PK 5OU; META-INF/PK 4OU;~bMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.7.0 Created-By: 10.0-b23 (Sun Microsystems Inc.) Main-Class: lev1generator.Lev1Generator Class-Path: X-COMMENT: Main-Class will be added automatically by build PK 5OU;lev1generator/PK 5OU;  lev1generator/Edge.class1. & ' ( ) *+,parentLlev1generator/Vertex;child useForNewickZuseForNewickTree/(Llev1generator/Vertex;Llev1generator/Vertex;)VCodeLineNumberTableLocalVariableTablethisLlev1generator/Edge; getParent()Llev1generator/Vertex; setParent(Llev1generator/Vertex;)VpgetChildsetChildcsetUseForNewick(Z)V trueOrFalsegetUseForNewick()ZsetUseForNewickTreegetUseForNewickTree SourceFile Edge.java -  lev1generator/Edgejava/lang/Object()V!    k****+*,    /* >*+  /* >*+ !" >* ()  !/*1 ">* 89 #!/*@ $%PK 5OU;6=g22lev1generator/InReader.class1f <= > ? @A < B C D E FGH I J K LM N OP QR QST inputContentsLjava/util/ArrayList; Signature)Ljava/util/ArrayList;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLlev1generator/InReader;fileNameLjava/lang/String;(Ljava/io/File;)ViI listOfFiles[Ljava/io/File; directoryLjava/io/File; returnInput()Ljava/util/ArrayList;+()Ljava/util/ArrayList; readInput inputLineexLjava/io/IOException;Ljava/io/FileNotFoundException;newFilemyDataLjava/io/BufferedReader; SourceFile InReader.java U java/io/File  2( VWjava/util/ArrayList  XY ZW [\ ]^java/io/BufferedReaderjava/io/FileReader ( _ `\a b\ cU dUjava/io/IOException eUjava/io/FileNotFoundExceptionlev1generator/InReaderjava/lang/Object()V isDirectory()Z listFiles()[Ljava/io/File;isFilegetName()Ljava/lang/String;add(Ljava/lang/Object;)Z(Ljava/io/Reader;)VreadLinejava/lang/Stringtrim trimToSizecloseprintStackTrace! !M**Y+"#$%&'(!A*+8*Y+ M>, ,2 *,2 W"&  #,:@"#*#)*%+,A$%A-./0!/*"&# $%12(!M*Y YY+M,YN-N*- W*,,RN-JN-,,:N-2N-,,"N-:,, : >FI>QV^a>invy>QVin"%+/ 01&5+679>GBIFOILJNNPQ;R=VGZI^OaLbNfPi?jAnGrIvOyLzN~PEGIOLNOQ#f #3'J45R46b45j45z4545$%7.89:;PK 5OU;Y++!lev1generator/Lev1Generator.class1 c  @   ??陙 ; ; @ ;         @       0 / / @ @ ; ! " #$%&'()*+, H H- . /0 1 H2 H3 H45 Q6 H78 H9: Q;<=>? ;@A ;B ;CD HEFG HI eJ KLM HNOPQRS TUV r W @X @YZ[\ ]^_`abcdefghVERSIONLjava/lang/String; ConstantValue(Ljava/lang/String;IIZZZ)VCodeLineNumberTableLocalVariableTableinLlev1generator/InReader;subNetthisLlev1generator/Lev1Generator; inputFileNamenInetworksToBeGneratedtreesZdotdotTreessubNetsCollectionLjava/util/ArrayList;printTraceLevel subNetsNo hybridRatioD heightRatioLocalVariableTypeTable)Ljava/util/ArrayList;main([Ljava/lang/String;)VposeLjava/io/IOException;brLjava/io/BufferedReader;inputargs[Ljava/lang/String; inFileName noNetworksgenerate(Ljava/util/ArrayList;IIDDIZZ)VadditionalSubNetnetwork1Llev1generator/Network;idotNet treesListfileNofilenetwork subNetCounteNewickj allNetworkspath Signature3(Ljava/util/ArrayList;IIDDIZZ)VmanualGenerator(Ljava/util/ArrayList;I)V selection2leafLlev1generator/Vertex;leavesinput2 nextSubNetdone2 selection subNetsCountdone-Ljava/util/ArrayList;-(Ljava/util/ArrayList;I)V isNumeric(Ljava/lang/String;)Znfe!Ljava/lang/NumberFormatException;str readInput()Ljava/lang/String; printList(Ljava/util/ArrayList;)Vlist,(Ljava/util/ArrayList;)V newickToDot(Z)VoutNamenewickcontentsfileNamefdir fileNames treeExtractor()V printHelp SourceFileLev1Generator.java java/util/ArrayList ijlev1generator/InReader k lm((16E,(18E,(20E,(22E,(24E,(26E,#H0)12i)10i)8i)6i)4i)2i,(((((((((31E,32E)28i,(29E,30E)27i)14i)#H0,25E)11i,23E)9i,21E)7i,19E)5i,17E)3i,15E)1i) no --help po q rs--inputjava/lang/StringBuilder tu v--nw xy --multiple z{7Sorry, number of networks is limited to 9999, stopping.