Revision: 2263
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2263&view=rev
Author: heeroyuy
Date: 2010-08-20 08:59:03 +0000 (Fri, 20 Aug 2010)
Log Message:
-----------
-added forgotten domain and range for data properties
Modified Paths:
--------------
trunk/examples/mutagenesis/mutagenesis.owl
trunk/examples/mutagenesis/train1.conf
trunk/examples/mutagenesis/train2.conf
trunk/src/dl-learner/org/dllearner/examples/Mutagenesis.java
Modified: trunk/examples/mutagenesis/mutagenesis.owl
===================================================================
--- trunk/examples/mutagenesis/mutagenesis.owl 2010-08-17 17:43:46 UTC (rev 2262)
+++ trunk/examples/mutagenesis/mutagenesis.owl 2010-08-20 08:59:03 UTC (rev 2263)
@@ -92,7 +92,10 @@
<!-- http://dl-learner.org/mutagenesis#logp -->
- <owl:DatatypeProperty rdf:about="http://dl-learner.org/mutagenesis#logp"/>
+ <owl:DatatypeProperty rdf:about="http://dl-learner.org/mutagenesis#logp">
+ <rdfs:domain rdf:resource="http://dl-learner.org/mutagenesis#Compound"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+ </owl:DatatypeProperty>
Modified: trunk/examples/mutagenesis/train1.conf
===================================================================
--- trunk/examples/mutagenesis/train1.conf 2010-08-17 17:43:46 UTC (rev 2262)
+++ trunk/examples/mutagenesis/train1.conf 2010-08-20 08:59:03 UTC (rev 2263)
@@ -1,8 +1,8 @@
import("mutagenesis.owl");
reasoner = fastInstanceChecker;
-algorithm = celoe;
-refexamples.noisePercentage = 11;
+algorithm = refexamples;
+refexamples.noisePercentage = 0;
refexamples.startClass = "http://dl-learner.org/mutagenesis#Compound";
refexamples.writeSearchTree = false;
refexamples.searchTreeFile = "log/mutagenesis/searchTree.log";
Modified: trunk/examples/mutagenesis/train2.conf
===================================================================
--- trunk/examples/mutagenesis/train2.conf 2010-08-17 17:43:46 UTC (rev 2262)
+++ trunk/examples/mutagenesis/train2.conf 2010-08-20 08:59:03 UTC (rev 2263)
@@ -2,109 +2,109 @@
reasoner = fastInstanceChecker;
algorithm = refexamples;
-refexamples.noisePercentage = 31;
+refexamples.noisePercentage = 0;
refexamples.startClass = "http://dl-learner.org/mutagenesis#Compound";
refexamples.writeSearchTree = false;
refexamples.searchTreeFile = "log/mutagenesis/searchTree.log";
-+"http://dl-learner.org/mutagenesis#d1"
-+"http://dl-learner.org/mutagenesis#d10"
+-"http://dl-learner.org/mutagenesis#d1"
+-"http://dl-learner.org/mutagenesis#d10"
-"http://dl-learner.org/mutagenesis#d100"
-+"http://dl-learner.org/mutagenesis#d101"
-+"http://dl-learner.org/mutagenesis#d102"
-+"http://dl-learner.org/mutagenesis#d103"
-+"http://dl-learner.org/mutagenesis#d104"
-+"http://dl-learner.org/mutagenesis#d105"
-+"http://dl-learner.org/mutagenesis#d106"
-+"http://dl-learner.org/mutagenesis#d107"
-+"http://dl-learner.org/mutagenesis#d108"
-+"http://dl-learner.org/mutagenesis#d109"
-+"http://dl-learner.org/mutagenesis#d11"
+-"http://dl-learner.org/mutagenesis#d101"
