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fixed permissions

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ddarriba committed Oct 28, 2015
1 parent 93d8a45 commit d22bea8b8bdc05cb3d8a91dc9adab2325fa07ac3
Showing with 8 additions and 12 deletions.
  1. 0 COPYING
  2. 0 INSTALL
  3. 0 THIRDPARTYLICENSES
  4. +8 −12 build.xml
  5. 0 src/main/java/META-INF/services/org.jdesktop.application.Application
  6. 0 src/main/java/es/uvigo/darwin/prottest/ProtTest.java
  7. 0 src/main/java/es/uvigo/darwin/prottest/consensus/Consensus.java
  8. 0 src/main/java/es/uvigo/darwin/prottest/consensus/package.html
  9. 0 src/main/java/es/uvigo/darwin/prottest/exe/AminoAcidRunEstimator.java
  10. 0 src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutionManager.java
  11. 0 src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutor.java
  12. 0 src/main/java/es/uvigo/darwin/prottest/exe/ParallelModelEstimator.java
  13. 0 src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
  14. 0 src/main/java/es/uvigo/darwin/prottest/exe/PhymlStreamGobbler.java
  15. 0 src/main/java/es/uvigo/darwin/prottest/exe/RaxMLAminoAcidRunEstimator.java
  16. 0 src/main/java/es/uvigo/darwin/prottest/exe/RaxMLStreamGobbler.java
  17. 0 src/main/java/es/uvigo/darwin/prottest/exe/RunEstimator.java
  18. 0 src/main/java/es/uvigo/darwin/prottest/exe/RunEstimatorImpl.java
  19. 0 src/main/java/es/uvigo/darwin/prottest/exe/StreamGobbler.java
  20. 0 src/main/java/es/uvigo/darwin/prottest/exe/package.html
  21. 0 src/main/java/es/uvigo/darwin/prottest/exe/util/TemporaryFileManager.java
  22. 0 src/main/java/es/uvigo/darwin/prottest/exe/util/package.html
  23. 0 src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacade.java
  24. 0 src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeImpl.java
  25. 0 src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeMPJ.java
  26. 0 src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeSequential.java
  27. 0 src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeThread.java
  28. 0 src/main/java/es/uvigo/darwin/prottest/facade/TreeFacade.java
  29. 0 src/main/java/es/uvigo/darwin/prottest/facade/TreeFacadeImpl.java
  30. 0 src/main/java/es/uvigo/darwin/prottest/facade/package.html
  31. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/DistributionStrategy.java
  32. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/Distributor.java
  33. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/DynamicDistributionStrategy.java
  34. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/HybridDistributionStrategy.java
  35. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/ImprovedDynamicDistributionStrategy.java
  36. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/MultipleDistributor.java
  37. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/StaticDistributionStrategy.java
  38. 0 src/main/java/es/uvigo/darwin/prottest/facade/strategy/package.html
  39. 0 src/main/java/es/uvigo/darwin/prottest/facade/thread/ThreadPoolSynchronizer.java
  40. 0 src/main/java/es/uvigo/darwin/prottest/facade/thread/package.html
  41. 0 src/main/java/es/uvigo/darwin/prottest/facade/util/ProtTestParameterVO.java
  42. 0 src/main/java/es/uvigo/darwin/prottest/facade/util/SelectionChunk.java
  43. 0 src/main/java/es/uvigo/darwin/prottest/facade/util/package.html
  44. 0 src/main/java/es/uvigo/darwin/prottest/global/AminoAcidApplicationGlobals.java
  45. 0 src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java
  46. 0 src/main/java/es/uvigo/darwin/prottest/global/ProtTestConsoleParameters.java
  47. 0 src/main/java/es/uvigo/darwin/prottest/global/ProtTestConstants.java
  48. 0 src/main/java/es/uvigo/darwin/prottest/global/RaxmlAminoAcidApplicationGlobals.java
  49. 0 src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java
  50. 0 src/main/java/es/uvigo/darwin/prottest/global/options/SerializableApplicationOptions.java
  51. 0 src/main/java/es/uvigo/darwin/prottest/global/options/package.html
  52. 0 src/main/java/es/uvigo/darwin/prottest/global/package.html
  53. 0 src/main/java/es/uvigo/darwin/prottest/model/AminoAcidModel.java
  54. 0 src/main/java/es/uvigo/darwin/prottest/model/Model.java
  55. 0 src/main/java/es/uvigo/darwin/prottest/model/package.html
