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JAL-2629 adjust log parameter slightly and reduce granularity
author
TZVanaalten
<TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Thu, 24 Aug 2017 14:41:40 +0000
(15:41 +0100)
committer
TZVanaalten
<TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Fri, 25 Aug 2017 16:21:04 +0000
(17:21 +0100)
src/jalview/gui/OptsAndParamsPage.java
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src/jalview/hmmer/HMMERParamStore.java
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src/jalview/ws/params/simple/LogarithmicParameter.java
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diff --git
a/src/jalview/gui/OptsAndParamsPage.java
b/src/jalview/gui/OptsAndParamsPage.java
index
44acdab
..
1505df8
100644
(file)
--- a/
src/jalview/gui/OptsAndParamsPage.java
+++ b/
src/jalview/gui/OptsAndParamsPage.java
@@
-589,7
+589,7
@@
public class OptsAndParamsPage
Double base = ((LogarithmicParameter) parameter).getBase();
Double value = Math.pow(
base,
Double base = ((LogarithmicParameter) parameter).getBase();
Double value = Math.pow(
base,
- slider.getValue());
+ slider.getValue() / 1000000f);
valueField.setText(formatDouble(value));
}
checkIfModified();
valueField.setText(formatDouble(value));
}
checkIfModified();
@@
-599,7
+599,7
@@
public class OptsAndParamsPage
public String formatDouble(Double value)
{
public String formatDouble(Double value)
{
- String string = String.format("%2.3f", value);
+ String string = String.format("%3.3f", value);
if (value < 0.001)
{
string = String.format("%3.3e", value);
if (value < 0.001)
{
string = String.format("%3.3e", value);
@@
-681,7
+681,7
@@
public class OptsAndParamsPage
{
Double base = ((LogarithmicParameter) parm).getBase();
Double value = Math.pow(base,
{
Double base = ((LogarithmicParameter) parm).getBase();
Double value = Math.pow(base,
- Double.parseDouble(parm.getValue()));
+ Double.parseDouble(parm.getValue()) / 1000000);
valueField.setText(formatDouble(value));
}
else
valueField.setText(formatDouble(value));
}
else
@@
-750,7
+750,8
@@
public class OptsAndParamsPage
eValue = Double.valueOf(valueField.getText());
dVal = Math.log(eValue) / Math
eValue = Double.valueOf(valueField.getText());
dVal = Math.log(eValue) / Math
- .log(((LogarithmicParameter) parameter).getBase());
+ .log(((LogarithmicParameter) parameter).getBase())
+ * 1000000;
if (validator.getMin() != null
&& validator.getMin().doubleValue() > dVal)
if (validator.getMin() != null
&& validator.getMin().doubleValue() > dVal)
diff --git
a/src/jalview/hmmer/HMMERParamStore.java
b/src/jalview/hmmer/HMMERParamStore.java
index
ab33c95
..
a4bf8e4
100644
(file)
--- a/
src/jalview/hmmer/HMMERParamStore.java
+++ b/
src/jalview/hmmer/HMMERParamStore.java
@@
-117,7
+117,7
@@
public class HMMERParamStore implements ParamDatastoreI
args.add(new LogarithmicParameter(
MessageManager.getString("label.seq_e_value"),
MessageManager.getString("label.seq_e_value_desc"), false,
args.add(new LogarithmicParameter(
MessageManager.getString("label.seq_e_value"),
MessageManager.getString("label.seq_e_value_desc"), false,
- -9.96578, -126d, 3.3219d, 2d));
+ -3d, -37.92977945, 1d, 10d));
/*
args.add(new DoubleParameter(
MessageManager.getString("label.seq_score"),
/*
args.add(new DoubleParameter(
MessageManager.getString("label.seq_score"),
@@
-127,7
+127,7
@@
public class HMMERParamStore implements ParamDatastoreI
args.add(new LogarithmicParameter(
MessageManager.getString("label.dom_e_value_desc"),
MessageManager.getString("label.dom_e_value_desc"), false,
args.add(new LogarithmicParameter(
MessageManager.getString("label.dom_e_value_desc"),
MessageManager.getString("label.dom_e_value_desc"), false,
- -9.96578, -126d, 3.3219d, 2d));
+ -3d, -37.92977945, 1d, 10d));
/*
args.add(new DoubleParameter(
MessageManager.getString("label.dom_score"),
/*
args.add(new DoubleParameter(
MessageManager.getString("label.dom_score"),
diff --git
a/src/jalview/ws/params/simple/LogarithmicParameter.java
b/src/jalview/ws/params/simple/LogarithmicParameter.java
index
4944d6b
..
91ed03a
100644
(file)
--- a/
src/jalview/ws/params/simple/LogarithmicParameter.java
+++ b/
src/jalview/ws/params/simple/LogarithmicParameter.java
@@
-71,8
+71,8
@@
public class LogarithmicParameter extends Option implements ParameterI
super(name, description, required, String.valueOf(defValue), null, null,
null);
defval = defValue;
super(name, description, required, String.valueOf(defValue), null, null,
null);
defval = defValue;
- this.min = min;
- this.max = max;
+ this.min = min * 1000000;
+ this.max = max * 1000000;
this.base = base;
}
this.base = base;
}
@@
-83,8
+83,8
@@
public class LogarithmicParameter extends Option implements ParameterI
super(name, description, required, String.valueOf(defValue),
String.valueOf(value), null, null);
defval = defValue;
super(name, description, required, String.valueOf(defValue),
String.valueOf(value), null, null);
defval = defValue;
- this.min = min;
- this.max = max;
+ this.min = min * 1000000;
+ this.max = max * 1000000;
this.base = base;
}
this.base = base;
}