Calculate score for smallest sequence + Bump to v1.0.3

Also throw exception when sequence is empty. Fixes #2
3D-e-Chem · May 19, 2016 · b2b80ad · b2b80ad
1 parent 0eee935
commit b2b80ad
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,18 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+## [1.0.3] - 2015-05-19
+
+### Fixed
+
+* Throw exception when sequence is empty
+
+## [1.0.2] - 2015-05-19
+
+### Fixed
+
+* exception when sequences are not same length (#2)
+
 ## [1.0.1] - 2015-05-04
 
 Initial release

diff --git a/feature/feature.xml b/feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.sstea.feature"
       label="ss-TEA"
-      version="1.0.1"
+      version="1.0.3"
       provider-name="Netherlands eScience Center">
 
    <description url="https://github.com/3D-e-Chem/knime-sstea">

diff --git a/feature/pom.xml b/feature/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-		<version>1.0.1</version>
+		<version>1.0.3</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.sstea.feature</artifactId>

diff --git a/p2/category.xml b/p2/category.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature url="features/nl.esciencecenter.e3dchem.sstea.feature-1.0.1.jar" id="nl.esciencecenter.e3dchem.sstea.feature" version="1.0.1">
+   <feature url="features/nl.esciencecenter.e3dchem.sstea.feature-1.0.3.jar" id="nl.esciencecenter.e3dchem.sstea.feature" version="1.0.3">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
-   <feature url="features/nl.esciencecenter.e3dchem.sstea.feature.source_1.0.1.jar" id="nl.esciencecenter.e3dchem.sstea.feature.source" version="1.0.1">
+   <feature url="features/nl.esciencecenter.e3dchem.sstea.feature.source_1.0.3.jar" id="nl.esciencecenter.e3dchem.sstea.feature.source" version="1.0.3">
       <category name="nl.esciencecenter.3D-e-Chem.sources"/>
    </feature>
    <category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">

diff --git a/p2/pom.xml b/p2/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
         <groupId>nl.esciencecenter.e3dchem.sstea</groupId>
-        <version>1.0.1</version>
+        <version>1.0.3</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.sstea.p2</artifactId>
     <packaging>eclipse-repository</packaging>

diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Subfamily specific two entropy analysis score
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sstea.plugin;singleton:=true
-Bundle-Version: 1.0.1
+Bundle-Version: 1.0.3
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.knime.core;bundle-version="[3.1.0,4.0.0)",
  org.knime.base;bundle-version="[3.1.0,4.0.0)"

diff --git a/plugin/pom.xml b/plugin/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-		<version>1.0.1</version>
+		<version>1.0.3</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.sstea.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>

diff --git a/plugin/src/nl/esciencecenter/e3dchem/sstea/Scorer.java b/plugin/src/nl/esciencecenter/e3dchem/sstea/Scorer.java
@@ -27,7 +27,10 @@ public List<Score> scoreit(Map<String, String> sequences, Set<String> subfamily_
             throw new KeySelectorException("Not all subfamily_members are in keys of sequences");
         }
 
-        int minimumSequenceLength = Collections.max(sequences.values()).length();
+        int minimumSequenceLength = Collections.min(sequences.values()).length();
+        if (minimumSequenceLength == 0) {
+            throw new IllegalArgumentException("Empty sequence");
+        }
         int outSideNr = sequences.size() - subfamily_members.size();
         int inSideNr = subfamily_members.size();
 

diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>nl.esciencecenter.e3dchem.sstea</groupId>
     <artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-    <version>1.0.1</version>
+    <version>1.0.3</version>
     <packaging>pom</packaging>
 
     <organization>

diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Tests
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sstea.tests
-Bundle-Version: 1.0.1
+Bundle-Version: 1.0.3
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.junit;bundle-version="4.12.0",
  org.knime.core;bundle-version="[3.1.0,4.0.0)",

diff --git a/tests/pom.xml b/tests/pom.xml
@@ -6,7 +6,7 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xs
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-		<version>1.0.1</version>
+		<version>1.0.3</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.sstea.tests</artifactId>

diff --git a/tests/src/nl/esciencecenter/e3dchem/sstea/ScorerTest.java b/tests/src/nl/esciencecenter/e3dchem/sstea/ScorerTest.java
@@ -146,4 +146,24 @@ public void conserved75_subfamily() throws KeySelectorException {
         assertEquals(expected, scores);
     }
 
+    @Test
+    public void jaggedSequence() throws KeySelectorException {
+        sequences.put("seq10", "ICK");
+        Set<String> subfamily_members = new HashSet<String>();
+        subfamily_members.add("seq1");
+        List<Score> scores = scorer.scoreit(sequences, subfamily_members);
+        assertEquals(scores.size(), 1);
+    }
+
+    @Test
+    public void emptySequence() throws KeySelectorException {
+        sequences.put("seq10", "");
+        Set<String> subfamily_members = new HashSet<String>();
+        subfamily_members.add("seq1");
+
+        thrown.expect(IllegalArgumentException.class);
+
+        scorer.scoreit(sequences, subfamily_members);
+    }
+
 }