  56. 0 src/main/java/es/uvigo/darwin/prottest/model/state/ModelEmptyLkState.java
  57. 0 src/main/java/es/uvigo/darwin/prottest/model/state/ModelFilledLkState.java
  58. 0 src/main/java/es/uvigo/darwin/prottest/model/state/ModelLkState.java
  59. 0 src/main/java/es/uvigo/darwin/prottest/model/state/package.html
  60. 0 src/main/java/es/uvigo/darwin/prottest/observer/ModelUpdaterObserver.java
  61. 0 src/main/java/es/uvigo/darwin/prottest/observer/ObservableModelUpdater.java
  62. 0 src/main/java/es/uvigo/darwin/prottest/observer/package.html
  63. 0 src/main/java/es/uvigo/darwin/prottest/package.html
  64. 0 src/main/java/es/uvigo/darwin/prottest/selection/AIC.java
  65. 0 src/main/java/es/uvigo/darwin/prottest/selection/AICc.java
  66. 0 src/main/java/es/uvigo/darwin/prottest/selection/BIC.java
  67. 0 src/main/java/es/uvigo/darwin/prottest/selection/DT.java
  68. 0 src/main/java/es/uvigo/darwin/prottest/selection/InformationCriterion.java
  69. 0 src/main/java/es/uvigo/darwin/prottest/selection/LNL.java
  70. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/AICSelectionModel.java
  71. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/AICcSelectionModel.java
  72. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/BICSelectionModel.java
  73. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/DTSelectionModel.java
  74. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/LNLSelectionModel.java
  75. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/SelectionModel.java
  76. 0 src/main/java/es/uvigo/darwin/prottest/selection/model/package.html
  77. 0 src/main/java/es/uvigo/darwin/prottest/selection/package.html
  78. 0 src/main/java/es/uvigo/darwin/prottest/selection/printer/AminoAcidPrintFramework.java
  79. 0 src/main/java/es/uvigo/darwin/prottest/selection/printer/PrintFramework.java
  80. 0 src/main/java/es/uvigo/darwin/prottest/selection/printer/package.html
  81. 0 src/main/java/es/uvigo/darwin/prottest/taxa/Taxon.java
  82. 0 src/main/java/es/uvigo/darwin/prottest/taxa/TaxonomicLevel.java
  83. 0 src/main/java/es/uvigo/darwin/prottest/taxa/package.html
  84. 0 src/main/java/es/uvigo/darwin/prottest/tree/TreeDistancesCache.java
  85. 0 src/main/java/es/uvigo/darwin/prottest/tree/TreeEuclideanDistancesCache.java
  86. 0 src/main/java/es/uvigo/darwin/prottest/tree/TreeUtils.java
  87. 0 src/main/java/es/uvigo/darwin/prottest/tree/WeightedTree.java
  88. 0 src/main/java/es/uvigo/darwin/prottest/tree/package.html
  89. 0 src/main/java/es/uvigo/darwin/prottest/util/FixedBitSet.java
  90. 0 src/main/java/es/uvigo/darwin/prottest/util/ProtTestAlignment.java
  91. 0 src/main/java/es/uvigo/darwin/prottest/util/StatFramework.java
  92. 0 src/main/java/es/uvigo/darwin/prottest/util/Utilities.java
  93. 0 src/main/java/es/uvigo/darwin/prottest/util/argumentparser/AminoAcidArgumentParser.java
  94. 0 src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java
  95. 0 src/main/java/es/uvigo/darwin/prottest/util/argumentparser/package.html
  96. 0 src/main/java/es/uvigo/darwin/prottest/util/attributable/Attributable.java
  97. 0 src/main/java/es/uvigo/darwin/prottest/util/attributable/AttributableHelper.java
  98. 0 src/main/java/es/uvigo/darwin/prottest/util/attributable/package.html
  99. 0 src/main/java/es/uvigo/darwin/prottest/util/checkpoint/CheckPointManager.java
  100. 0 src/main/java/es/uvigo/darwin/prottest/util/checkpoint/package.html
  101. 0 src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/ApplicationStatus.java
  102. 0 src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/ProtTestStatus.java
  103. 0 src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/package.html
  104. 0 src/main/java/es/uvigo/darwin/prottest/util/collection/ModelCollection.java
  105. 0 src/main/java/es/uvigo/darwin/prottest/util/collection/ParallelModelCollection.java
  106. 0 src/main/java/es/uvigo/darwin/prottest/util/collection/ParallelModelQueue.java
  107. 0 src/main/java/es/uvigo/darwin/prottest/util/collection/SingleModelCollection.java
  108. 0 src/main/java/es/uvigo/darwin/prottest/util/collection/package.html
  109. 0 src/main/java/es/uvigo/darwin/prottest/util/comparator/AminoAcidModelNaturalComparator.java
