Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/KernelQMatrix.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/KernelQMatrix.java (revision 101)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/KernelQMatrix.java (revision 149)
@@ -3,4 +3,5 @@
import edu.berkeley.compbio.jlibsvm.SolutionVector;
import edu.berkeley.compbio.jlibsvm.kernel.KernelFunction;
+import org.jetbrains.annotations.NotNull;
import java.util.Arrays;
@@ -22,5 +23,5 @@
// --------------------------- CONSTRUCTORS ---------------------------
- KernelQMatrix(KernelFunction kernel, int numExamples, int cacheRows)
+ KernelQMatrix(@NotNull KernelFunction
kernel, int numExamples, int cacheRows)
{
this.kernel = kernel;
@@ -134,7 +135,7 @@
{
return "QMatrix hits = " + hits + ", misses = " + misses + ", widemisses = " + widemisses
- + ", diagonalhits = " + diagonalhits + ", diagonalmisses = " + diagonalmisses + ", rate = "
- + (float) (hits + diagonalhits) / (float) (hits + diagonalhits + misses + widemisses
- + diagonalmisses) + ", size = " + data.length;
+ + ", diagonalhits = " + diagonalhits + ", diagonalmisses = " + diagonalmisses + ", rate = "
+ + (float) (hits + diagonalhits) / (float) (hits + diagonalhits + misses + widemisses
+ + diagonalmisses) + ", size = " + data.length;
}
Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/BasicKernelQMatrix.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/BasicKernelQMatrix.java (revision 69)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/BasicKernelQMatrix.java (revision 149)
@@ -3,4 +3,5 @@
import edu.berkeley.compbio.jlibsvm.SolutionVector;
import edu.berkeley.compbio.jlibsvm.kernel.KernelFunction;
+import org.jetbrains.annotations.NotNull;
/**
@@ -12,5 +13,5 @@
// --------------------------- CONSTRUCTORS ---------------------------
- public BasicKernelQMatrix(KernelFunction
kernel, int numExamples, int maxCachedRank)
+ public BasicKernelQMatrix(@NotNull KernelFunction
kernel, int numExamples, int maxCachedRank)
{
super(kernel, numExamples, maxCachedRank);
Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/BooleanInvertingKernelQMatrix.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/BooleanInvertingKernelQMatrix.java (revision 69)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/qmatrix/BooleanInvertingKernelQMatrix.java (revision 149)
@@ -3,4 +3,5 @@
import edu.berkeley.compbio.jlibsvm.SolutionVector;
import edu.berkeley.compbio.jlibsvm.kernel.KernelFunction;
+import org.jetbrains.annotations.NotNull;
/**
@@ -12,5 +13,5 @@
// --------------------------- CONSTRUCTORS ---------------------------
- public BooleanInvertingKernelQMatrix(KernelFunction
kernel, int numExamples, int maxCachedRank)
+ public BooleanInvertingKernelQMatrix(@NotNull KernelFunction
kernel, int numExamples, int maxCachedRank)
{
super(kernel, numExamples, maxCachedRank);
Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/ImmutableSvmParameterGrid.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/ImmutableSvmParameterGrid.java (revision 102)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/ImmutableSvmParameterGrid.java (revision 149)
@@ -41,4 +41,8 @@
{
super(copyFrom);
+
+ //default
+ Cset = new HashSet();
+ Cset.add(1f);
}
@@ -46,4 +50,9 @@
{
super(copyFrom);
+
+ //default
+ //Cset = new HashSet();
+ //Cset.add(1f);
+
//Cset = copyFrom.Cset;
//kernelSet = copyFrom.kernelSet;
@@ -59,4 +68,14 @@
{
ImmutableSvmParameterPoint.Builder builder = ImmutableSvmParameterPoint.asBuilder(this);
+
+ if (Cset == null || Cset.isEmpty())
+ {
+ throw new SvmException("Can't build a grid with no C values");
+ }
+
+ if (kernelSet == null || kernelSet.isEmpty())
+ {
+ throw new SvmException("Can't build a grid with no kernels");
+ }
if (Cset.size() == 1 && kernelSet.size() == 1)
Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/ImmutableSvmParameterPoint.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/ImmutableSvmParameterPoint.java (revision 102)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/ImmutableSvmParameterPoint.java (revision 149)
@@ -16,5 +16,11 @@
super(copyFrom);
C = copyFrom.C;
+
kernel = copyFrom.kernel;
+
+ if (kernel == null)
+ {
+ throw new SvmException("Can't build a parameter set with no kernel");
+ }
}
Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/legacyexec/svm_toy.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/legacyexec/svm_toy.java (revision 113)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/legacyexec/svm_toy.java (revision 149)
@@ -4,5 +4,4 @@
import edu.berkeley.compbio.jlibsvm.ContinuousModel;
import edu.berkeley.compbio.jlibsvm.DiscreteModel;
-import edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter;
import edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint;
