source: tags/arb-6.0.5/SOURCE_TOOLS/dep.4dummy

Last change on this file was 11401, checked in by westram, 10 years ago
  • reintegrates 'tree' into 'trunk':
    • consensus trees:
      • support for merging partial trees ("worked" before, but results were crap; implements #65)
      • generated trees are automatically re-rooted and -ordered
      • always list source trees in consensus-tree-comment; show info about partial trees
      • fixed progress bar
    • made GBT_TREE a base class of other tree classes (implements #31)
    • save tree properties in properties (not in DB)
    • new functions 'Remove zombies/marked from ALL trees'
    • tree load/save: layout fixes
    • unit tests
      • added tests for basic tree modifications (PARSIMONY)
    • performance:
      • compute_tree updates tree information in one traversal
      • tree generators are now capable to generate any type of tree (w/o needing to copy it once)
    • bugfixes:
      • NNI (of marked species) was also always performed for colored species
      • centered beautify-order is stable now
      • improved 'search optimal root'
  • adds:
File size: 5.0 KB
Line 
1ARB_GDE/ARB_GDE.dummy: SL/AW_NAME/AW_NAME.dummy SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy
2AWTC/AWTC.dummy: SERVERCNTRL/SERVERCNTRL.dummy WINDOW/WINDOW.dummy
3AWTI/AWTI.dummy: GENOM_IMPORT/GENOM_IMPORT.dummy SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy SL/SEQIO/SEQIO.dummy
4CONSENSUS_TREE/CONSENSUS_TREE.dummy: SL/ROOTED_TREE/ROOTED_TREE.dummy
5CONVERTALN/CONVERTALN.dummy: ARBDB/ARBDB.dummy
6DBSERVER/DBSERVER.dummy: SERVERCNTRL/SERVERCNTRL.dummy
7DIST/DIST.dummy: CONSENSUS_TREE/CONSENSUS_TREE.dummy SERVERCNTRL/SERVERCNTRL.dummy SL/ARB_TREE/ARB_TREE.dummy SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy SL/MACROS/MACROS.dummy SL/NDS/NDS.dummy SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy
8EDIT4/EDIT4.dummy: ARB_GDE/ARB_GDE.dummy RNA3D/RNA3D.dummy SECEDIT/SECEDIT.dummy SL/AW_HELIX/AW_HELIX.dummy SL/FAST_ALIGNER/FAST_ALIGNER.dummy SL/MACROS/MACROS.dummy SL/NDS/NDS.dummy SL/TRANSLATE/TRANSLATE.dummy STAT/STAT.dummy
9GENOM/GENOM.dummy: SL/DB_UI/DB_UI.dummy SL/LOCATION/LOCATION.dummy SL/NDS/NDS.dummy SL/TRANSLATE/TRANSLATE.dummy
10GENOM_IMPORT/GENOM_IMPORT.dummy: GENOM/GENOM.dummy SL/REGEXPR/REGEXPR.dummy
11GL/glAW/libglAW.dummy: WINDOW/WINDOW.dummy
12HELP_SOURCE/arb_help2xml.dummy: XML/XML.dummy
13ISLAND_HOPPING/ISLAND_HOPPING.dummy: ARBDB/ARBDB.dummy
14MERGE/MERGE.dummy: SL/DB_UI/DB_UI.dummy SL/MACROS/MACROS.dummy SL/TREE_ADMIN/TREE_ADMIN.dummy
15MULTI_PROBE/MULTI_PROBE.dummy: SERVERCNTRL/SERVERCNTRL.dummy SL/REGEXPR/REGEXPR.dummy SL/TREEDISP/TREEDISP.dummy
16NALIGNER/NALIGNER.dummy: SERVERCNTRL/SERVERCNTRL.dummy SL/HELIX/HELIX.dummy
17NAMES/NAMES.dummy: NAMES_COM/NAMES_COM.dummy SERVERCNTRL/SERVERCNTRL.dummy
18NTREE/NTREE.dummy: ARB_GDE/ARB_GDE.dummy AWTI/AWTI.dummy CONSENSUS_TREE/CONSENSUS_TREE.dummy MERGE/MERGE.dummy MULTI_PROBE/MULTI_PROBE.dummy PRIMER_DESIGN/PRIMER_DESIGN.dummy PROBE_DESIGN/PROBE_DESIGN.dummy SEQ_QUALITY/SEQ_QUALITY.dummy SL/INSDEL/INSDEL.dummy SL/REFENTRIES/REFENTRIES.dummy SL/TREE_READ/TREE_READ.dummy SL/TREE_WRITE/TREE_WRITE.dummy STAT/STAT.dummy
19PARSIMONY/PARSIMONY.dummy: SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy SL/MACROS/MACROS.dummy SL/TREEDISP/TREEDISP.dummy
