Author: ghannum
Date: 2010-06-25 17:08:39 -0700 (Fri, 25 Jun 2010)
New Revision: 20673
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/BooleanVector.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/ByteMatrix.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/FloatVector.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/IntMatrix.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/SNodeModule.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/LinpackSVD.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/PartialSVD.java
Log:
Fixed a few minor bugs
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -275,7 +275,7 @@
int sharedNodeCount =0;
for (int i=0; i< nodeIndicesB.length; i++){
- if (hashSet.contains(new Integer(nodeIndicesB[i]))){
+ if (hashSet.contains(Integer.valueOf(nodeIndicesB[i]))){
sharedNodeCount++;
}
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/BooleanVector.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/BooleanVector.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/BooleanVector.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -111,7 +111,7 @@
return out;
}
- public synchronized void add(boolean val)
+ public void add(boolean val)
{
if (data.length==0) data = new boolean[10];
else if (this.size==data.length) data =
BooleanVector.resize(data,data.length*2);
@@ -125,7 +125,7 @@
this.add(Boolean.valueOf(val));
}
- public synchronized void addAll(boolean[] vals)
+ public void addAll(boolean[] vals)
{
if (data.length<this.size+vals.length) data =
BooleanVector.resize(data,data.length+vals.length);
@@ -133,7 +133,7 @@
this.add(d);
}
- public synchronized void addAll(Collection<Boolean> vals)
+ public void addAll(Collection<Boolean> vals)
{
if (data.length<this.size+vals.size()) data =
BooleanVector.resize(data,data.length+vals.size());
@@ -141,7 +141,7 @@
this.add(d);
}
- public synchronized void addAll(BooleanVector vals)
+ public void addAll(BooleanVector vals)
{
if (data.length<this.size+vals.size()) data =
BooleanVector.resize(data,data.length+vals.size());
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/ByteMatrix.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/ByteMatrix.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/ByteMatrix.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -728,7 +728,7 @@
sum = sum / (valcount - 1);
- return java.lang.Math.sqrt(.5);
+ return sum;
}
public DoubleVector stdByRow()
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/FloatVector.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/FloatVector.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/FloatVector.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -271,7 +271,7 @@
}
public void set(int i, Integer val) {
- data[i] = new Float(val);
+ data[i] = Float.valueOf(val);
}
public void set(List<Integer> indices, float val) {
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/IntMatrix.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/IntMatrix.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/data/IntMatrix.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -691,7 +691,7 @@
sum = sum / (valcount - 1);
- return java.lang.Math.sqrt(.5);
+ return sum;
}
public DoubleVector stdByRow()
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/SNodeModule.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/SNodeModule.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/SNodeModule.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -52,7 +52,7 @@
if (c instanceof SNodeModule)
{
SNodeModule other = (SNodeModule)c;
- if (other.id == this.id &&
other.members.equals(this.members)) return true;
+ if (other.id.equals(this.id) &&
other.members.equals(this.members)) return true;
else return false;
}else return false;
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/LinpackSVD.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/LinpackSVD.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/LinpackSVD.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -172,7 +172,7 @@
e[j] = A[k][j];
}
- if (wantu & (k < nct))
+ if (wantu && (k < nct))
{
// Place the transformation in U for subsequent
back
// multiplication.
@@ -203,7 +203,7 @@
e[k] = -e[k];
- if ((k+1 < m) & (e[k] != 0.0))
+ if ((k+1 < m) && (e[k] != 0.0))
{
// Apply the transformation.
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/PartialSVD.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/PartialSVD.java
2010-06-25 23:56:07 UTC (rev 20672)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/math/svd/PartialSVD.java
2010-06-26 00:08:39 UTC (rev 20673)
@@ -3,7 +3,7 @@
public class PartialSVD extends SVD
{
- private final double epsilon = 1e-8;
+ private static final double epsilon = 1e-8;
public PartialSVD(double[][] M, int k)
{
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