/
pom.xml
183 lines (169 loc) · 5.14 KB
/
pom.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
<?xml version="1.0" encoding="UTF-8"?>
<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">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.0.2</version>
</parent>
<artifactId>biojava-structure</artifactId>
<name>biojava-structure</name>
<description>The protein structure modules of BioJava.</description>
<licenses>
<license>
<name>GNU LGPL v2</name>
<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<dependencies>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>${ciftools.artifact}</artifactId>
<version>${ciftools.version}</version>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-api</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-serialization</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-codec</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.0.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.0.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>java3d</groupId>
<artifactId>vecmath</artifactId>
<version>1.3.1</version>
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
<!-- Pin! Java 8 requires 1.4.0 -->
<version>1.4.0</version>
</dependency>
<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
Note versions are set in parent pom in dependency management section -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
<!-- Used for json deserialization in PDBStatus -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.13.4.2</version>
</dependency>
<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<!-- Testing related dependencies -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<version>1.6</version>
<scope>test</scope>
</dependency>
<!-- Junit5 dependencies, defined in parent pom. -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
</dependency>
<dependency>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</dependency>
</dependencies>
<properties>
<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
<timestamp>${maven.build.timestamp}</timestamp>
</properties>
<build>
<plugins>
<!-- Excluding demo package is required for avoiding namespace clashes
(demo package is in all modules) for signing the jar. See issue #387 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<excludes>
<exclude>demo/**</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
</plugin>
</plugins>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<includes>
<include>**/*.cif.gz</include>
<include>**/*.pdb.gz</include>
<include>**/*.mat</include>
<include>**/*.xml</include>
</includes>
</resource>
</resources>
</build>
</project>