+-"http://dl-learner.org/mutagenesis#d102"
+-"http://dl-learner.org/mutagenesis#d103"
+-"http://dl-learner.org/mutagenesis#d104"
+-"http://dl-learner.org/mutagenesis#d105"
+-"http://dl-learner.org/mutagenesis#d106"
+-"http://dl-learner.org/mutagenesis#d107"
+-"http://dl-learner.org/mutagenesis#d108"
+-"http://dl-learner.org/mutagenesis#d109"
+-"http://dl-learner.org/mutagenesis#d11"
-"http://dl-learner.org/mutagenesis#d110"
-"http://dl-learner.org/mutagenesis#d111"
-+"http://dl-learner.org/mutagenesis#d112"
+-"http://dl-learner.org/mutagenesis#d112"
-"http://dl-learner.org/mutagenesis#d113"
-"http://dl-learner.org/mutagenesis#d114"
-+"http://dl-learner.org/mutagenesis#d115"
+-"http://dl-learner.org/mutagenesis#d115"
-"http://dl-learner.org/mutagenesis#d116"
-+"http://dl-learner.org/mutagenesis#d117"
-+"http://dl-learner.org/mutagenesis#d118"
+-"http://dl-learner.org/mutagenesis#d117"
+-"http://dl-learner.org/mutagenesis#d118"
-"http://dl-learner.org/mutagenesis#d119"
-+"http://dl-learner.org/mutagenesis#d12"
+-"http://dl-learner.org/mutagenesis#d12"
-"http://dl-learner.org/mutagenesis#d120"
-+"http://dl-learner.org/mutagenesis#d121"
-+"http://dl-learner.org/mutagenesis#d122"
+-"http://dl-learner.org/mutagenesis#d121"
+-"http://dl-learner.org/mutagenesis#d122"
-"http://dl-learner.org/mutagenesis#d123"
-"http://dl-learner.org/mutagenesis#d124"
-+"http://dl-learner.org/mutagenesis#d125"
-+"http://dl-learner.org/mutagenesis#d126"
-+"http://dl-learner.org/mutagenesis#d127"
-+"http://dl-learner.org/mutagenesis#d128"
+-"http://dl-learner.org/mutagenesis#d125"
+-"http://dl-learner.org/mutagenesis#d126"
+-"http://dl-learner.org/mutagenesis#d127"
+-"http://dl-learner.org/mutagenesis#d128"
-"http://dl-learner.org/mutagenesis#d129"
-+"http://dl-learner.org/mutagenesis#d13"
+-"http://dl-learner.org/mutagenesis#d13"
-"http://dl-learner.org/mutagenesis#d130"
-"http://dl-learner.org/mutagenesis#d131"
-"http://dl-learner.org/mutagenesis#d132"
-"http://dl-learner.org/mutagenesis#d133"
-+"http://dl-learner.org/mutagenesis#d134"
+-"http://dl-learner.org/mutagenesis#d134"
-"http://dl-learner.org/mutagenesis#d135"
-+"http://dl-learner.org/mutagenesis#d136"
-+"http://dl-learner.org/mutagenesis#d137"
+-"http://dl-learner.org/mutagenesis#d136"
+-"http://dl-learner.org/mutagenesis#d137"
-"http://dl-learner.org/mutagenesis#d138"
-"http://dl-learner.org/mutagenesis#d139"
-"http://dl-learner.org/mutagenesis#d14"
-+"http://dl-learner.org/mutagenesis#d140"
+-"http://dl-learner.org/mutagenesis#d140"
-"http://dl-learner.org/mutagenesis#d141"
-"http://dl-learner.org/mutagenesis#d142"
-"http://dl-learner.org/mutagenesis#d143"
-"http://dl-learner.org/mutagenesis#d144"
-+"http://dl-learner.org/mutagenesis#d145"
-+"http://dl-learner.org/mutagenesis#d146"
+-"http://dl-learner.org/mutagenesis#d145"
+-"http://dl-learner.org/mutagenesis#d146"
-"http://dl-learner.org/mutagenesis#d147"
-+"http://dl-learner.org/mutagenesis#d148"
-+"http://dl-learner.org/mutagenesis#d149"
