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Commit d081b12

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hilbertglmhilbertglm
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Changed the version to 7.1.0-SNAPSHOT. Made changes per review.
1 parent 26b21d7 commit d081b12

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15 files changed

+36
-36
lines changed

15 files changed

+36
-36
lines changed

‎biojava-aa-prop/pom.xml‎

Lines changed: 3 additions & 3 deletions
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@@ -2,7 +2,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-alignment/pom.xml‎

Lines changed: 2 additions & 2 deletions
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@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
7-
<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-alignment</artifactId>
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<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-core/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-core</artifactId>

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaStreamer.java‎

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@@ -10,6 +10,7 @@
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.UncheckedIOException;
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import java.nio.file.Path;
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import java.util.Collections;
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import java.util.Iterator;
@@ -27,7 +28,7 @@
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* for use in a functional programming paradigm.
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*
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* @author Gary Murphy
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* @since 7.0.3
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* @since 7.1.0
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*/
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public class FastaStreamer {
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@@ -135,12 +136,12 @@ private ProteinSequence next(FastaReader<ProteinSequence, AminoAcidCompound> rea
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}
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if (iterator.hasNext()) {
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Map.Entry<String, ProteinSequence> entry = iterator.next();
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return createSequence(entry.getKey(), entry.getValue());
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return createSequence(entry.getValue());
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}
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closed = true;
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reader.close();
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} catch (IOException exception) {
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throw new RuntimeException(String.format("I/O error reading the FASTA file from '%s'", getPath()));
144+
throw new UncheckedIOException(String.format("I/O error reading the FASTA file from '%s'", getPath()), exception);
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}
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return null;
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}
@@ -153,11 +154,10 @@ private ProteinSequence next(FastaReader<ProteinSequence, AminoAcidCompound> rea
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* this is an opportunity for the implementer to build specific information into the user collection space
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* of the sequence
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*
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* @param header the original header
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* @param sequence the protein sequence
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* @return the sequence
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*/
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protected ProteinSequence createSequence(String header, ProteinSequence sequence) {
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protected ProteinSequence createSequence(ProteinSequence sequence) {
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return sequence;
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}
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‎biojava-genome/pom.xml‎

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@@ -3,7 +3,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-genome</artifactId>
@@ -71,13 +71,13 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-integrationtest/pom.xml‎

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@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-integrationtest</artifactId>
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<packaging>jar</packaging>
@@ -40,7 +40,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
43-
<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>

‎biojava-modfinder/pom.xml‎

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@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.0.3-SNAPSHOT</version>
7+
<version>7.1.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-modfinder</artifactId>
1010
<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
34-
<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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<type>jar</type>
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<scope>compile</scope>
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</dependency>

‎biojava-ontology/pom.xml‎

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@@ -4,7 +4,7 @@
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<parent>
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<groupId>org.biojava</groupId>
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<artifactId>biojava</artifactId>
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<version>7.0.3-SNAPSHOT</version>
7+
<version>7.1.0-SNAPSHOT</version>
88
</parent>
99

1010
<artifactId>biojava-ontology</artifactId>

‎biojava-protein-comparison-tool/pom.xml‎

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@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
7-
<version>7.0.3-SNAPSHOT</version>
7+
<version>7.1.0-SNAPSHOT</version>
88
</parent>
99

1010
<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
39-
<version>7.0.3-SNAPSHOT</version>
39+
<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
45-
<version>7.0.3-SNAPSHOT</version>
45+
<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<dependency>
5353
<groupId>org.biojava</groupId>
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<artifactId>biojava-structure-gui</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>net.sourceforge.jmol</groupId>

‎biojava-protein-disorder/pom.xml‎

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@@ -3,7 +3,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.0.3-SNAPSHOT</version>
6+
<version>7.1.0-SNAPSHOT</version>
77
</parent>
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<artifactId>biojava-protein-disorder</artifactId>
99
<packaging>jar</packaging>
@@ -63,7 +63,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.0.3-SNAPSHOT</version>
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<version>7.1.0-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or
6969
scopes here) -->

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