Better API, throw IOException publically.

core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>beam</artifactId>
         <groupId>uk.ac.ebi.beam</groupId>
-        <version>1.1-SNAPSHOT</version>
+        <version>1.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

core/src/test/java/uk/ac/ebi/beam/GraphBuilderTest.java

@@ -32,6 +32,8 @@
 import org.junit.Assert;
 import org.junit.Test;
 
+import java.io.IOException;
+
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.assertThat;
 import static uk.ac.ebi.beam.Configuration.DoubleBond.OPPOSITE;
@@ -42,7 +44,7 @@
 public class GraphBuilderTest {
 
     @Test
-    public void clockwise_parity() throws InvalidSmilesException {
+    public void clockwise_parity() throws IOException {
 
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomBuilder.aliphatic("C").build())
@@ -64,7 +66,7 @@ public void clockwise_parity() throws InvalidSmilesException {
     }
 
     @Test
-    public void anticlockwise_parity() throws InvalidSmilesException {
+    public void anticlockwise_parity() throws IOException {
 
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomBuilder.aliphatic("C").build())
@@ -86,7 +88,7 @@ public void anticlockwise_parity() throws InvalidSmilesException {
     }
 
     @Test
-    public void e_1_2_difluroethene() throws InvalidSmilesException {
+    public void e_1_2_difluroethene() throws IOException {
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomImpl.AliphaticSubset.Fluorine)
                     .add(AtomImpl.AliphaticSubset.Carbon)
@@ -101,7 +103,7 @@ public void e_1_2_difluroethene() throws InvalidSmilesException {
     }
 
     @Test
-    public void z_1_2_difluroethene() throws InvalidSmilesException {
+    public void z_1_2_difluroethene() throws IOException {
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomImpl.AliphaticSubset.Fluorine)
                     .add(AtomImpl.AliphaticSubset.Carbon)
@@ -117,7 +119,7 @@ public void z_1_2_difluroethene() throws InvalidSmilesException {
 
 
     @Test
-    public void conjugated_consider_existing() throws InvalidSmilesException {
+    public void conjugated_consider_existing() throws IOException {
         // the second configuration considers the existing configuration
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomImpl.AliphaticSubset.Fluorine)
@@ -138,7 +140,7 @@ public void conjugated_consider_existing() throws InvalidSmilesException {
     }
 
     @Test
-    public void conjugated_resolve_conflict() throws InvalidSmilesException {
+    public void conjugated_resolve_conflict() throws IOException {
         // assigning the second one first means we have to consider this
         // on the first one
         GraphBuilder gb = GraphBuilder.create(5);
@@ -160,7 +162,7 @@ public void conjugated_resolve_conflict() throws InvalidSmilesException {
     }
 
     @Test
-    public void conjugated_resolve_conflict2() throws InvalidSmilesException {
+    public void conjugated_resolve_conflict2() throws IOException {
         // we assign the first, third then second - the second one cause
         // a conflict and we must flip one of the others
         GraphBuilder gb = GraphBuilder.create(5);
@@ -213,7 +215,7 @@ public void resolveConflict3() throws Exception {
     }
 
     @Test
-    public void all_trans_octatetraene() throws InvalidSmilesException {
+    public void all_trans_octatetraene() throws IOException {
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomImpl.AliphaticSubset.Carbon)
                     .add(AtomImpl.AliphaticSubset.Carbon)
@@ -240,7 +242,7 @@ public void all_trans_octatetraene() throws InvalidSmilesException {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void impossible_octatetraene() throws InvalidSmilesException {
+    public void impossible_octatetraene() throws IOException {
         GraphBuilder gb = GraphBuilder.create(5);
         Graph g = gb.add(AtomImpl.AliphaticSubset.Carbon)
                     .add(AtomImpl.AliphaticSubset.Carbon)
@@ -302,7 +304,7 @@ public void correctCyclicDb() {
     }
 
     @Test
-    public void suppress_benzene() throws InvalidSmilesException {
+    public void suppress_benzene() throws IOException {
         GraphBuilder gb = GraphBuilder.create(5);
         assertThat(gb.add(Element.Carbon, 1)
                             .add(Element.Carbon, 1)
@@ -320,7 +322,7 @@ public void suppress_benzene() throws InvalidSmilesException {
     }
 
     @Test
-    public void buildExtendedTetrahedral() throws InvalidSmilesException {
+    public void buildExtendedTetrahedral() throws IOException {
         GraphBuilder gb = GraphBuilder.create(4);
         gb = gb.add(Element.Carbon, 3)
                .add(Element.Carbon, 1)

core/src/test/java/uk/ac/ebi/beam/GraphTest.java

@@ -33,6 +33,7 @@
 import org.junit.Assert;
 import org.junit.Test;
 
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
@@ -492,7 +493,7 @@ public void invalidPermutation() {
                    containsString("C1C[N@@]2CC[C@H]1C2"));
     }
 
-    @Test public void cisplatin() throws InvalidSmilesException {
+    @Test public void cisplatin() throws IOException {
         Graph g = Graph.fromSmiles("[NH3][Pt@SP1]([NH3])(Cl)Cl");
         assertThat(g.topologyOf(1).type(),
                    is(Configuration.Type.SquarePlanar));
@@ -501,7 +502,7 @@ public void invalidPermutation() {
                    is("[NH3][Pt@SP3]([NH3])(Cl)Cl"));
     }
 