-+"http://dl-learner.org/mutagenesis#d15"
+-"http://dl-learner.org/mutagenesis#d148"
+-"http://dl-learner.org/mutagenesis#d149"
+-"http://dl-learner.org/mutagenesis#d15"
-"http://dl-learner.org/mutagenesis#d150"
-+"http://dl-learner.org/mutagenesis#d151"
-+"http://dl-learner.org/mutagenesis#d152"
-+"http://dl-learner.org/mutagenesis#d153"
+-"http://dl-learner.org/mutagenesis#d151"
+-"http://dl-learner.org/mutagenesis#d152"
+-"http://dl-learner.org/mutagenesis#d153"
-"http://dl-learner.org/mutagenesis#d154"
-"http://dl-learner.org/mutagenesis#d155"
-"http://dl-learner.org/mutagenesis#d156"
-+"http://dl-learner.org/mutagenesis#d157"
-+"http://dl-learner.org/mutagenesis#d158"
-+"http://dl-learner.org/mutagenesis#d159"
-+"http://dl-learner.org/mutagenesis#d16"
+-"http://dl-learner.org/mutagenesis#d157"
+-"http://dl-learner.org/mutagenesis#d158"
+-"http://dl-learner.org/mutagenesis#d159"
+-"http://dl-learner.org/mutagenesis#d16"
-"http://dl-learner.org/mutagenesis#d160"
-+"http://dl-learner.org/mutagenesis#d161"
-+"http://dl-learner.org/mutagenesis#d162"
-+"http://dl-learner.org/mutagenesis#d163"
-+"http://dl-learner.org/mutagenesis#d164"
-+"http://dl-learner.org/mutagenesis#d165"
-+"http://dl-learner.org/mutagenesis#d166"
-+"http://dl-learner.org/mutagenesis#d167"
+-"http://dl-learner.org/mutagenesis#d161"
+-"http://dl-learner.org/mutagenesis#d162"
+-"http://dl-learner.org/mutagenesis#d163"
+-"http://dl-learner.org/mutagenesis#d164"
+-"http://dl-learner.org/mutagenesis#d165"
+-"http://dl-learner.org/mutagenesis#d166"
+-"http://dl-learner.org/mutagenesis#d167"
-"http://dl-learner.org/mutagenesis#d168"
-+"http://dl-learner.org/mutagenesis#d169"
+-"http://dl-learner.org/mutagenesis#d169"
-"http://dl-learner.org/mutagenesis#d17"
-+"http://dl-learner.org/mutagenesis#d170"
-+"http://dl-learner.org/mutagenesis#d171"
-+"http://dl-learner.org/mutagenesis#d172"
-+"http://dl-learner.org/mutagenesis#d173"
-+"http://dl-learner.org/mutagenesis#d174"
+-"http://dl-learner.org/mutagenesis#d170"
+-"http://dl-learner.org/mutagenesis#d171"
+-"http://dl-learner.org/mutagenesis#d172"
+-"http://dl-learner.org/mutagenesis#d173"
+-"http://dl-learner.org/mutagenesis#d174"
-"http://dl-learner.org/mutagenesis#d175"
-+"http://dl-learner.org/mutagenesis#d176"
-+"http://dl-learner.org/mutagenesis#d177"
-+"http://dl-learner.org/mutagenesis#d178"
+-"http://dl-learner.org/mutagenesis#d176"
+-"http://dl-learner.org/mutagenesis#d177"
+-"http://dl-learner.org/mutagenesis#d178"
-"http://dl-learner.org/mutagenesis#d179"
-+"http://dl-learner.org/mutagenesis#d18"
-+"http://dl-learner.org/mutagenesis#d180"
+-"http://dl-learner.org/mutagenesis#d18"
+-"http://dl-learner.org/mutagenesis#d180"
-"http://dl-learner.org/mutagenesis#d181"
-"http://dl-learner.org/mutagenesis#d182"
-+"http://dl-learner.org/mutagenesis#d183"
-+"http://dl-learner.org/mutagenesis#d184"
+-"http://dl-learner.org/mutagenesis#d183"
+-"http://dl-learner.org/mutagenesis#d184"
-"http://dl-learner.org/mutagenesis#d185"
-"http://dl-learner.org/mutagenesis#d186"