  110. 0 src/main/java/es/uvigo/darwin/prottest/util/comparator/LKComparator.java
  111. 0 src/main/java/es/uvigo/darwin/prottest/util/comparator/ModelDistributionHeuristic.java
  112. 0 src/main/java/es/uvigo/darwin/prottest/util/comparator/ModelWeightComparator.java
  113. 0 src/main/java/es/uvigo/darwin/prottest/util/comparator/package.html
  114. 0 src/main/java/es/uvigo/darwin/prottest/util/exception/AlignmentParseException.java
  115. 0 src/main/java/es/uvigo/darwin/prottest/util/exception/ImportException.java
  116. 0 src/main/java/es/uvigo/darwin/prottest/util/exception/ModelOptimizationException.java
  117. 0 src/main/java/es/uvigo/darwin/prottest/util/exception/ProtTestCheckedException.java
  118. 0 src/main/java/es/uvigo/darwin/prottest/util/exception/ProtTestInternalException.java
  119. 0 src/main/java/es/uvigo/darwin/prottest/util/exception/TreeFormatException.java
  120. 0 src/main/java/es/uvigo/darwin/prottest/util/factory/ProtTestFactory.java
  121. 0 src/main/java/es/uvigo/darwin/prottest/util/factory/package.html
  122. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
  123. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/ImportHelper.java
  124. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusExporter.java
  125. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusImporter.java
  126. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusTreeReader.java
  127. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/SimpleNewickTreeReader.java
  128. 0 src/main/java/es/uvigo/darwin/prottest/util/fileio/TreeReader.java
  129. 0 src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogFormatter.java
  130. 0 src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogger.java
  131. 0 src/main/java/es/uvigo/darwin/prottest/util/package.html
  132. 0 src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestFormattedOutput.java
  133. 0 src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestPrinter.java
  134. 0 src/main/java/es/uvigo/darwin/xprottest/CreditsBox.java
  135. 0 src/main/java/es/uvigo/darwin/xprottest/PreferencesView.java
  136. 0 src/main/java/es/uvigo/darwin/xprottest/XProtTestAboutBox.java
  137. 0 src/main/java/es/uvigo/darwin/xprottest/XProtTestApp.java
  138. 0 src/main/java/es/uvigo/darwin/xprottest/XProtTestView.java
  139. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/FrequenciesView.java
  140. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/TreeView.java
  141. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/TreeWrapper.java
  142. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/consensus/Consensus.java
  143. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/consensus/resources/Consensus.properties
  144. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/resources/FrequenciesView.properties
  145. 0 src/main/java/es/uvigo/darwin/xprottest/analysis/resources/TreeView.properties
  146. 0 src/main/java/es/uvigo/darwin/xprottest/compute/OptionsView.java
  147. 0 src/main/java/es/uvigo/darwin/xprottest/compute/RunningFrame.java
  148. 0 src/main/java/es/uvigo/darwin/xprottest/compute/resources/OptionsView.properties
  149. 0 src/main/java/es/uvigo/darwin/xprottest/compute/resources/RunningFrame.properties
  150. 0 src/main/java/es/uvigo/darwin/xprottest/resources/CreditsBox.properties
  151. 0 src/main/java/es/uvigo/darwin/xprottest/resources/PreferencesView.properties
  152. 0 src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestAboutBox.properties
  153. 0 src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestApp.properties
  154. 0 src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestView.properties
  155. BIN src/main/java/es/uvigo/darwin/xprottest/resources/about.png
  156. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon0.png
  157. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon1.png
  158. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon10.png
  159. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon11.png
  160. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon12.png
  161. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon13.png
  162. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon14.png
  163. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon2.png