| }k--trees--dot --dottreesUnrecognised argument ' ', stopping.$Please note that there can be up to ~  t1 trees consistent with a network generatated from  subNets (possibly even more if input subNet has more than one reticulation). Extracting trees can take a long time, additionally the output file size may cause problems. AYou may consider allocating more memmory to JVM. Proceed? [y/n] kjava/io/BufferedReaderjava/io/InputStreamReader    java/io/IOExceptionIO error y Ylev1generator/Lev1Generator s } java/lang/String000000Generating network...  of  eNewick file: .netlev1generator/Network       lev1generator/OutWriter  .dot .tre all.net (no,input)Current network: SELECT subNet: !SELECT subNet and press enter... *SELECT LEAF TO BE REPLACED BY THIS subNet: m [%3d] %s java/lang/Object lev1generator/Vertex  SELECT leaf and press enter...  leaf selected:  finished...Conctructed network: NETWORKS/network.netjava/lang/NumberFormatExceptionuser.dir / java/io/File    Reading... enewick trees contained t Writing...*Lev1Generator Version 1.0, 20 October 2009.----------------------------------------------%Usage: java Level1Generator [options][options] can be:r--input : file containing network(s) in eNewick format, if not specified the default subNet is used. N--n : number of subNets to be used by the generator. The default is 2. --multiple : number of networks to be generated, the default is 1. If more than one network is generated, additional file (all.net), containing eNewick strings is generated n--trees : Extracts trees consistent with generated network(s). Outputs .tre file for each generated network. o--dot : Generates 'dot' representation of generated network(s). Outputs .dot file for each generated network. --dottrees : Generates 'dot' representation of ALL trees consistent with generated network(s). Outputs .dot file for each tree. Use with caution! 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"# $ %& ' ( ) * + , - . / 0 1234 5 678 69 : ; < = >? @A BC D E FG HI JK L MN OP@Y QRST UV WX YZ[ \ ]^_`abc d e fg fhijkl fmn opq rs 1tu vw a x y z { | a* } ~  a   o       1       @    verticesLjava/util/ArrayList; Signature-Ljava/util/ArrayList;hybridstreesContainedInNetwork)Ljava/util/ArrayList;rootLlev1generator/Vertex;randomGeneratorLjava/util/Random;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLlev1generator/Network; newickStringLjava/lang/String; addSubNet(Llev1generator/Network;I)IsuffixvrtsubNet subNetCountIaddedZleafToAttachToreplaceLeafWithSubNet1(Llev1generator/Network;ILlev1generator/Vertex;)ZileafremoveRandomLeaves(II)ImaxLeavesToDestroyrandomLeavesToDestroyparentcremovedname randomIntleavesToRemoveprintTraceLeveldestroyedCount loopCount"getRandomNumberOfVerticesToDestroy()ImaxVerticesToDestroyrandomVerticesToDestroyhardMaxVerticesToDestroyrandomlyPermute(DDI)Irandom doDestroy hybridRateD heightRatehybRatehgtRatetryDestroyInnerVertexpchild vertexIdx wasHybridtryToDestroyVertexgetMaxVerticesToDestroymaxcleanup(I)VremoveItnitLjava/util/ListIterator;LocalVariableTypeTable0Ljava/util/ListIterator; getNoLeavesvleaves getNoHybridshyb addNameSuffixcurrentsfxgetRoot()Llev1generator/Vertex; readNewickchild1name1 newickStrnodeNameLjava/lang/StringBuffer; nodeLengthtreeName readingLengthreadingTreeNameisHybrid hybridCount hybridNames currentNodeid