From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 28 Apr 2011 15:17:21 +0000 (+0000)
Subject: Add method to SequenceUtil to clean the protein sequence
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a16efab90029be12793ac062994de9627b8f3046;p=jabaws.git

Add method to SequenceUtil to clean the protein sequence

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4047 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/build.xml b/build.xml
index fc99421..3d4535e 100644
--- a/build.xml
+++ b/build.xml
@@ -128,23 +128,7 @@
 			<compilerarg value="-Xlint:-unchecked" />
 			<classpath refid="project.classpath" />
 		</javac>
-		<!-- Complile the engines -->
-		<javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
-			<compilerarg value="-Xlint:-all" />
-			<compilerarg value="-Xlint:-unchecked" />
-			<classpath refid="project.classpath" />
-		</javac>
-		<!-- Complile the runners -->
-		<javac srcdir="${basedir}/runner" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
-			<compilerarg value="-Xlint:-unchecked" />
-			<classpath refid="project.classpath" />
-		</javac>
-		<!-- Complile the webservices -->
-		<javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
-			<compilerarg value="-Xlint:-unchecked" />
-			<classpath refid="project.classpath" />
-		</javac>
-
+	
 	</target>
 
 
diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index d0a6cd7..4d61d2a 100644
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -170,6 +170,17 @@ public final class SequenceUtil {
 	}
 
 	/**
+	 * Remove all non AA chars from the sequence
+	 * 
+	 * @param sequence
+	 *            the sequence to clean
+	 * @return cleaned sequence
+	 */
+	public static String cleanProteinSequence(String sequence) {
+		return SequenceUtil.NON_AA.matcher(sequence).replaceAll("");
+	}
+
+	/**
 	 * @param sequence
 	 * @return true is the sequence is a protein sequence, false overwise
 	 */
diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index b6e74ae..3e351bf 100644
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -83,6 +83,31 @@ public class SequenceUtilTester {
 	}
 
 	@Test()
+	public void testCleanProteinSequence() {
+		String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
+		assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
+		// This will still be NON protein sequence despite having only correct
+		// letters because the letters match perfectly the nucleotide sequence!
+		assertFalse(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(dirtySeq)));
+
+		String notaSeq = "atgc1tgatgcatgcatgatgmctga";
+		assertFalse(SequenceUtil.isProteinSequence(notaSeq));
+		assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(notaSeq)));
+
+		String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
+		assertTrue(SequenceUtil.isProteinSequence(AAseq));
+		assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(AAseq)));
+		AAseq += "XU";
+
+		assertFalse(SequenceUtil.isProteinSequence(AAseq));
+		assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(AAseq)));
+	}
+
+	@Test()
 	public void testReadWriteFasta() {
 
 		try {
diff --git a/website/archive/datamodel-1.2.jar b/website/archive/datamodel-1.2.jar
index 4c7cffc..ecbf161 100644
Binary files a/website/archive/datamodel-1.2.jar and b/website/archive/datamodel-1.2.jar differ
diff --git a/website/archive/datamodel-src-1.2.jar b/website/archive/datamodel-src-1.2.jar
index 6b324de..06610ed 100644
Binary files a/website/archive/datamodel-src-1.2.jar and b/website/archive/datamodel-src-1.2.jar differ