  164. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon3.png
  165. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon4.png
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  167. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon6.png
  168. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon7.png
  169. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon8.png
  170. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon9.png
  171. BIN src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/idle-icon.png
  172. BIN src/main/java/es/uvigo/darwin/xprottest/resources/prottestlogo.gif
  173. BIN src/main/java/es/uvigo/darwin/xprottest/resources/splash.png
  174. 0 src/main/java/es/uvigo/darwin/xprottest/results/Bundle.properties
  175. 0 src/main/java/es/uvigo/darwin/xprottest/results/ErrorLogView.java
  176. 0 src/main/java/es/uvigo/darwin/xprottest/results/ResultsView.java
  177. 0 src/main/java/es/uvigo/darwin/xprottest/results/resources/ErrorLogView.properties
  178. 0 src/main/java/es/uvigo/darwin/xprottest/results/resources/ResultsView.properties
  179. 0 src/main/java/es/uvigo/darwin/xprottest/util/BrowserLauncher.java
  180. 0 src/main/java/es/uvigo/darwin/xprottest/util/OptimizationStrategyWrapper.java
  181. 0 src/main/java/es/uvigo/darwin/xprottest/util/TextAreaAppender.java
  182. 0 src/main/java/es/uvigo/darwin/xprottest/util/TextAreaWriter.java
  183. 0 src/main/resources/COPYING
  184. 0 src/main/resources/README
  185. 0 src/main/resources/THIRDPARTYLICENSES
  186. 0 src/main/resources/examples/COX2_PF0016/alignment
  187. 0 src/main/resources/examples/COX2_PF0016/tree
  188. 0 src/main/resources/examples/HIV1.2008.pol.nex
  189. 0 src/main/resources/examples/Ribosomal_L5_PF00673/alignment
  190. 0 src/main/resources/examples/Ribosomal_L5_PF00673/tree
  191. 0 src/main/resources/filecluster8.conf.template
  192. 0 src/main/resources/machines
  193. 0 src/main/resources/models/FLU
  194. BIN src/main/resources/mpj.tar.gz
  195. 0 src/main/resources/prottest.properties
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@@ -2,7 +2,8 @@
<project name="prottest-3.4.1" default="jar" basedir=".">
<property name="src.dir" location="src/main/java" />
<property name="bin.dir" location="build/classes" />
<property name="build.base.dir" location="build" />
<property name="build.dir" location="${build.base.dir}/classes" />
<property name="lib.dir" location="lib" />
<property name="dist.dir" location="dist" />
<property name="exe.dir" location="${dist.dir}/bin" />
@@ -27,32 +28,27 @@
</target>
<target name="compile" description="Compile code">
<mkdir dir="${bin.dir}" />
<mkdir dir="${build.dir}" />
<mkdir dir="${lib.dir}" />
<property environment="env" />
<property name="java6.boot.classpath" value="${env.JAVA6_BOOTCLASSES}" />
<javac srcdir="${src.dir}" destdir="${bin.dir}" includeAntRuntime="no"
<javac srcdir="${src.dir}" destdir="${build.dir}" includeAntRuntime="no"
target="1.6" source="1.6" bootclasspath="${java5.boot.classpath}"
classpathref="lib.path" debug="${compile.debug}">
</javac>
<!--
<copy todir="${bin.dir}/models">
<fileset dir="${src.resources.dir}/models" includes="**/*.xml,**/*.properties,**/*.gif,**/*.ico" />
</copy>
-->
</target>
<target name="jar" depends="compile" description="Build jar">
<mkdir dir="${dist.dir}" />
<jar jarfile="${jarfile}" basedir="${bin.dir}" manifest="manifest.mf">
<jar jarfile="${jarfile}" basedir="${build.dir}" manifest="manifest.mf">
<fileset id="jar.additional" dir="${src.dir}">
<include name="**/*.properties" />
<include name="**/*.png" />
<include name="**/*.gif" />
<include name="**/*.html" />
</fileset>
<!-- Merge library jars into final jar file
<zipgroupfileset refid="lib.jars"/>-->
<!-- Merge library jars into final jar file-->
<!--<zipgroupfileset refid="lib.jars"/>-->
</jar>
<mkdir dir="${dist.dir}/lib" />
<copy todir="${dist.dir}/lib">
@@ -75,7 +71,7 @@
</target>
<target name="clean" description="Remove build and dist directories">
<delete dir="${bin.dir}" />
<delete dir="${build.base.dir}" />
<delete dir="${dist.dir}" />
</target>
</project>
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0 src/main/resources/mpj.tar.gz 100755 → 100644
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