-+"http://dl-learner.org/mutagenesis#d187"
+-"http://dl-learner.org/mutagenesis#d187"
-"http://dl-learner.org/mutagenesis#d188"
-"http://dl-learner.org/mutagenesis#d189"
-"http://dl-learner.org/mutagenesis#d19"
@@ -117,93 +117,93 @@
-"http://dl-learner.org/mutagenesis#d196"
+"http://dl-learner.org/mutagenesis#d197"
-"http://dl-learner.org/mutagenesis#d2"
-+"http://dl-learner.org/mutagenesis#d20"
-+"http://dl-learner.org/mutagenesis#d21"
-+"http://dl-learner.org/mutagenesis#d22"
-+"http://dl-learner.org/mutagenesis#d23"
-+"http://dl-learner.org/mutagenesis#d24"
-+"http://dl-learner.org/mutagenesis#d25"
-+"http://dl-learner.org/mutagenesis#d26"
-+"http://dl-learner.org/mutagenesis#d27"
-+"http://dl-learner.org/mutagenesis#d28"
-+"http://dl-learner.org/mutagenesis#d29"
+-"http://dl-learner.org/mutagenesis#d20"
+-"http://dl-learner.org/mutagenesis#d21"
+-"http://dl-learner.org/mutagenesis#d22"
+-"http://dl-learner.org/mutagenesis#d23"
+-"http://dl-learner.org/mutagenesis#d24"
+-"http://dl-learner.org/mutagenesis#d25"
+-"http://dl-learner.org/mutagenesis#d26"
+-"http://dl-learner.org/mutagenesis#d27"
+-"http://dl-learner.org/mutagenesis#d28"
+-"http://dl-learner.org/mutagenesis#d29"
-"http://dl-learner.org/mutagenesis#d3"
-+"http://dl-learner.org/mutagenesis#d30"
-+"http://dl-learner.org/mutagenesis#d31"
-+"http://dl-learner.org/mutagenesis#d32"
-+"http://dl-learner.org/mutagenesis#d33"
+-"http://dl-learner.org/mutagenesis#d30"
+-"http://dl-learner.org/mutagenesis#d31"
+-"http://dl-learner.org/mutagenesis#d32"
+-"http://dl-learner.org/mutagenesis#d33"
-"http://dl-learner.org/mutagenesis#d34"
-+"http://dl-learner.org/mutagenesis#d35"
+-"http://dl-learner.org/mutagenesis#d35"
-"http://dl-learner.org/mutagenesis#d36"
-+"http://dl-learner.org/mutagenesis#d37"
+-"http://dl-learner.org/mutagenesis#d37"
-"http://dl-learner.org/mutagenesis#d38"
-"http://dl-learner.org/mutagenesis#d39"
-+"http://dl-learner.org/mutagenesis#d4"
+-"http://dl-learner.org/mutagenesis#d4"
-"http://dl-learner.org/mutagenesis#d40"
-+"http://dl-learner.org/mutagenesis#d41"
+-"http://dl-learner.org/mutagenesis#d41"
-"http://dl-learner.org/mutagenesis#d42"
-+"http://dl-learner.org/mutagenesis#d43"
-+"http://dl-learner.org/mutagenesis#d44"
-+"http://dl-learner.org/mutagenesis#d45"
-+"http://dl-learner.org/mutagenesis#d46"
-+"http://dl-learner.org/mutagenesis#d47"
-+"http://dl-learner.org/mutagenesis#d48"
-+"http://dl-learner.org/mutagenesis#d49"
+-"http://dl-learner.org/mutagenesis#d43"
+-"http://dl-learner.org/mutagenesis#d44"
+-"http://dl-learner.org/mutagenesis#d45"
+-"http://dl-learner.org/mutagenesis#d46"
+-"http://dl-learner.org/mutagenesis#d47"
+-"http://dl-learner.org/mutagenesis#d48"
+-"http://dl-learner.org/mutagenesis#d49"
-"http://dl-learner.org/mutagenesis#d5"
-+"http://dl-learner.org/mutagenesis#d50"
-+"http://dl-learner.org/mutagenesis#d51"
-+"http://dl-learner.org/mutagenesis#d52"
-+"http://dl-learner.org/mutagenesis#d53"
-+"http://dl-learner.org/mutagenesis#d54"