mergeHybrids()Vv0h1v1jh0"prepareHybridsForExtendedNewickOut noParentsvertexextractTreesFromNetwork(I)Inewicknextvertex0maskAllButOneHybridInEdges(Llev1generator/Vertex;I)VexcludeprintTreesContainedInNetwork(Z)Ljava/util/ArrayList;printOut totalHybridsexpected totalTrees,(Z)Ljava/util/ArrayList;printExtendedNewickStringgetExtendedNewickString()Ljava/lang/String; getDotNetworkdot getLeaves()Ljava/util/ArrayList;/()Ljava/util/ArrayList; SourceFile Network.java java/util/ArrayList java/util/Random   lev1generator/Vertex  java/lang/StringBuilder        Leaf %s replaced with network java/lang/Object   RANDOM LEAF REMOVAL     -CANDIDATE LEAF %s @ %4d, desroyedCount = %3d   /DESTroyed leaf %10s @ %4d, desroyedCount = %3d   /DESTroyed parent %s @ %4d, desroyedCount = %3d /CANDIDATE CHERRY %s @ %4d, desroyedCount = %3d 1Destroyed vertex %10s @ %4d, desroyedCount = %3d   Destroyed leaf %10s  RANDOMLY PERMUTE (p) CANDIDATE to destroy %s 6HYBRID (or RootToHybridLink %s: random=%d, hybRate=%d 4HybChild or CherryParrent %s: random=%d, hgtRate=%d (p) try to destroy vertex %s  REMOVED vertex < > outdegree = , STATS:   PARENT:  (p) destroyed parent %s  CHILD:  (p) destroyed child %s $ (p) not leaf but bypassed %s : (p) not leaf, NOT bypassed %s - --::<>::--     SHOULD CLEAN UP...  because indeg==outdeg==1 because indeg==outdeg==01 because isHybrida & (parent isSubRoot or isRoot) #H  HAD TO REMOVE ERRONOUS HYBRID  "ERRRRROR in Network.java cleanup() sub java/lang/StringBuffer         lev1generator/VertexComparator       JIOHandler.java; one and only one of hybrid nodes must have descendants (?)    ;   \Extracting trees consistent with network, there are %d reticulations, so %d trees expected cSOME KIND OF ERROR - Trees contained in the network = %d, total expected = %d, as hybridCount = %d  Trees contained in the network:java/lang/Stringextended newick:  strict digraph net { }lev1generator/NetworksizenextIntget(I)Ljava/lang/Object;isLeaf()Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toStringremovereplaceWithSubNet(Llev1generator/Network;)VupdateVerticesList,(Ljava/util/ArrayList;)Ljava/util/ArrayList;java/lang/SystemoutLjava/io/PrintStream;getNamejava/io/PrintStreamprintf<(Ljava/lang/String;[Ljava/lang/Object;)Ljava/io/PrintStream;println isHybridChild getParentAt(I)Llev1generator/Vertex;isRoot isSubRootjava/lang/IntegervalueOf(I)Ljava/lang/Integer; removeChild(Llev1generator/Vertex;)V isRedundant createBypass(Ljava/lang/Object;)ZisCherryParent destroyVertex(I)Z getOutDegree getChildAtisRootToHybridLinkgetNameForNewickgetInfo getInDegree canBeRemoved listIterator()Ljava/util/ListIterator;java/util/ListIteratorhasNext()Ljava/lang/Object; startsWith(Ljava/lang/String;)ZlengthexitsetName setIsRootaddcharAt(I)CaddChild(Llev1generator/Vertex;)ZtrimequalsIgnoreCasesetIsToBeHybrid(Z)V(C)Ljava/lang/StringBuffer;java/util/Collectionssort)(Ljava/util/List;Ljava/util/Comparator;)VgetIsToBeHybridendsWithsplit'(Ljava/lang/String;)[Ljava/lang/String;getParentEdgeAt(I)Llev1generator/Edge;(Llev1generator/Edge;)Verrlev1generator/EdgesetUseForNewickgenerateNewickTreesetUseForNewickTreejava/lang/Mathpow(DD)DgenerateENewickgenerateDotNetwork!s+**Y*Y*+*Y "#$%&*'++0>*Y 6{* * 6* :MEY:+*W+**Y>*B34 567$829B<Z=`>j?p@ADFGHZ*2W~G66* * :-nf^YS WY:+*W+**Y6 r*>RTU V6WKXcYiZs[y\]^TcdRc. q  !"5*#l6*  `6l 6666 dh* * >* ::$%: %&%'$(YSY)SY)S W# %& %' *$+YSY)SY)S W*W ,? 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