Skip to content

Commit 3cad165

Browse files
shaunmahonyshaunmahony
committed
Major repo change in preparation for move to github.
Changing the namespace to org.seqcode.* Tidied and documented the lib dependencies.
1 parent 579ab1e commit 3cad165

File tree

1,486 files changed

+9745
-8615
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

1,486 files changed

+9745
-8615
lines changed

‎LICENSE‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
Copyright (c) 2014 Shaun Mahony
2+
3+
Permission is hereby granted, free of charge, to any person obtaining a copy
4+
of this software and associated documentation files (the "Software"), to deal
5+
in the Software without restriction, including without limitation the rights
6+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
7+
copies of the Software, and to permit persons to whom the Software is
8+
furnished to do so, subject to the following conditions:
9+
10+
The above copyright notice and this permission notice shall be included in
11+
all copies or substantial portions of the Software.
12+
13+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
14+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
15+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
16+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
17+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
18+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
19+
THE SOFTWARE.

‎build.xml‎

Lines changed: 11 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -109,36 +109,13 @@
109109
<property name="pwfiles.path" value="${pwfiles.basepath}/${pwset}"/>
110110
</target>
111111

112-
<target name="unjarwd" unless="build.unjar.dir.present">
113-
<mkdir dir="${build.unjar.dir}.tmp" />
114-
<unjar dest="${build.unjar.dir}.tmp">
115-
<fileset dir="${lib.dir}">
116-
<include name="ApacheCommons/*.jar"/>
117-
<include name="batik/batik-1.7/*.jar"/>
118-
<include name="biojava/biojava-1.5/*.jar"/>
119-
<include name="colt/*.jar"/>
120-
<include name="flanagan/*.jar"/>
121-
<include name="jahmm/*.jar"/>
122-
<include name="jfreechart/jfreechar-1.0.6/*.jar"/>
123-
<include name="junit/*.jar"/>
124-
<include name="libsvm/*.jar"/>
125-
<include name="pal-1.5.1/*.jar"/>
126-
<include name="picard/*.jar"/>
127-
<include name="ojdbc/ojdbc14.jar"/>
128-
<include name="mysql-connector/mysql-connector-java-3.1.12-bin.jar"/>
129-
<include name="log4j/*.jar"/>
130-
</fileset>
131-
</unjar>
132-
<move file="${build.unjar.dir}.tmp" tofile="${build.unjar.dir}" />
133-
</target>
134-
135-
<!-- ======================================================================= -->
112+
<!-- ======================================================================= -->
136113
<!-- Target: makemultigpsjar -->
137-
<!-- Depends: build, unjarwd, setpwfilespath -->
114+
<!-- Depends: build, unjarall, setpwfilespath -->
138115
<!-- Description: Compiles all the client source files and builds the jar -->
139116
<!-- for MultiGPS. ant -Dpwset=mahonylab makemultigpsjar -->
140117
<!-- ======================================================================= -->
141-
<target name="makemultigpsjar" depends="build, unjarwd, setpwfilespath">
118+
<target name="makemultigpsjar" depends="build, unjarall, setpwfilespath">
142119
<delete dir="${build.unjar.dir}/META-INF"/>
143120
<jar destfile="${build.dist.dir}/multigps.${pwset}.jar" manifest="manifests/multigps_manifest.txt">
144121
<fileset dir="${build.classes.dir}" includes="**/*.class"/>
@@ -153,11 +130,11 @@
153130

154131
<!-- ======================================================================= -->
155132
<!-- Target: makeseqviewjar -->
156-
<!-- Depends: build, unjarwd, setpwfilespath -->
133+
<!-- Depends: build, unjarall, setpwfilespath -->
157134
<!-- Description: Compiles all the client source files and builds the jar -->
158135
<!-- for the seqview browser. ant -Dpwset=mahonylab makeseqviewjar -->
159136
<!-- ======================================================================= -->
160-
<target name="makeseqviewjar" depends="build, unjarwd, setpwfilespath">
137+
<target name="makeseqviewjar" depends="build, unjarall, setpwfilespath">
161138
<delete dir="${build.unjar.dir}/META-INF"/>
162139
<jar destfile="${build.dist.dir}/seqview.${pwset}.jar" manifest="manifests/seqview_manifest.txt">
163140
<fileset dir="${build.classes.dir}" includes="**/*.class"/>
@@ -172,11 +149,11 @@
172149

173150
<!-- ======================================================================= -->
174151
<!-- Target: makesigniftestjar -->
175-
<!-- Depends: build, unjarwd, setpwfilespath -->
152+
<!-- Depends: build, unjarall, setpwfilespath -->
176153
<!-- Description: Compiles all the client source files and builds the jar -->
177154
<!-- for the seqview browser. ant -Dpwset=pughlab makesigniftestjar -->
178155
<!-- ======================================================================= -->
179-
<target name="makesigniftestjar" depends="build, unjarwd, setpwfilespath">
156+
<target name="makesigniftestjar" depends="build, unjarall, setpwfilespath">
180157
<delete dir="${build.unjar.dir}/META-INF"/>
181158
<jar destfile="${build.dist.dir}/SignificanceTester.${pwset}.jar" manifest="manifests/signiftest_manifest.txt">
182159
<fileset dir="${build.classes.dir}" includes="**/*.class"/>
@@ -213,7 +190,7 @@
213190
<mkdir dir="${build.unjar.dir}.tmp" />
214191
<unjar dest="${build.unjar.dir}.tmp">
215192
<fileset dir="${lib.dir}">
216-
<include name="ApacheCommons/commons-cli-1.2.jar"/>
193+
<include name="apache-commons/commons-cli-1.3.1.jar"/>
217194
</fileset>
218195
</unjar>
219196
<move file="${build.unjar.dir}.tmp" tofile="${build.unjar.dir}" />
@@ -228,7 +205,7 @@
228205
deprecation="yes"
229206
compiler="modern"
230207
verbose="no">
231-
<include name="edu/psu/compbio/seqcode/gse/projects/readdb/*.java"/>
208+
<include name="org/seqcode/gse/projects/readdb/*.java"/>
232209
</javac>
233210
</target>
234211
<target name="makereaddbjar" depends="compilereaddb, unjarcli">
@@ -240,9 +217,9 @@
240217
tofile="${build.unjar.dir}/Apache-Commons-Cli-LICENSE.txt"/>
241218
<move file="${build.unjar.dir}/META-INF/NOTICE.txt"
242219
tofile="${build.unjar.dir}/Apache-Commons-Cli-NOTICE.txt"/>
243-
<copy file="${src.dir}/edu/psu/compbio/seqcode/gse/projects/readdb/HOWTO"
220+
<copy file="${src.dir}/org/seqcode/gse/projects/readdb/HOWTO"
244221
tofile="${build.classes.dir}/HOWTO"/>
245-
<copy file="${src.dir}/edu/psu/compbio/seqcode/gse/projects/readdb/LICENSE"
222+
<copy file="${src.dir}/org/seqcode/gse/projects/readdb/LICENSE"
246223
tofile="${build.classes.dir}/LICENSE"/>
247224
<delete dir="${build.unjar.dir}/META-INF"/>
248225
<jar destfile="${build.dist.dir}/gse-readdb.jar">

‎db-schemas/annotations.oracle‎

Lines changed: 0 additions & 166 deletions
This file was deleted.

0 commit comments

Comments
 (0)