+-"http://dl-learner.org/mutagenesis#d50"
+-"http://dl-learner.org/mutagenesis#d51"
+-"http://dl-learner.org/mutagenesis#d52"
+-"http://dl-learner.org/mutagenesis#d53"
+-"http://dl-learner.org/mutagenesis#d54"
-"http://dl-learner.org/mutagenesis#d55"
-+"http://dl-learner.org/mutagenesis#d56"
-+"http://dl-learner.org/mutagenesis#d57"
-+"http://dl-learner.org/mutagenesis#d58"
-+"http://dl-learner.org/mutagenesis#d59"
-+"http://dl-learner.org/mutagenesis#d6"
-+"http://dl-learner.org/mutagenesis#d60"
-+"http://dl-learner.org/mutagenesis#d61"
+-"http://dl-learner.org/mutagenesis#d56"
+-"http://dl-learner.org/mutagenesis#d57"
+-"http://dl-learner.org/mutagenesis#d58"
+-"http://dl-learner.org/mutagenesis#d59"
+-"http://dl-learner.org/mutagenesis#d6"
+-"http://dl-learner.org/mutagenesis#d60"
+-"http://dl-learner.org/mutagenesis#d61"
-"http://dl-learner.org/mutagenesis#d62"
-+"http://dl-learner.org/mutagenesis#d63"
-+"http://dl-learner.org/mutagenesis#d64"
+-"http://dl-learner.org/mutagenesis#d63"
+-"http://dl-learner.org/mutagenesis#d64"
-"http://dl-learner.org/mutagenesis#d65"
-"http://dl-learner.org/mutagenesis#d66"
-+"http://dl-learner.org/mutagenesis#d67"
-+"http://dl-learner.org/mutagenesis#d68"
-+"http://dl-learner.org/mutagenesis#d69"
+-"http://dl-learner.org/mutagenesis#d67"
+-"http://dl-learner.org/mutagenesis#d68"
+-"http://dl-learner.org/mutagenesis#d69"
-"http://dl-learner.org/mutagenesis#d7"
-"http://dl-learner.org/mutagenesis#d70"
-+"http://dl-learner.org/mutagenesis#d71"
-+"http://dl-learner.org/mutagenesis#d72"
+-"http://dl-learner.org/mutagenesis#d71"
+-"http://dl-learner.org/mutagenesis#d72"
-"http://dl-learner.org/mutagenesis#d73"
-+"http://dl-learner.org/mutagenesis#d74"
-+"http://dl-learner.org/mutagenesis#d75"
+-"http://dl-learner.org/mutagenesis#d74"
+-"http://dl-learner.org/mutagenesis#d75"
-"http://dl-learner.org/mutagenesis#d76"
-"http://dl-learner.org/mutagenesis#d77"
-"http://dl-learner.org/mutagenesis#d78"
-+"http://dl-learner.org/mutagenesis#d79"
-+"http://dl-learner.org/mutagenesis#d8"
-+"http://dl-learner.org/mutagenesis#d80"
-+"http://dl-learner.org/mutagenesis#d81"
-+"http://dl-learner.org/mutagenesis#d82"
-+"http://dl-learner.org/mutagenesis#d83"
+-"http://dl-learner.org/mutagenesis#d79"
+-"http://dl-learner.org/mutagenesis#d8"
+-"http://dl-learner.org/mutagenesis#d80"
+-"http://dl-learner.org/mutagenesis#d81"
+-"http://dl-learner.org/mutagenesis#d82"
+-"http://dl-learner.org/mutagenesis#d83"
-"http://dl-learner.org/mutagenesis#d84"
-+"http://dl-learner.org/mutagenesis#d85"
-+"http://dl-learner.org/mutagenesis#d86"
-+"http://dl-learner.org/mutagenesis#d87"
+-"http://dl-learner.org/mutagenesis#d85"
+-"http://dl-learner.org/mutagenesis#d86"
+-"http://dl-learner.org/mutagenesis#d87"
-"http://dl-learner.org/mutagenesis#d88"
-"http://dl-learner.org/mutagenesis#d89"
-"http://dl-learner.org/mutagenesis#d9"
-+"http://dl-learner.org/mutagenesis#d90"
-+"http://dl-learner.org/mutagenesis#d91"
-+"http://dl-learner.org/mutagenesis#d92"
