Skip to content

Commit 8fe919a

Browse files
author
Jacob Litman
committed
Updated POMs in preparation for hosting as separate Maven repository; a few comments and log messages also got slightly refactored. Everything seems ready for public Biojava-FFX integration (with the caveat that it will be a separate branch on account of unsolvable API clashes).
1 parent ffdc278 commit 8fe919a

File tree

24 files changed

+78
-78
lines changed

24 files changed

+78
-78
lines changed

‎biojava-aa-prop/pom.xml‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,12 @@
11
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
22
<parent>
3-
<artifactId>biojava</artifactId>
3+
<artifactId>biojava-ffx</artifactId>
44
<groupId>org.biojava</groupId>
55
<version>4.1.1-SNAPSHOT</version>
66
</parent>
77
<modelVersion>4.0.0</modelVersion>
8-
<artifactId>biojava-aa-prop</artifactId>
9-
<name>biojava-aa-prop</name>
8+
<artifactId>biojava-aa-prop-ffx</artifactId>
9+
<name>biojava-aa-prop-ffx</name>
1010
<url>http://www.biojava.org</url>
1111

1212
<build>
@@ -59,12 +59,12 @@
5959
<dependencies>
6060
<dependency>
6161
<groupId>org.biojava</groupId>
62-
<artifactId>biojava-core</artifactId>
62+
<artifactId>biojava-core-ffx</artifactId>
6363
<version>4.1.1-SNAPSHOT</version>
6464
</dependency>
6565
<dependency>
6666
<groupId>org.biojava</groupId>
67-
<artifactId>biojava-structure</artifactId>
67+
<artifactId>biojava-structure-ffx</artifactId>
6868
<version>4.1.1-SNAPSHOT</version>
6969
</dependency>
7070

‎biojava-aa-prop/src/main/assembly/assembly.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@
1212

1313
<!-- <useAllReactorProjects>true</useAllReactorProjects> -->
1414
<includes>
15-
<include>org.biojava:biojava-core</include>
16-
<include>org.biojava:biojava-structure</include>
15+
<include>org.biojava:biojava-core-ffx</include>
16+
<include>org.biojava:biojava-structure-ffx</include>
1717

1818
</includes>
1919
<binaries>

‎biojava-alignment/pom.xml‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,12 @@
22
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
33
<modelVersion>4.0.0</modelVersion>
44
<parent>
5-
<artifactId>biojava</artifactId>
5+
<artifactId>biojava-ffx</artifactId>
66
<groupId>org.biojava</groupId>
77
<version>4.1.1-SNAPSHOT</version>
88
</parent>
9-
<artifactId>biojava-alignment</artifactId>
10-
<name>biojava-alignment</name>
9+
<artifactId>biojava-alignment-ffx</artifactId>
10+
<name>biojava-alignment-ffx</name>
1111

1212
<url>http://maven.apache.org</url>
1313
<properties>
@@ -36,13 +36,13 @@
3636
</dependency>
3737
<dependency>
3838
<groupId>org.biojava</groupId>
39-
<artifactId>biojava-core</artifactId>
39+
<artifactId>biojava-core-ffx</artifactId>
4040
<version>4.1.1-SNAPSHOT</version>
4141
<scope>compile</scope>
4242
</dependency>
4343
<dependency>
4444
<groupId>org.biojava</groupId>
45-
<artifactId>biojava-phylo</artifactId>
45+
<artifactId>biojava-phylo-ffx</artifactId>
4646
<version>4.1.1-SNAPSHOT</version>
4747
<scope>compile</scope>
4848
</dependency>

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/aaindex/ScaledSubstitutionMatrix.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@
3232

3333

3434
/**
35-
* The biojava-alignment module represents substitution matrices with short
35+
* The biojava-alignment-ffx module represents substitution matrices with short
3636
* values. This is for performance reasons. Some substitution matrices, however,
3737
* are provided as float values with up to 2 decimal places.
3838
* <p>

‎biojava-core/pom.xml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
<?xml version="1.0" encoding="UTF-8"?>
22
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
33
<parent>
4-
<artifactId>biojava</artifactId>
4+
<artifactId>biojava-ffx</artifactId>
55
<groupId>org.biojava</groupId>
66
<version>4.1.1-SNAPSHOT</version>
77
</parent>
88
<modelVersion>4.0.0</modelVersion>
9-
<artifactId>biojava-core</artifactId>
10-
<name>biojava-core</name>
9+
<artifactId>biojava-core-ffx</artifactId>
10+
<name>biojava-core-ffx</name>
1111
<url>http://www.biojava.org</url>
1212
<organization>
1313
<name>BioJava</name>

