updating some hard coded paths

andreasprlic · andreasprlic · commit 5f94ec71acae · 2015-01-29T17:38:29.000-08:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
@@ -84,7 +84,7 @@ public static IUPACParser getInstance() {
     return IOD.INSTANCE;
   }
 
-  public static final String      IUPAC_LOCATION = "org/biojava3/core/sequence/iupac.txt";
+  public static final String      IUPAC_LOCATION = "/org/biojava/nbio/core/sequence/iupac.txt";
 
   private InputStream              is;
   private List<IUPACTable>         tables;
diff --git a/biojava-core/src/main/resources/org/biojava/nbio/core/sequence/iupac.txt b/biojava-core/src/main/resources/org/biojava/nbio/core/sequence/iupac.txt
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
@@ -61,13 +61,13 @@ public class TranslationTest {
 	@BeforeClass
 	public static void parseSequences() {
 		InputStream cdsIs = new ClasspathResource(
-				"org/biojava3/core/sequence/BRCA2-cds.fasta").getInputStream();
+				"/org/biojava/nbio/core/sequence/BRCA2-cds.fasta").getInputStream();
 		InputStream pepIs = new ClasspathResource(
-				"org/biojava3/core/sequence/BRCA2-peptide.fasta").getInputStream();
+				"/org/biojava/nbio/core/sequence/BRCA2-peptide.fasta").getInputStream();
 		InputStream volDnaIs = new ClasspathResource(
-				"org/biojava3/core/sequence/volvox-cds.fasta").getInputStream();
+				"/org/biojava/nbio/core/sequence/volvox-cds.fasta").getInputStream();
 		InputStream volPepIs = new ClasspathResource(
-				"org/biojava3/core/sequence/volvox-peptide.fasta").getInputStream();
+				"/org/biojava/nbio/core/sequence/volvox-peptide.fasta").getInputStream();
 
 		try {
 			FastaReader<DNASequence, NucleotideCompound> dnaReader = new FastaReader<DNASequence, NucleotideCompound>(cdsIs,
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java
@@ -184,7 +184,7 @@ private String doXMLSerialization(ModifiedCompound mc) throws IOException{
 	}
 
 	public void testFlatFileParsing(){
-		InputStream inStream = this.getClass().getResourceAsStream("/org/biojava3/protmod/parser/modifiedCompound.xml");
+		InputStream inStream = this.getClass().getResourceAsStream("/org/biojava/nbio/protmod/parser/modifiedCompound.xml");
 		assertNotNull(inStream);
 		try {
 			String xml = convertStreamToString(inStream);
diff --git a/pom.xml b/pom.xml
@@ -44,7 +44,7 @@
 		<connection>scm:git:git://github.com/biojava/biojava.git</connection>
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
-		<tag>biojava-4.0.0</tag>
+
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

Original file line number	Diff line number	Diff line change
`@@ -84,7 +84,7 @@ public static IUPACParser getInstance() {`
`84`	`84`	`return IOD.INSTANCE;`
`85`	`85`	`}`
`86`	`86`
`87`		`- public static final String IUPAC_LOCATION = "org/biojava3/core/sequence/iupac.txt";`
	`87`	`+ public static final String IUPAC_LOCATION = "/org/biojava/nbio/core/sequence/iupac.txt";`
`88`	`88`
`89`	`89`	`private InputStream is;`
`90`	`90`	`private List<IUPACTable> tables;`
Original file line number	Diff line number	Diff line change
`@@ -184,7 +184,7 @@ private String doXMLSerialization(ModifiedCompound mc) throws IOException{`
`184`	`184`	`}`
`185`	`185`
`186`	`186`	`public void testFlatFileParsing(){`
`187`		`- InputStream inStream = this.getClass().getResourceAsStream("/org/biojava3/protmod/parser/modifiedCompound.xml");`
	`187`	`+ InputStream inStream = this.getClass().getResourceAsStream("/org/biojava/nbio/protmod/parser/modifiedCompound.xml");`
`188`	`188`	`assertNotNull(inStream);`
`189`	`189`	`try {`
`190`	`190`	`String xml = convertStreamToString(inStream);`