20PERLTOOLS/arb_proto_2_xsub.dummy: ARBDB/ARBDB.dummy
21PHYLO/PHYLO.dummy: AWT/AWT.dummy SL/MACROS/MACROS.dummy SL/MATRIX/MATRIX.dummy
22PRIMER_DESIGN/PRIMER_DESIGN.dummy: AWT/AWT.dummy
23PROBE/PROBE.dummy: PROBE_COM/PROBE_COM.dummy SERVERCNTRL/SERVERCNTRL.dummy SL/HELIX/HELIX.dummy SL/PTCLEAN/PTCLEAN.dummy
24PROBE_DESIGN/PROBE_DESIGN.dummy: SERVERCNTRL/SERVERCNTRL.dummy SL/TREEDISP/TREEDISP.dummy
25RNA3D/RNA3D.dummy: AWT/AWT.dummy GL/glAW/glAW.dummy GL/glpng/glpng.dummy SL/HELIX/HELIX.dummy
26SECEDIT/SECEDIT.dummy: AWT/AWT.dummy SL/HELIX/HELIX.dummy SL/PRONUC/PRONUC.dummy
27SEQ_QUALITY/SEQ_QUALITY.dummy: SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy
28SERVERCNTRL/SERVERCNTRL.dummy: ARBDB/ARBDB.dummy PROBE_COM/PROBE_COM.dummy
29SL/ALIVIEW/ALIVIEW.dummy: SL/FILTER/FILTER.dummy
30SL/AP_TREE/AP_TREE.dummy: AWT/AWT.dummy SL/ARB_TREE/ARB_TREE.dummy
31SL/ARB_TREE/ARB_TREE.dummy: SL/ROOTED_TREE/ROOTED_TREE.dummy SL/SEQUENCE/SEQUENCE.dummy
32SL/AW_HELIX/AW_HELIX.dummy: SL/HELIX/HELIX.dummy WINDOW/WINDOW.dummy
33SL/AW_NAME/AW_NAME.dummy: AWT/AWT.dummy SERVERCNTRL/SERVERCNTRL.dummy
34SL/CB/CB.dummy: CORE/CORE.dummy
35SL/DB_QUERY/DB_QUERY.dummy: SL/ITEMS/ITEMS.dummy
36SL/DB_SCANNER/DB_SCANNER.dummy: SL/AW_NAME/AW_NAME.dummy SL/ITEMS/ITEMS.dummy
37SL/DB_UI/DB_UI.dummy: AWTC/AWTC.dummy SL/DB_QUERY/DB_QUERY.dummy SL/DB_SCANNER/DB_SCANNER.dummy
38SL/FAST_ALIGNER/FAST_ALIGNER.dummy: AWT/AWT.dummy AWTC/AWTC.dummy ISLAND_HOPPING/ISLAND_HOPPING.dummy SL/FILTER/FILTER.dummy SL/HELIX/HELIX.dummy
39SL/FILTER/FILTER.dummy: ARBDB/ARBDB.dummy
40SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: AWT/AWT.dummy SL/ALIVIEW/ALIVIEW.dummy SL/HELIX/HELIX.dummy
41SL/HELIX/HELIX.dummy: ARBDB/ARBDB.dummy
42SL/INSDEL/INSDEL.dummy: SL/FILTER/FILTER.dummy
43SL/ITEMS/ITEMS.dummy: AWT/AWT.dummy
44SL/LOCATION/LOCATION.dummy: ARBDB/ARBDB.dummy
45SL/MACROS/MACROS.dummy: WINDOW/WINDOW.dummy
46SL/MATRIX/MATRIX.dummy: WINDOW/WINDOW.dummy
47SL/NDS/NDS.dummy: SL/ITEMS/ITEMS.dummy
48SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: SL/MATRIX/MATRIX.dummy
49SL/PRONUC/PRONUC.dummy: ARBDB/ARBDB.dummy
50SL/PTCLEAN/PTCLEAN.dummy: ARBDB/ARBDB.dummy
51SL/REFENTRIES/REFENTRIES.dummy: WINDOW/WINDOW.dummy
52SL/REGEXPR/REGEXPR.dummy: CORE/CORE.dummy
53SL/ROOTED_TREE/ROOTED_TREE.dummy: ARBDB/ARBDB.dummy
54SL/SEQIO/SEQIO.dummy: SL/FILTER/FILTER.dummy XML/XML.dummy
55SL/SEQUENCE/SEQUENCE.dummy: SL/ALIVIEW/ALIVIEW.dummy SL/PRONUC/PRONUC.dummy
56SL/TRANSLATE/TRANSLATE.dummy: SL/PRONUC/PRONUC.dummy
57SL/TREEDISP/TREEDISP.dummy: SL/AP_TREE/AP_TREE.dummy SL/NDS/NDS.dummy
58SL/TREE_ADMIN/TREE_ADMIN.dummy: WINDOW/WINDOW.dummy
59SL/TREE_READ/TREE_READ.dummy: ARBDB/ARBDB.dummy
60SL/TREE_WRITE/TREE_WRITE.dummy: XML/XML.dummy
61STAT/STAT.dummy: SL/AP_TREE/AP_TREE.dummy SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy SL/ITEMS/ITEMS.dummy
62TOOLS/arb_consensus_tree.dummy: CONSENSUS_TREE/CONSENSUS_TREE.dummy SL/TREE_READ/TREE_READ.dummy SL/TREE_WRITE/TREE_WRITE.dummy
63TOOLS/arb_probe.dummy: SERVERCNTRL/SERVERCNTRL.dummy SL/REGEXPR/REGEXPR.dummy
64TOOLS/arb_test.dummy: ARBDB/ARBDB.dummy
65WETC/WETC.dummy: AWT/AWT.dummy
66XML/XML.dummy: CORE/CORE.dummy
67ARBDB/ARBDB.dummy: CORE/CORE.dummy
68AWT/AWT.dummy: WINDOW/WINDOW.dummy
69WINDOW/WINDOW.dummy: ARBDB/ARBDB.dummy
70CORE/CORE.dummy:
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