‎biojava-genome/pom.xml‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
<?xml version="1.0" encoding="UTF-8"?>
22
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
33
<parent>
4-
<artifactId>biojava</artifactId>
4+
<artifactId>biojava-ffx</artifactId>
55
<groupId>org.biojava</groupId>
66
<version>4.1.1-SNAPSHOT</version>
77
</parent>
88
<modelVersion>4.0.0</modelVersion>
9-
<artifactId>biojava-genome</artifactId>
10-
<name>biojava-genome</name>
9+
<artifactId>biojava-genome-ffx</artifactId>
10+
<name>biojava-genome-ffx</name>
1111
<repositories>
1212
<repository>
1313
<id>biojava-maven-repo</id>
@@ -57,13 +57,13 @@
5757
</dependency>
5858
<dependency>
5959
<groupId>org.biojava</groupId>
60-
<artifactId>biojava-core</artifactId>
60+
<artifactId>biojava-core-ffx</artifactId>
6161
<version>4.1.1-SNAPSHOT</version>
6262
<scope>compile</scope>
6363
</dependency>
6464
<dependency>
6565
<groupId>org.biojava</groupId>
66-
<artifactId>biojava-alignment</artifactId>
66+
<artifactId>biojava-alignment-ffx</artifactId>
6767
<version>4.1.1-SNAPSHOT</version>
6868
<scope>compile</scope>
6969
</dependency>

‎biojava-integrationtest/pom.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,13 +2,13 @@
22
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
33
<modelVersion>4.0.0</modelVersion>
44
<parent>
5-
<artifactId>biojava</artifactId>
5+
<artifactId>biojava-ffx</artifactId>
66
<groupId>org.biojava</groupId>
77
<version>4.1.1-SNAPSHOT</version>
88
</parent>
9-
<artifactId>biojava-integrationtest</artifactId>
9+
<artifactId>biojava-integrationtest-ffx</artifactId>
1010
<packaging>jar</packaging>
11-
<name>biojava-integrationtest</name>
11+
<name>biojava-integrationtest-ffx</name>
1212
<url>http://www.biojava.org</url>
1313
<properties>
1414
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -22,7 +22,7 @@
2222
</dependency>
2323
<dependency>
2424
<groupId>org.biojava</groupId>
25-
<artifactId>biojava-structure</artifactId>
25+
<artifactId>biojava-structure-ffx</artifactId>
2626
<version>4.1.1-SNAPSHOT</version>
2727
</dependency>
2828
<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-modfinder/pom.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,12 @@
22
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
33
<modelVersion>4.0.0</modelVersion>
44
<parent>
5-
<artifactId>biojava</artifactId>
5+
<artifactId>biojava-ffx</artifactId>
66
<groupId>org.biojava</groupId>
77
<version>4.1.1-SNAPSHOT</version>
88
</parent>
9-
<artifactId>biojava-modfinder</artifactId>
10-
<name>biojava-modfinder</name>
9+
<artifactId>biojava-modfinder-ffx</artifactId>
10+
<name>biojava-modfinder-ffx</name>
1111
<url>http://www.biojava.org</url>
1212
<properties>
1313
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -21,7 +21,7 @@
2121
</dependency>
2222
<dependency>
2323
<groupId>org.biojava</groupId>
24-
<artifactId>biojava-structure</artifactId>
24+
<artifactId>biojava-structure-ffx</artifactId>
2525
<version>4.1.1-SNAPSHOT</version>
2626
<type>jar</type>
2727
<scope>compile</scope>

‎biojava-ontology/pom.xml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,12 +3,12 @@
33
<modelVersion>4.0.0</modelVersion>
44
<parent>
55
<groupId>org.biojava</groupId>
6-
<artifactId>biojava</artifactId>
6+
<artifactId>biojava-ffx</artifactId>
77
<version>4.1.1-SNAPSHOT</version>
88
</parent>
99

10-
<artifactId>biojava-ontology</artifactId>
11-
<name>biojava-ontology</name>
10+
<artifactId>biojava-ontology-ffx</artifactId>
11+
<name>biojava-ontology-ffx</name>
1212
<url>http://maven.apache.org</url>
1313

1414
<dependencies>

‎biojava-phylo/pom.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
<?xml version="1.0" encoding="UTF-8"?>
22
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
33
<parent>
4-
<artifactId>biojava</artifactId>
4+
<artifactId>biojava-ffx</artifactId>
55
<groupId>org.biojava</groupId>
66
<version>4.1.1-SNAPSHOT</version>
77
</parent>
88
<modelVersion>4.0.0</modelVersion>
9-
<artifactId>biojava-phylo</artifactId>
10-
<name>biojava-phylo</name>
9+
<artifactId>biojava-phylo-ffx</artifactId>
10+
<name>biojava-phylo-ffx</name>
1111

1212
<url>http://www.biojava.org</url>
1313
<build>
@@ -30,7 +30,7 @@
3030
</dependency>
3131
<dependency>
3232
<groupId>org.biojava</groupId>
33-
<artifactId>biojava-core</artifactId>
33+
<artifactId>biojava-core-ffx</artifactId>
3434
<version>4.1.1-SNAPSHOT</version>
3535
<scope>compile</scope>
3636
</dependency>

0 commit comments

Comments
 (0)