(type, newScaler);
+ }
+
+ private static void init() {
+ if (typeToScalerMap != null)
+ throw new IllegalStateException("already initialised!");
+ typeToScalerMap = new TreeMap<String, Scaler>();
+
+ typeToScalerMap.put("linear", new LinearScaler());
+ typeToScalerMap.put("rank", new RankScaler());
+ }
+}
Copied: cytoscape/trunk/tests/cytoscape/util/LinearScalerTest.java (from rev
20541, cytoscape/trunk/tests/cytoscape/util/MathUtilTest.java)
===================================================================
--- cytoscape/trunk/tests/cytoscape/util/LinearScalerTest.java
(rev 0)
+++ cytoscape/trunk/tests/cytoscape/util/LinearScalerTest.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -0,0 +1,26 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class LinearScalerTest extends TestCase {
+ public void test() {
+ final Scaler linearScaler = new LinearScaler();
+ final double[] unscaledValues = new double[] { 3.0, 10.2, 5.4,
3.0, 7.7 };
+ final double MIN = 0.0;
+ final double MAX = 1.0;
+ final double[] scaledValues =
linearScaler.scale(unscaledValues, MIN, MAX);
+ boolean foundMin = false;
+ boolean foundMax = false;
+ for (final double d : scaledValues) {
+ if (MathUtil.almostEqual(MIN, d))
+ foundMin = true;
+ if (MathUtil.almostEqual(MAX, d))
+ foundMax = true;
+ assertTrue(d >= MIN && d <= MAX);
+ }
+ assertTrue(foundMin);
+ assertTrue(foundMax);
+ }
+}
\ No newline at end of file
Deleted: cytoscape/trunk/tests/cytoscape/util/ProbabilityScalerTest.java
===================================================================
--- cytoscape/trunk/tests/cytoscape/util/ProbabilityScalerTest.java
2010-06-15 20:15:40 UTC (rev 20545)
+++ cytoscape/trunk/tests/cytoscape/util/ProbabilityScalerTest.java
2010-06-15 21:04:21 UTC (rev 20546)
@@ -1,108 +0,0 @@
-package cytoscape.util;
-
-
-import junit.framework.*;
-
-
-public class ProbabilityScalerTest extends TestCase {
- public void testNoRanking() {
- final float[] distinctValues = getDistinctValues();
- final float[] unscaledValues1 = (float[])distinctValues.clone();
-
- final StringBuilder errorMessage = new StringBuilder();
- final float[] scaledValues1 =
ProbabilityScaler.scale(distinctValues, ScalingMethod.NONE,
-
errorMessage);
-
- for (int i = 0; i < unscaledValues1.length; ++i)
- assertEquals(unscaledValues1[i], scaledValues1[i]);
-
- final float[] valuesWithDups = getDistinctValues();
- final float[] unscaledValues2 = (float[])valuesWithDups.clone();
-
- final float[] scaledValues2 =
ProbabilityScaler.scale(valuesWithDups, ScalingMethod.NONE,
-
errorMessage);
-
- for (int i = 0; i < unscaledValues2.length; ++i)
- assertEquals(unscaledValues2[i], scaledValues2[i]);
- }
-
- public void testLinearUpper() {
- final float[] distinctValues = getDistinctValues();
-
- final StringBuilder errorMessage = new StringBuilder();
- final float [] scaledValues1 =
ProbabilityScaler.scale(distinctValues, ScalingMethod.LINEAR_UPPER,
-
errorMessage);
- final float[] expectedValues1 = new float[] { 0.5999999f,
0.6449999f, 0.74999994f, 0.9f };
- for (int i = 0; i < expectedValues1.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues1[i],
scaledValues1[i]));
-
- final float[] valuesWithDups = getValuesWithDups();
- final float [] scaledValues2 =
ProbabilityScaler.scale(valuesWithDups, ScalingMethod.LINEAR_UPPER,
-
errorMessage);
- final float[] expectedValues2 = new float[] { 0.5625f,
0.61875f, 0.61875f, 0.61875f, 0.75f, 0.9375f, 0.9375f };
- for (int i = 0; i < expectedValues2.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues2[i],
scaledValues2[i]));
- }
-
- public void testLinearLower() {
- final float[] distinctValues = getDistinctValues();
-
- final StringBuilder errorMessage = new StringBuilder();
- final float [] scaledValues1 =
ProbabilityScaler.scale(distinctValues, ScalingMethod.LINEAR_LOWER,
-
errorMessage);
- final float[] expectedValues1 = new float[] { 0.9f,
0.85499996f, 0.74999994f, 0.5999999f };
- for (int i = 0; i < expectedValues1.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues1[i],
scaledValues1[i]));
-
- final float[] valuesWithDups = getValuesWithDups();
- final float [] scaledValues2 =
ProbabilityScaler.scale(valuesWithDups, ScalingMethod.LINEAR_LOWER,
-
errorMessage);
- final float[] expectedValues2 = new float[] { 0.9375f,
0.88125f, 0.88125f, 0.88125f, 0.75f, 0.5625f, 0.5625f };