-+"http://dl-learner.org/mutagenesis#d93"
-+"http://dl-learner.org/mutagenesis#d94"
-+"http://dl-learner.org/mutagenesis#d95"
-+"http://dl-learner.org/mutagenesis#d96"
-+"http://dl-learner.org/mutagenesis#d97"
+-"http://dl-learner.org/mutagenesis#d90"
+-"http://dl-learner.org/mutagenesis#d91"
+-"http://dl-learner.org/mutagenesis#d92"
+-"http://dl-learner.org/mutagenesis#d93"
+-"http://dl-learner.org/mutagenesis#d94"
+-"http://dl-learner.org/mutagenesis#d95"
+-"http://dl-learner.org/mutagenesis#d96"
+-"http://dl-learner.org/mutagenesis#d97"
-"http://dl-learner.org/mutagenesis#d98"
-+"http://dl-learner.org/mutagenesis#d99"
+-"http://dl-learner.org/mutagenesis#d99"
+"http://dl-learner.org/mutagenesis#e1"
-"http://dl-learner.org/mutagenesis#e10"
-"http://dl-learner.org/mutagenesis#e11"
Modified: trunk/src/dl-learner/org/dllearner/examples/Mutagenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Mutagenesis.java 2010-08-17 17:43:46 UTC (rev 2262)
+++ trunk/src/dl-learner/org/dllearner/examples/Mutagenesis.java 2010-08-20 08:59:03 UTC (rev 2263)
@@ -141,6 +141,19 @@
String kbString = "DPDOMAIN(" + getURI2("charge") + ") = "
+ getURI2("Atom") + ".\n";
kbString += "DPRANGE(" + getURI2("charge") + ") = DOUBLE.\n";
+
+ kbString += "DPDOMAIN(" + getURI2("logp") + ") = "
+ + getURI2("Compound") + ".\n";
+ kbString += "DPRANGE(" + getURI2("logp") + ") = DOUBLE.\n";
+
+ kbString += "DPDOMAIN(" + getURI2("act") + ") = "
+ + getURI2("Compound") + ".\n";
+ kbString += "DPRANGE(" + getURI2("act") + ") = DOUBLE.\n";
+
+ kbString += "DPDOMAIN(" + getURI2("lumo") + ") = "
+ + getURI2("Compound") + ".\n";
+ kbString += "DPRANGE(" + getURI2("lumo") + ") = DOUBLE.\n";
+
kbString += "OPDOMAIN(" + getURI2("hasAtom") + ") = "
+ getURI2("Compound") + ".\n";
kbString += "OPRANGE(" + getURI2("hasAtom") + ") = " + getURI2("Atom")
@@ -153,8 +166,10 @@
+ ".\n";
kbString += "OPRANGE(" + getURI2("inBond") + ") = " + getURI2("Atom")
+ ".\n";
- kbString += "OPDOMAIN(" + getURI2("hasStructure") + ") = " + getURI2("Compound") + ".\n";
- kbString += "OPRANGE(" + getURI2("inStructure") + ") = " + getURI2("RingStructure") + ".\n";
+ kbString += "OPDOMAIN(" + getURI2("hasStructure") + ") = "
+ + getURI2("Compound") + ".\n";
+ kbString += "OPRANGE(" + getURI2("inStructure") + ") = "
+ + getURI2("RingStructure") + ".\n";
KB kb2 = KBParser.parseKBFile(kbString);
kb.addKB(kb2);
@@ -176,32 +191,31 @@
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
System.out.println("OK (" + time + ").");
-
+
// generating first conf file
System.out.print("Generatin first conf file ... ");
startTime = System.nanoTime();
File confTrainFile = new File("examples/mutagenesis/train1.conf");
Files.clearFile(confTrainFile);
generateConfFile(confTrainFile);
- String[] trainingFiles = new String[] { "s1.pl", "s2.pl",
- "s3.pl", "s4.pl", "s5.pl", "s6.pl", "s7.pl",
- "s8.pl", "s9.pl", "s10.pl"};
-
+ String[] trainingFiles = new String[] { "s1.pl", "s2.pl", "s3.pl",