import edu.berkeley.compbio.jlibsvm.MutableSvmProblem;
@@ -16,5 +15,4 @@
import edu.berkeley.compbio.jlibsvm.kernel.GammaKernel;
import edu.berkeley.compbio.jlibsvm.kernel.GaussianRBFKernel;
-import edu.berkeley.compbio.jlibsvm.kernel.KernelFunction;
import edu.berkeley.compbio.jlibsvm.kernel.LinearKernel;
import edu.berkeley.compbio.jlibsvm.kernel.PolynomialKernel;
@@ -71,5 +69,5 @@
byte current_value = 1;
- ImmutableSvmParameter param;
+ ImmutableSvmParameterPoint param;
@@ -292,5 +290,5 @@
}
- ImmutableSvmParameterPoint.Builder paramBuilder = new ImmutableSvmParameterPoint.Builder();
+ ImmutableSvmParameterPoint.Builder paramPointBuilder = new ImmutableSvmParameterPoint.Builder();
// default values
@@ -300,11 +298,11 @@
param.gamma = 0;
param.coef0 = 0;*/
- paramBuilder.nu = 0.5f;
- paramBuilder.cache_size = 40;
- paramBuilder.C = 1;
- paramBuilder.eps = 1e-3f;
- paramBuilder.p = 0.1f;
- paramBuilder.shrinking = true;
- paramBuilder.probability = false;
+ paramPointBuilder.nu = 0.5f;
+ paramPointBuilder.cache_size = 40;
+ paramPointBuilder.C = 1;
+ paramPointBuilder.eps = 1e-3f;
+ paramPointBuilder.p = 0.1f;
+ paramPointBuilder.shrinking = true;
+ paramPointBuilder.probability = false;
//param.nr_weight = 0;
//param.weightLabel = new int[0];
@@ -355,29 +353,29 @@
break;
case 'n':
- paramBuilder.nu = Float.parseFloat(argv[i]);
+ paramPointBuilder.nu = Float.parseFloat(argv[i]);
break;
case 'm':
- paramBuilder.cache_size = Float.parseFloat(argv[i]);
+ paramPointBuilder.cache_size = Float.parseFloat(argv[i]);
break;
case 'c':
- paramBuilder.C = Float.parseFloat(argv[i]);
+ paramPointBuilder.C = Float.parseFloat(argv[i]);
break;
case 'e':
- paramBuilder.eps = Float.parseFloat(argv[i]);
+ paramPointBuilder.eps = Float.parseFloat(argv[i]);
break;
case 'p':
- paramBuilder.p = Float.parseFloat(argv[i]);
+ paramPointBuilder.p = Float.parseFloat(argv[i]);
break;
case 'h':
- paramBuilder.shrinking = Boolean.parseBoolean(argv[i]);
+ paramPointBuilder.shrinking = Boolean.parseBoolean(argv[i]);
break;
case 'b':
- paramBuilder.probability = Boolean.parseBoolean(argv[i]);
+ paramPointBuilder.probability = Boolean.parseBoolean(argv[i]);
break;
case 'u':
- paramBuilder.redistributeUnbalancedC = Boolean.parseBoolean(argv[i]);
+ paramPointBuilder.redistributeUnbalancedC = Boolean.parseBoolean(argv[i]);
break;
case 'w':
- paramBuilder.putWeight(Integer.parseInt(argv[i - 1].substring(2)), Float.parseFloat(argv[i]));
+ paramPointBuilder.putWeight(Integer.parseInt(argv[i - 1].substring(2)), Float.parseFloat(argv[i]));
break;
default:
@@ -386,21 +384,21 @@
}
- KernelFunction kernel;
+ //final KernelFunction kernel;
switch (kernel_type)
{
case svm_train.LINEAR:
- kernel = new LinearKernel();
+ paramPointBuilder.kernel = new LinearKernel();
break;
case svm_train.POLY:
- kernel = new PolynomialKernel(degree, gamma, coef0);
+ paramPointBuilder.kernel = new PolynomialKernel(degree, gamma, coef0);
break;
case svm_train.RBF:
- kernel = new GaussianRBFKernel(gamma);
+ paramPointBuilder.kernel = new GaussianRBFKernel(gamma);
break;
case svm_train.SIGMOID:
- kernel = new SigmoidKernel(gamma, coef0);
+ paramPointBuilder.kernel = new SigmoidKernel(gamma, coef0);
break;
case svm_train.PRECOMPUTED:
- kernel = new PrecomputedKernel();
+ paramPointBuilder.kernel = new PrecomputedKernel();
break;
default:
@@ -408,6 +406,7 @@
}
+
SVM svm;
- param = paramBuilder.build();
+ param = paramPointBuilder.build();
switch (svm_type)
{
@@ -468,7 +467,7 @@
else if (svm_type == svm_train.EPSILON_SVR || svm_type == svm_train.NU_SVR)
{
- if (kernel instanceof GammaKernel && ((GammaKernel) kernel).getGamma() == 0f)
- {
- ((GammaKernel) kernel).setGamma(1.0f);
+ if (param.kernel instanceof GammaKernel && ((GammaKernel) param.kernel).getGamma() == 0f)
+ {
+ ((GammaKernel) param.kernel).setGamma(1.0f);
//gamma = 1;
}
@@ -512,5 +511,5 @@
window_gc.drawLine(0, 0, 0, YLEN - 1);
- int p = (int) (paramBuilder.p * YLEN);
+ int p = (int) (paramPointBuilder.p * YLEN);
for (int i = 1; i < XLEN; i++)
{
@@ -541,7 +540,7 @@
else
{
- if (kernel instanceof GammaKernel && ((GammaKernel) kernel).getGamma() == 0f)
- {
- ((GammaKernel) kernel).setGamma(0.5f);
+ if (param.kernel instanceof GammaKernel && ((GammaKernel) param.kernel).getGamma() == 0f)
+ {
+ ((GammaKernel) param.kernel).setGamma(0.5f);
//gamma = 0.5f;
}
Index: trunk/src/main/java/edu/berkeley/compbio/jlibsvm/legacyexec/svm_train.java
===================================================================
--- trunk/src/main/java/edu/berkeley/compbio/jlibsvm/legacyexec/svm_train.java (revision 132)
+++ trunk/src/main/java/edu/berkeley/compbio/jlibsvm/legacyexec/svm_train.java (revision 149)
@@ -229,5 +229,7 @@
break;
case 'c':
+ // override the default
builder.Cset = new HashSet();
+
for (String s : argv[i].split(","))
{