From: pvtroshin Date: Thu, 3 Feb 2011 10:13:15 +0000 (+0000) Subject: Disembl further implementation X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=commitdiff_plain;h=6ff5fdd71d597d015fdc1df7eb0a352f8086eaa9 Disembl further implementation git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3663 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/conf/Executable.properties b/conf/Executable.properties index 2e4e419..b8e7723 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -72,14 +72,15 @@ jronn.cluster.cpunum=4 jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 -### Disembl configuration - NOT DISTRIBUTED ### +### Disembl configuration Tisean - Disembl dependancy cannot be redistributed (!) ### #local.disembl.bin.windows= local.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py cluster.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py -#disembl.parameters.file=conf/settings/JronnParameters.xml +disembl.parameters.file=conf/settings/DisemblParameters.xml disembl.limits.file=conf/settings/DisemblLimits.xml disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +### AACon configuration ### local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe local.aacon.bin=/sw/java/latest/bin/java cluster.aacon.bin=/sw/java/latest/bin/java diff --git a/conf/settings/DisemblParameters.xml b/conf/settings/DisemblParameters.xml index 9e50d5d..3820a35 100644 --- a/conf/settings/DisemblParameters.xml +++ b/conf/settings/DisemblParameters.xml @@ -3,17 +3,82 @@ compbio.runner.disorder.Disembl = - Default parameters should not be changed! - Normally the default parameters should not be changed. - If the query protein sequence is very long, >1000 residues, you can download the predictions and - use a local graph/plotting tool such as Grace or OpenOffice.org to plot and zoom the data. - Having identified the potential disordered regions, you should now have a good basis for setting - up expression vectors and/or comparing the data with obtained structural data. - - -sg + Savitzky-Golay smoothing frame + Algorithm Parameter: Savitzky-Golay smoothing frame + sg prog_docs/disembl.html - 1 + 8 + + Integer + 1 + 30 + - + + + diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java index 716859f..8f4256f 100644 --- a/runner/compbio/runner/disorder/Disembl.java +++ b/runner/compbio/runner/disorder/Disembl.java @@ -20,6 +20,7 @@ import java.util.Map; import org.apache.log4j.Logger; import compbio.data.sequence.Score; +import compbio.engine.client.CommandBuilder; import compbio.engine.client.Executable; import compbio.engine.client.PipedExecutable; import compbio.engine.client.SkeletalExecutable; @@ -43,6 +44,12 @@ import compbio.runner.Util; * 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file' * print 'Mode: "default"(nothing) or "scores" which will give scores per * residue in TAB separated format' + * + * Internal parameters names are: sj + * + * //TODO? pw jd ct rt lt + * + * the order is preserved */ public class Disembl extends SkeletalExecutable implements @@ -53,6 +60,7 @@ public class Disembl extends SkeletalExecutable // Cache for Limits information private static LimitsManager limits; + // CHECK THIS !!! public static final String KEY_VALUE_SEPARATOR = Util.SPACE; public Disembl() { @@ -114,4 +122,15 @@ public class Disembl extends SkeletalExecutable return this.getClass(); } + @Override + public CommandBuilder getParameters(ExecProvider provider) { + // If Savitzky-Golay smoothing parameter is specified then set it + String val = cbuilder.getParamValue("sg"); + log.info("DisEMBL sav-gol value: " + val); + if (val != null) { + cbuilder.removeParam("sg"); + cbuilder.setFirst(val); + } + return super.getParameters(provider); + } } diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java index 1460b52..82aa4a3 100644 --- a/testsrc/compbio/data/sequence/SequenceUtilTester.java +++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java @@ -123,7 +123,7 @@ public class SequenceUtilTester { Map aseqs = SequenceUtil.readJRonn(fio); assertNotNull(aseqs); assertEquals(aseqs.size(), 3); - Score aseq = aseqs.get(0); + Score aseq = aseqs.get("Foobar"); assertNotNull(aseq); assertNotNull(aseq.getScores()); // System.out.println(aseq); diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java index 859c4ae..a18b2c4 100644 --- a/testsrc/compbio/runner/conservation/AAConTester.java +++ b/testsrc/compbio/runner/conservation/AAConTester.java @@ -190,7 +190,7 @@ public class AAConTester { assertNotNull(al1.getResults()); HashSet annotations = confAAcon.getResults(); assertNotNull(annotations); - assertEquals(annotations.size(), 1); + assertEquals(annotations.size(), 18); assertEquals(al1.getResults(), annotations); } catch (JobSubmissionException e) { e.printStackTrace(); diff --git a/website/prog_docs/disembl.pdf b/website/prog_docs/disembl.pdf new file mode 100644 index 0000000..30a667a Binary files /dev/null and b/website/prog_docs/disembl.pdf differ