+ "s4.pl", "s5.pl", "s6.pl", "s7.pl", "s8.pl", "s9.pl", "s10.pl" };
+
for (String file : trainingFiles) {
- generatePositiveExamples(prologDirectory + "188/" + file);
+ generatePositiveExamples(prologDirectory + "188/" + file);
}
appendExamples(confTrainFile, positiveExamples);
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
System.out.println("OK (" + time + ").");
-
-
+
// generating second conf file
System.out.print("Generatin second conf file ... ");
File confSecondTrainFile = new File("examples/mutagenesis/train2.conf");
Files.clearFile(confSecondTrainFile);
generateConfFile(confSecondTrainFile);
- generatePositiveExamples(prologDirectory + "42/all.pl");
+ positiveExamples.clear();
+ generatePositiveExamples(prologDirectory + "42/all.pl");
appendExamples(confSecondTrainFile, positiveExamples);
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
@@ -213,27 +227,30 @@
String confHeader = "import(\"mutagenesis.owl\");\n\n";
confHeader += "reasoner = fastInstanceChecker;\n";
confHeader += "algorithm = refexamples;\n";
- confHeader += "refexamples.noisePercentage = 31;\n";
+ confHeader += "refexamples.noisePercentage = 0;\n";
confHeader += "refexamples.startClass = " + getURI2("Compound") + ";\n";
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/mutagenesis/searchTree.log\";\n";
confHeader += "\n";
Files.appendFile(file, confHeader);
}
-
- private static void generatePositiveExamples(String fileName) throws FileNotFoundException {
+
+ private static void generatePositiveExamples(String fileName)
+ throws FileNotFoundException {
Scanner input = new Scanner(new File(fileName), "UTF-8");
String trainingContent = "";
- while ( input.hasNextLine() ) {
+
+ while (input.hasNextLine()) {
trainingContent = input.nextLine();
- if(trainingContent.startsWith("active")) {
+ if (trainingContent.startsWith("active")) {
int start = trainingContent.indexOf("(") + 1;
int end = trainingContent.indexOf(")");
- String individual = trainingContent.substring(start,end);
+ String individual = trainingContent.substring(start, end);
positiveExamples.add(individual);
}
}
}
+
private static List<Axiom> mapClause(Clause clause) throws IOException,
ParseException {
List<Axiom> axioms = new LinkedList<Axiom>();
@@ -509,19 +526,21 @@
ringStructureTypes.add(structureClass);
}
}
-
+
/**
- * This method
+ * This method
+ *
* @param file
* @param examples
*/
public static void appendExamples(File file, List<String> examples) {
StringBuffer content = new StringBuffer();
- for(String compound : compounds) {
- if(examples.contains(compound.toString())) {
- content.append("+\""+getIndividual(compound)+"\"\n");
+ for (String compound : compounds) {
+ if (examples.contains(compound.toString())) {
+ content.append("+\"" + getIndividual(compound) + "\"\n");
} else {
- content.append("-\""+getIndividual(compound.toString())+"\"\n");
+ content.append("-\"" + getIndividual(compound.toString())
+ + "\"\n");
}
}
Files.appendFile(file, content.toString());
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