PK 7 META-INF/PK 7a\META-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_09-b01 (Sun Microsystems Inc.) Main-Class: EvolMAP.ENSEMBL_Splice_Remover Class-Path: X-COMMENT: Main-Class will be added automatically by build PK 7EvolMAP/PK 7ensembl_splice_remover/PK 7)j$EvolMAP/ENSEMBL_Splice_Remover.class1 Bs At uvw sx y z {|} ~ s     6 6 6 6   " A A  u 1 1 A A 1 uINPUTS[Ljava/lang/String;OUTPUTSRUN_FROM_CONSOLEZ()VCodeLineNumberTableLocalVariableTablethis LEvolMAP/ENSEMBL_Splice_Remover;main([Ljava/lang/String;)VcurrentSequence2LEvolMAP/Sequence; geneName2Ljava/lang/String;jIcurrentSequencegeneNamei input_name output_namedbLEvolMAP/GeneDatabase; deleteListLjava/util/Vector;outputLjava/io/FileWriter;kargsLocalVariableTypeTable'Ljava/util/Vector; Exceptions create_file$(Ljava/io/File;)Ljava/io/FileWriter;eLjava/io/IOException;filenameLjava/io/File;fatal(Ljava/lang/String;)Vmessage SourceFileENSEMBL_Splice_Remover.java HI FG java/lang/StringBuilderReading fasta file  nEvolMAP/GeneDatabase Hjava/util/Vector Gene  finished. 1 Tgene:  transcript: 2 T 6Ensembl splices successfully removed. New fasta size:  java/io/File Hn ghcould not open output file mn line.separator n IOutput written to file [Incorrect number of arguments. Two inputs required are Ensembl input and output file names. CDNew genome size: EDjava/io/FileWriter Hjava/io/IOException Program terminating java/lang/String human.v41.fa rat.v41.fa mus.v41.fa chimp.v41.fa dog.v41.fa human.v41.ufa rat.v41.ufa mus.v41.ufa chimp.v41.ufa dog.v41.ufaEvolMAP/ENSEMBL_Splice_Removerjava/lang/Objectjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;Z)Vsize()I(I)Ljava/lang/StringBuilder;java/lang/IntegervalueOf(I)Ljava/lang/Integer;indexOf(Ljava/lang/Object;)IgetGene(I)LEvolMAP/Sequence;EvolMAP/Sequenceheader(Ljava/lang/String;)I substring(II)Ljava/lang/String;equals(Ljava/lang/Object;)Zsequencelengthadd toStringWhole getProperty&(Ljava/lang/String;)Ljava/lang/String;writeclose(Ljava/io/File;)Vexit(I)V!AB CD ED FGHIJ/*KL MN OPJ4 Ȳ **2L*2MY+ Y+ N Y :6-d+p"Y -::!:`6-w-: :  !   :  8 WW oY -!d "Y,#$:%&6-:&Y-'()*+Y,, ɲ- <. Y.2 M Y N6,dY -,::!:`6,-u,:: !:  6-W-W rY/,-!d "Y02#$:%&6,9-&Y,'()*+JKFQ - 7!@"N$\%{'()*+-/1234579&:)=<?G@JCUDX/^"dJLMOQROTUVY [ ^`$a,b:dYffgihqiujlnpqrstvxy|~"%/2n8b>_pz^LlQR hST UVWRXTC!YV@YVZT[T7\]@^_k`ajQRfST UVqWRuXT/YV}?YV$\],^_pQ`abVcDd@^e,^ef3 ghJL 1Y*2L 3K  L ij kl mnJPY*4 5KL oTpIJeE6Y7SY8SY9SY:SY;S.6YSY?SY@S0K @qrPK 7 EvolMAP/GeneDatabase.class1+ Q & & & & & & & %   & &    & &     &  % & %  % + + + 1 & 4 &  & I    % + J I I % %allGenes[LEvolMAP/Sequence;speciesLjava/lang/String; species_list[Ljava/lang/String;species_start_indexes[I LENGTH_MINI LENGTH_MAXREMOVE_X_CHARACTERSZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLEvolMAP/GeneDatabase;sequenceDatabaseFile Exceptions(Ljava/lang/String;Z)V countFirst((Ljava/lang/String;[LEvolMAP/Sequence;)Vgenes getAllGenes()[LEvolMAP/Sequence;setSpeciesIndexes()VseqLEvolMAP/Sequence;i speciesNamesLjava/util/Vector;speciesStartIndexesLocalVariableTypeTable&Ljava/util/Vector;'Ljava/util/Vector;getSpeciesStartIndex(Ljava/lang/String;)IgetGeneByPreComputedIndex&(Ljava/lang/String;)LEvolMAP/Sequence; gene_name!getGeneLocationByPreComputedIndexstLjava/util/StringTokenizer; nextToken speciesOrderspeciesStartIndexsetScoreMatrixPositionsgetSpeciesGenes*(Ljava/lang/String;)LEvolMAP/GeneDatabase; speciesGenesspeciesGenesArray speciesBase&Ljava/util/Vector;size()IgetGene(I)LEvolMAP/Sequence;getGeneByAnyNameggetGeneByName2getAllGenesByName2'([Ljava/lang/String;)Ljava/util/Vector;currentSequence geneNames foundGenes Signature;([Ljava/lang/String;)Ljava/util/Vector; readSequencescurrent_sequence_namecurrent_sequencefileNameinputLjava/io/BufferedReader;number_of_sequencesline open_file((Ljava/io/File;)Ljava/io/BufferedReader;eLjava/io/IOException;filenameLjava/io/File; more_records(Ljava/io/Reader;)ZrLjava/io/Reader; read_a_line,(Ljava/io/BufferedReader;)Ljava/lang/String;toString()Ljava/lang/String; returnStringtoStringCompact SourceFileGeneDatabase.java _o Z[ \[ ]^ TU h no RSjava/util/Vector    java/lang/String VW XY java/lang/Integer    ~z java/util/StringTokenizer_ _   z yz jSomething wrong going on with indexes. Check method getGeneLocationByPreComputedIndex in GeneDatabase.java ` [EvolMAP/SequenceEvolMAP/GeneDatabase _j U  java/lang/StringBuilder-Read error in getAllGenesByName2 file-- gene  not found in database  java/io/File _` java/io/IOException"Could not open gene database file >  oProblem reading file. line.separator   !X "#A Fasta file  is opened and $ sequences read.java/io/BufferedReaderjava/io/FileReader _% _&' ( ) * java/lang/Objectcontains(Ljava/lang/Object;)ZaddvalueOf(I)Ljava/lang/Integer;get(I)Ljava/lang/Object;intValueequals'(Ljava/lang/String;Ljava/lang/String;)V hasMoreTokens()ZparseIntjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintlnscoreMatrixPositionheader(Ljava/lang/CharSequence;)Z getGeneName2append-(Ljava/lang/String;)Ljava/lang/StringBuilder; startsWith(Ljava/lang/String;)Zcloselength getProperty&(Ljava/lang/String;)Ljava/lang/String; substring(II)Ljava/lang/String; replaceAll8(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;(I)Ljava/lang/StringBuilder;(Ljava/io/File;)V(Ljava/io/Reader;)Vjava/io/ReaderreadyreadLine toStringWhole!&QRSTUVWXYZ[\[]^_`av&***'***+*b" !%c&de&fUg4_ha&***'***+*b"! 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