-    @Test public void trigonalBipyramidal() throws InvalidSmilesException {
+    @Test public void trigonalBipyramidal() throws IOException {
         Graph g = Graph.fromSmiles("S[As@TB1](F)(Cl)(Br)N");
         assertThat(g.topologyOf(1).type(),
                    is(Configuration.Type.TrigonalBipyramidal));
@@ -510,7 +511,7 @@ public void invalidPermutation() {
                    is("S[As@@](F)(Br)(Cl)N"));
     }
 
-    @Test public void trigonalBipyramidal2() throws InvalidSmilesException {
+    @Test public void trigonalBipyramidal2() throws IOException {
         Graph g = Graph.fromSmiles("S[As@TB2](F)(Cl)(Br)N");
         assertThat(g.topologyOf(1).type(),
                    is(Configuration.Type.TrigonalBipyramidal));
@@ -519,7 +520,7 @@ public void invalidPermutation() {
                    is("S[As@](F)(Br)(Cl)N"));
     }
 
-    @Test public void trigonalBipyramidal15() throws InvalidSmilesException {
+    @Test public void trigonalBipyramidal15() throws IOException {
         Graph g = Graph.fromSmiles("F[As@TB15](Cl)(S)(Br)N");
         assertThat(g.topologyOf(1).type(),
                    is(Configuration.Type.TrigonalBipyramidal));
@@ -528,7 +529,7 @@ public void invalidPermutation() {
                    is("F[As@TB17](Cl)(Br)(S)N"));
     }
 
-    @Test public void octahedral1() throws InvalidSmilesException {
+    @Test public void octahedral1() throws IOException {
         Graph g = Graph.fromSmiles("C[Co@](F)(Cl)(Br)(I)S");
         assertThat(g.topologyOf(1).type(),
                    is(Configuration.Type.Octahedral));

core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java

@@ -2,6 +2,8 @@
 
 import org.junit.Test;
 
+import java.io.IOException;
+
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;
@@ -403,7 +405,7 @@ static void test(String delocalised, String localised) throws Exception {
     }
 
 
-    @Test public void biphenylene() throws InvalidSmilesException
+    @Test public void biphenylene() throws IOException
     {
         String smi = "c1cccc2-c3ccccc3-c12";
         assertThat(Graph.fromSmiles(smi).kekule().toSmiles(),

exec/pom.xml

@@ -9,7 +9,7 @@
   <parent>
     <artifactId>beam</artifactId>
     <groupId>uk.ac.ebi.beam</groupId>
-    <version>1.1-SNAPSHOT</version>
+    <version>1.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

exec/src/main/java/uk/ac/ebi/beam/Anonymise.java

@@ -6,6 +6,8 @@
 
 import joptsimple.OptionSet;
 
+import java.io.IOException;
+
 /**
  * Anonymise SMILES input to all '*' atoms. Bond orders can optionally be emitted.
  */
@@ -23,7 +25,7 @@ Functor createFunctor(OptionSet optionSet) {
         final boolean bondorders = optionSet.has("bo");
         return new Functor() {
             @Override
-            String map(String str) throws InvalidSmilesException {
+            String map(String str) throws IOException {
 
                 Graph g = Graph.fromSmiles(str);
 

exec/src/main/java/uk/ac/ebi/beam/Aromatise.java

@@ -6,6 +6,8 @@
 
 import joptsimple.OptionSet;
 
+import java.io.IOException;
+
 /**
  * Simple module simply Kekulises then emits and normalised
  * (by beam's model) aromatic form of the SMILES.
@@ -20,7 +22,7 @@ public Aromatise() {
     Functor createFunctor(OptionSet optionSet) {
         return new Functor() {
             @Override
-            String map(String str) throws InvalidSmilesException {
+            String map(String str) throws IOException {
                 return Graph.fromSmiles(str).kekule().aromatic().toSmiles() + suffixedId(str);
             }
         };

exec/src/main/java/uk/ac/ebi/beam/FunctorCmdLnModule.java

@@ -284,6 +284,6 @@ static String escapeForPrintf(String str) {
     }
 
     abstract class Functor {
-        abstract String map(String str) throws InvalidSmilesException;
+        abstract String map(String str) throws IOException;
     }
 }

exec/src/main/java/uk/ac/ebi/beam/Shuffle.java

@@ -51,7 +51,7 @@ void process(BufferedReader brdr, BufferedWriter bwtr, InputCounter counter, Opt
             report("%d => %d\n", cnt, gencnt);
     }
 
-    private Set<String> generate(String str, int n, int m) throws InvalidSmilesException {
+    private Set<String> generate(String str, int n, int m) throws IOException {
 
         final Set<String> smis = new HashSet<String>();
 

func/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>beam</artifactId>
         <groupId>uk.ac.ebi.beam</groupId>
-        <version>1.1-SNAPSHOT</version>
+        <version>1.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

pom.xml

@@ -7,7 +7,7 @@
     <description>SMILES parsing and generation library for cheminformatics</description>
     <url>http://www.github.com/johnmay/beam/</url>
     <packaging>pom</packaging>
-    <version>1.1-SNAPSHOT</version>
+    <version>1.1</version>
     <modules>
         <module>core</module>
         <module>func</module>