- for (int i = 0; i < expectedValues2.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues2[i],
scaledValues2[i]));
- }
-
- public void testRankUpper() {
- final float[] distinctValues = getDistinctValues();
-
- final StringBuilder errorMessage = new StringBuilder();
- final float [] scaledValues1 =
ProbabilityScaler.scale(distinctValues, ScalingMethod.RANK_UPPER,
-
errorMessage);
- final float[] expectedValues1 = new float[] { 0.9375f, 0.8125f,
0.6875f, 0.5625f };
- for (int i = 0; i < expectedValues1.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues1[i],
scaledValues1[i]));
-
- final float[] valuesWithDups = getValuesWithDups();
- final float [] scaledValues2 =
ProbabilityScaler.scale(valuesWithDups, ScalingMethod.RANK_UPPER,
-
errorMessage);
- final float[] expectedValues2 = new float[] { 0.96428573f,
0.82142854f, 0.82142854f, 0.82142854f, 0.67857146f, 0.5714286f, 0.5714286f };
- for (int i = 0; i < expectedValues2.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues2[i],
scaledValues2[i]));
- }
-
- public void testRankLower() {
- final float[] distinctValues = getDistinctValues();
-
- final StringBuilder errorMessage = new StringBuilder();
- final float [] scaledValues1 =
ProbabilityScaler.scale(distinctValues, ScalingMethod.RANK_LOWER,
-
errorMessage);
- final float[] expectedValues1 = new float[] { 0.5625f, 0.6875f,
0.8125f, 0.9375f };
- for (int i = 0; i < expectedValues1.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues1[i],
scaledValues1[i]));
-
- final float[] valuesWithDups = getValuesWithDups();
- final float [] scaledValues2 =
ProbabilityScaler.scale(valuesWithDups, ScalingMethod.RANK_LOWER,
-
errorMessage);
- final float[] expectedValues2 = new float[] { 0.53571427f,
0.67857146f, 0.67857146f, 0.67857146f, 0.82142854f, 0.92857146f };
- for (int i = 0; i < expectedValues2.length; ++i)
- assertTrue(MathUtil.almostEqual(expectedValues2[i],
scaledValues2[i]));
- }
-
- static private float[] getDistinctValues() {
- return new float[] { 0.2f, 0.5f, 1.2f, 2.2f };
- }
-
- static private float[] getValuesWithDups() {
- return new float[] { 0.2f, 0.5f, 0.5f, 0.5f, 1.2f, 2.2f, 2.2f };
- }
-}
Copied: cytoscape/trunk/tests/cytoscape/util/RankScalerTest.java (from rev
20541, cytoscape/trunk/tests/cytoscape/util/MathUtilTest.java)
===================================================================
--- cytoscape/trunk/tests/cytoscape/util/RankScalerTest.java
(rev 0)
+++ cytoscape/trunk/tests/cytoscape/util/RankScalerTest.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -0,0 +1,26 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class RankScalerTest extends TestCase {
+ public void test() {
+ final Scaler linearScaler = new RankScaler();
+ final double[] unscaledValues = new double[] { 3.0, 10.2, 5.4,
3.0, 7.7 };
+ final double MIN = 0.0;
+ final double MAX = 1.0;
+ final double[] scaledValues =
linearScaler.scale(unscaledValues, MIN, MAX);
+ boolean foundMin = false;
+ boolean foundMax = false;
+ for (final double d : scaledValues) {
+ if (MathUtil.almostEqual(MIN, d))
+ foundMin = true;
+ if (MathUtil.almostEqual(MAX, d))
+ foundMax = true;
+ assertTrue(d >= MIN && d <= MAX);
+ }
+ assertFalse(foundMin);
+ assertFalse(foundMax);
+ }
+}
\ No newline at end of file
Copied: cytoscape/trunk/tests/cytoscape/util/ScalerFactoryTest.java (from rev
20541, cytoscape/trunk/tests/cytoscape/util/MathUtilTest.java)
===================================================================
--- cytoscape/trunk/tests/cytoscape/util/ScalerFactoryTest.java
(rev 0)
+++ cytoscape/trunk/tests/cytoscape/util/ScalerFactoryTest.java 2010-06-15
21:04:21 UTC (rev 20546)
@@ -0,0 +1,24 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class ScalerFactoryTest extends TestCase {
+ public void testGetKnownScaler() {
+ final Scaler linearScaler = ScalerFactory.getScaler("linear");
+ assertTrue(linearScaler instanceof LinearScaler);
+
+ final Scaler rankScaler = ScalerFactory.getScaler("rank");
+ assertTrue(rankScaler instanceof RankScaler);
+ }
+
+ public void testGetUnknownScaler() {
+ try {
+ final Scaler scaler = ScalerFactory.getScaler("random
junk!#$");
+ fail();
+ } catch (final IllegalArgumentException e) {
+ assertTrue(true);
+ }
+ }
+}
\ No newline at end of file
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