Commit 390c032d authored by Rui Chen's avatar Rui Chen

[BioJava] Added a new fasta file(large). Added patch file for fixing stdout...

[BioJava] Added a new fasta file(large). Added patch file for fixing stdout problem and building problem
parent 90246a83
Pipeline #3119 canceled with stage
in 4 minutes and 38 seconds
......@@ -3,7 +3,6 @@ benchmark biojava
thread-model per_cpu
jars "AAProperties-jar-with-dependencies.jar";
size default args "${SCRATCH}/dat/test.fasta"
size default args "${SCRATCH}/dat/core_set_aligned.fasta"
output
stdout digest 0xd31deba48b76595f822b43217afefd6fec3aefb9,
stderr digest 0xda39a3ee5e6b4b0d3255bfef95601890afd80709;
\ No newline at end of file
stdout digest 0x039481f64d66930f41e2beb9f87131e08b9c2553;
\ No newline at end of file
diff -Nur build/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java tempbuild/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
--- build/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java 2018-12-11 13:56:09.000000000 +0800
+++ tempbuild/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java 2018-12-13 17:08:05.000000000 +0800
+++ tempbuild/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java 2018-12-13 19:01:29.000000000 +0800
@@ -88,7 +88,7 @@
compute(output, entry.getValue().getOriginalHeader(), entry.getValue().getSequenceAsString().trim(), delimiter, aaTable, propertyList, specificList,
decimalPlace);
......@@ -10,3 +10,31 @@ diff -Nur build/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Comm
}
public static void run(String[] args) throws Exception{
diff -Nur build/pom.xml tempbuild/pom.xml
--- build/pom.xml 2018-12-11 13:56:11.000000000 +0800
+++ tempbuild/pom.xml 2018-12-13 19:03:33.000000000 +0800
@@ -664,16 +664,16 @@
<module>biojava-core</module>
<module>biojava-alignment</module>
<module>biojava-structure</module>
- <module>biojava-structure-gui</module>
- <module>biojava-genome</module>
- <module>biojava-modfinder</module>
- <module>biojava-ws</module>
- <module>biojava-protein-disorder</module>
+ <!--<module>biojava-structure-gui</module>-->
+ <!--<module>biojava-genome</module>-->
+ <!--<module>biojava-modfinder</module>-->
+ <!--<module>biojava-ws</module>-->
+ <!--<module>biojava-protein-disorder</module>-->
<module>biojava-aa-prop</module>
- <module>biojava-survival</module>
- <module>biojava-ontology</module>
+ <!--<module>biojava-survival</module>-->
+ <!--<module>biojava-ontology</module>-->
<!-- Keep integration tests last -->
- <module>biojava-integrationtest</module>
+ <!--<module>biojava-integrationtest</module>-->
</modules>
<inceptionYear>2000</inceptionYear>
<issueManagement>
......@@ -32,12 +32,13 @@
<target name="bm-build">
<exec executable="${mvn-exe}" dir="${bm-build-dir}" failonerror="yes">
<arg value="clean"/>
<arg value="install"/>
</exec>
</target>
<target name="jar">
<copy file="${bm-build-dir}/biojava-aa-prop/target/AAProperties-jar-with-dependencies.jar"
tofile="${bm-jars}/${bm-name}-${bm-version}.jar"/>
todir="${bm-jars}"/>
</target>
</project>
</project>
\ No newline at end of file
This diff is collapsed.
......@@ -10,7 +10,7 @@ public class BioJava extends Benchmark {
String[] args;
public BioJava(Config config, File scratch, File data) throws Exception {
super(config, scratch, data, false);
super(config, scratch, data);
Class<?> clazz = Class.forName("org.biojava.nbio.aaproperties.CommandPrompt", true, loader);
this.method = clazz.getMethod("main", String[].class);
}
......@@ -23,9 +23,6 @@ public class BioJava extends Benchmark {
@Override
public void iterate(String size) throws Exception {
System.out.println(System.out.toString());
this.method.invoke(null, (Object) new String[]{"-i", args[0], "-a"});
System.out.println(System.out.toString());
System.out.println("in here I am out");
}
}
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