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Revision c37c8506

Added by Ben Stöver about 5 years ago

Plugin molecular.lib refactored to use direct project dependencies. This should not be merged into trunk, since this is only for development state. (Currently the trunk is anyway already using different Maven dependencies.)
Adjustments to recent changes in JPhyloIO.

View differences:

eu.etaxonomy.taxeditor.molecular.lib/.classpath
1 1
<?xml version="1.0" encoding="UTF-8"?>
2 2
<classpath>
3
	<classpathentry exported="true" kind="lib" path="lib/commons-collections4-4.1.jar"/>
4
	<classpathentry exported="true" kind="lib" path="lib/core-1.9.2.jar"/>
5
	<classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2.jar"/>
3
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.biojava1/bin/"/>
6 4
	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
7 5
	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
8 6
	<classpathentry exported="true" kind="lib" path="lib/owlapi-xmlutils-4.1.4.jar"/>
9
	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
10
	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2-SNAPSHOT.jar"/>
11
	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
12
	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swt-2-SNAPSHOT.jar"/>
13
	<classpathentry exported="true" kind="lib" path="lib/jphyloio-core-0-SNAPSHOT.jar"/>
14
	<classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0-SNAPSHOT.jar"/>
15
	<classpathentry exported="true" kind="lib" path="lib/libralign-core-0-SNAPSHOT.jar"/>
16
	<classpathentry exported="true" kind="lib" path="lib/libralign-swt-0-SNAPSHOT.jar"/>
17
	<classpathentry exported="true" kind="lib" path="lib/tic-core-2-SNAPSHOT.jar"/>
18
	<classpathentry exported="true" kind="lib" path="lib/tic-swt-2-SNAPSHOT.jar"/>
7
	<classpathentry exported="true" kind="lib" path="lib/commons-collections4-4.1.jar"/>
8
	<classpathentry exported="true" kind="lib" path="lib/core-1.9.2.jar"/>
9
	<classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2.jar"/>
10
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.bio/bin"/>
11
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.core/bin"/>
12
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.swing/bin"/>
13
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.swt/bin"/>
14
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.core/bin"/>
15
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.io/bin"/>
16
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.swt/bin"/>
17
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.tic.core/bin"/>
18
	<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.tic.swt/bin"/>
19
	<classpathentry exported="true" kind="lib" path="lib/JPhyloIO/bin" sourcepath="lib/JPhyloIO/bin"/>
19 20
	<classpathentry kind="output" path="target/classes"/>
20 21
</classpath>
eu.etaxonomy.taxeditor.molecular.lib/.project
26 26
		<nature>org.eclipse.pde.PluginNature</nature>
27 27
		<nature>org.eclipse.jdt.core.javanature</nature>
28 28
	</natures>
29
	<linkedResources>
30
		<link>
31
			<name>lib/JPhyloIO</name>
32
			<type>2</type>
33
			<locationURI>WORKSPACE_LOC/JPhyloIO</locationURI>
34
		</link>
35
		<link>
36
			<name>lib/info.bioinfweb.commons.bio</name>
37
			<type>2</type>
38
			<locationURI>WORKSPACE_LOC/info.bioinfweb.commons.bio</locationURI>
39
		</link>
40
		<link>
41
			<name>lib/info.bioinfweb.commons.core</name>
42
			<type>2</type>
43
			<locationURI>WORKSPACE_LOC/info.bioinfweb.commons.core</locationURI>
44
		</link>
45
		<link>
46
			<name>lib/info.bioinfweb.commons.swing</name>
47
			<type>2</type>
48
			<locationURI>WORKSPACE_LOC/info.bioinfweb.commons.swing</locationURI>
49
		</link>
50
		<link>
51
			<name>lib/info.bioinfweb.commons.swt</name>
52
			<type>2</type>
53
			<locationURI>WORKSPACE_LOC/info.bioinfweb.commons.swt</locationURI>
54
		</link>
55
		<link>
56
			<name>lib/info.bioinfweb.libralign.biojava1</name>
57
			<type>2</type>
58
			<locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.biojava1</locationURI>
59
		</link>
60
		<link>
61
			<name>lib/info.bioinfweb.libralign.core</name>
62
			<type>2</type>
63
			<locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.core</locationURI>
64
		</link>
65
		<link>
66
			<name>lib/info.bioinfweb.libralign.io</name>
67
			<type>2</type>
68
			<locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.io</locationURI>
69
		</link>
70
		<link>
71
			<name>lib/info.bioinfweb.libralign.swt</name>
72
			<type>2</type>
73
			<locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.swt</locationURI>
74
		</link>
75
		<link>
76
			<name>lib/info.bioinfweb.tic.core</name>
77
			<type>2</type>
78
			<locationURI>WORKSPACE_LOC/info.bioinfweb.tic.core</locationURI>
79
		</link>
80
		<link>
81
			<name>lib/info.bioinfweb.tic.swt</name>
82
			<type>2</type>
83
			<locationURI>WORKSPACE_LOC/info.bioinfweb.tic.swt</locationURI>
84
		</link>
85
	</linkedResources>
29 86
</projectDescription>
eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
5 5
Bundle-Version: 4.2.0.qualifier
6 6
Bundle-ClassPath: .,
7 7
 lib/owlapi-xmlutils-4.1.4.jar,
8
 lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
9
 lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
10
 lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,
11
 lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,
12
 lib/jphyloio-core-0-SNAPSHOT.jar,
13
 lib/libralign-biojava1-0-SNAPSHOT.jar,
14
 lib/libralign-core-0-SNAPSHOT.jar,
15
 lib/libralign-swt-0-SNAPSHOT.jar,
16
 lib/tic-core-2-SNAPSHOT.jar,
17
 lib/tic-swt-2-SNAPSHOT.jar,
18 8
 lib/commons-collections4-4.1.jar,
19 9
 lib/core-1.9.2.jar,
20
 lib/sequencing-1.9.2.jar
10
 lib/sequencing-1.9.2.jar,
11
 lib/info.bioinfweb.commons.bio/bin/,
12
 lib/info.bioinfweb.commons.core/bin/,
13
 lib/info.bioinfweb.commons.swing/bin/,
14
 lib/info.bioinfweb.commons.swt/bin/,
15
 lib/info.bioinfweb.libralign.core/bin/,
16
 lib/info.bioinfweb.libralign.io/bin/,
17
 lib/info.bioinfweb.libralign.swt/bin/,
18
 lib/info.bioinfweb.tic.core/bin/,
19
 lib/info.bioinfweb.tic.swt/bin/,
20
 lib/JPhyloIO/bin/,
21
 lib/info.bioinfweb.libralign.biojava1/bin/
21 22
Export-Package: info.bioinfweb.commons,
22 23
 info.bioinfweb.commons.appversion,
23 24
 info.bioinfweb.commons.beans,
......
36 37
 info.bioinfweb.jphyloio,
37 38
 info.bioinfweb.jphyloio.dataadapters,
38 39
 info.bioinfweb.jphyloio.dataadapters.implementations,
39
 info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter,
40
 info.bioinfweb.jphyloio.dataadapters.implementations.store,
40 41
 info.bioinfweb.jphyloio.dataadapters.implementations.receivers,
41 42
 info.bioinfweb.jphyloio.events,
42 43
 info.bioinfweb.jphyloio.events.meta,
......
48 49
 info.bioinfweb.jphyloio.formats.mega,
49 50
 info.bioinfweb.jphyloio.formats.newick,
50 51
 info.bioinfweb.jphyloio.formats.nexml,
51
 info.bioinfweb.jphyloio.formats.nexml.nexmlreceivers,
52 52
 info.bioinfweb.jphyloio.formats.nexus,
53 53
 info.bioinfweb.jphyloio.formats.nexus.blockhandlers,
54 54
 info.bioinfweb.jphyloio.formats.nexus.commandreaders,
......
60 60
 info.bioinfweb.jphyloio.formats.pde,
61 61
 info.bioinfweb.jphyloio.formats.phylip,
62 62
 info.bioinfweb.jphyloio.formats.phyloxml,
63
 info.bioinfweb.jphyloio.formats.phyloxml.elementreader,
63 64
 info.bioinfweb.jphyloio.formats.text,
64 65
 info.bioinfweb.jphyloio.formats.xml,
65 66
 info.bioinfweb.jphyloio.formats.xtg,
66
 info.bioinfweb.jphyloio.tools,
67
 info.bioinfweb.jphyloio.utils,
68
 info.bioinfweb.jphyloio.objecttranslation,
69
 info.bioinfweb.jphyloio.objecttranslation.implementations,
67 70
 info.bioinfweb.libralign,
68 71
 info.bioinfweb.libralign.actions,
69 72
 info.bioinfweb.libralign.alignmentarea,
eu.etaxonomy.taxeditor.molecular.lib/build.properties
1 1
bin.includes = META-INF/,\
2 2
               lib/tic-swt-2.0.0-preview-1.jar,\
3
               lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,\
4
               lib/bioinfweb-commons-core-2-SNAPSHOT.jar,\
5
               lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,\
6
               lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,\
7
               lib/jphyloio-core-0-SNAPSHOT.jar,\
8
               lib/libralign-biojava1-0-SNAPSHOT.jar,\
9
               lib/libralign-core-0-SNAPSHOT.jar,\
10
               lib/libralign-swt-0-SNAPSHOT.jar,\
11
               lib/tic-core-2-SNAPSHOT.jar,\
12
               lib/tic-swt-2-SNAPSHOT.jar,\
13 3
               lib/commons-collections4-4.1.jar,\
14 4
               lib/core-1.9.2.jar,\
15
               lib/sequencing-1.9.2.jar
5
               lib/sequencing-1.9.2.jar,\
6
               lib/info.bioinfweb.commons.bio/bin/,\
7
               lib/info.bioinfweb.commons.core/bin/,\
8
               lib/info.bioinfweb.commons.swing/bin/,\
9
               lib/info.bioinfweb.commons.swt/bin/,\
10
               lib/info.bioinfweb.libralign.core/bin/,\
11
               lib/info.bioinfweb.libralign.io/bin/,\
12
               lib/info.bioinfweb.libralign.swt/bin/,\
13
               lib/info.bioinfweb.tic.core/bin/,\
14
               lib/info.bioinfweb.tic.swt/bin/,\
15
               lib/JPhyloIO/bin/,\
16
               lib/info.bioinfweb.libralign.biojava1/bin/
16 17
               lib/jphyloio-core-0-SNAPSHOT.jar,\
17 18
               lib/owlapi-xmlutils-4.1.4.jar
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java
18 18
import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter;
19 19
import info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter;
20 20
import info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter;
21
import info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter.StoreObjectListDataAdapter;
21
import info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter;
22 22
import info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent;
23 23
import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent;
24 24
import info.bioinfweb.jphyloio.events.SequenceTokensEvent;
eu.etaxonomy.taxeditor/rcp.target
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<?pde version="3.8"?><target name="Eclipse Indigo Target" sequenceNumber="7">
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<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">
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<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">
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</location>
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</locations>
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</target>
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