PK |4 META-INF/PK |4]pMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.6.2 Created-By: 1.5.0_05-b05 (Sun Microsystems Inc.) Main-Class: cositoms.CosiToMs X-COMMENT: Main-Class will be added automatically by build PK |4 cositoms/PK |4pcositoms/CosiSample.class1O 2 3 45 678 9: ; <=> ?@A BCD sampleLines[Ljava/lang/String;segsitesI()VCodeLineNumberTableLocalVariableTablethisLcositoms/CosiSample;getSampleLines()[Ljava/lang/String; readSample(Ljava/io/BufferedReader;II)VtkLjava/util/StringTokenizer;chromLjava/lang/String;brLjava/io/BufferedReader;seqs iterationsiline ExceptionsE getSegsites()I SourceFileCosiSample.java   java/lang/StringF GHjava/util/StringTokenizer I JK JH  LM20 N/cositoms/CosiSamplejava/lang/Objectjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;(Ljava/lang/String;)V nextToken&(Ljava/lang/String;)Ljava/lang/String;replaceD(Ljava/lang/CharSequence;Ljava/lang/CharSequence;)Ljava/lang/String;length!< **   /*  !(x:*6a+:Y: W W: :  : : **S+WF%& ()*%+-,5-8.?/J0U1Z2c4l(r7w8R%G"#84$%xx&'x(x)j*u+%,-.//*; 01PK |4cositoms/CosiToMs.class1 #E FGH IJ KLM NO PQ RS NT U VW E X Y IZ [ \ []^ E_ ` a bcdef()VCodeLineNumberTableLocalVariableTablethisLcositoms/CosiToMs;main([Ljava/lang/String;)VsampleLcositoms/CosiSample;infileLjava/io/FileReader;brLjava/io/BufferedReader;outputLcositoms/NewMsOutputFile;outfileLjava/io/FileWriter;bwLjava/io/BufferedWriter;iIerrorLjava/io/FileNotFoundException;error2Ljava/io/IOException;args[Ljava/lang/String;seqs iterations SourceFile CosiToMs.java $%g hi3use: j klm nojava/io/FileReader $ljava/io/BufferedReader $pcositoms/NewMsOutputFile $qjava/io/FileWriterjava/io/BufferedWriter $r stcositoms/CosiSample uv wx ky z% {%java/io/FileNotFoundExceptionjava/lang/StringBuilderFile not found: |} |~ java/io/IOException IO error: cositoms/CosiToMsjava/lang/Objectjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)Vjava/lang/IntegerparseInt(Ljava/lang/String;)I(Ljava/io/Reader;)V(II)V(Ljava/io/Writer;)V writeHeader(Ljava/io/BufferedWriter;)V readSample(Ljava/io/BufferedReader;II)V writeSample0(Ljava/io/BufferedWriter;Lcositoms/CosiSample;)V(I)Vcloseflushappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;!"#$%&3*' ( )* +,& * *2<*2=Y*2NY- : Y : Y*2 :Y:6,Y:   -:NY-NY!- 'n#$%(),(-2/=0I1T2[5d6m7v895<=>C?@CABE(z m-. (s/02i12=^34IR56TG78^=9:;<=>?@A:B:CDPK |4\\cositoms/NewMsOutputFile.class1Z 3 4 56 37 8 9:; < => =?@AB CDEF CGHI iterationsIseqs(II)VCodeLineNumberTableLocalVariableTablethisLcositoms/NewMsOutputFile; pIterationspSeqs writeHeader(Ljava/io/BufferedWriter;)VbwLjava/io/BufferedWriter; ExceptionsJ writeSample0(Ljava/io/BufferedWriter;Lcositoms/CosiSample;)VpSampleLcositoms/CosiSample;samplei sampleLines[Ljava/lang/String; SourceFileNewMsOutputFile.java K  java/lang/StringBuilderms LM LN  -s 111 OPQ RS TK111// segsites: U VW positions:  XYcositoms/NewMsOutputFilejava/lang/Objectjava/io/IOException()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/BufferedWriterwrite(Ljava/lang/String;)VnewLinecositoms/CosiSample getSegsites()IgetSampleLines()[Ljava/lang/String;!Y***   !"#$>+Y* *  + + + +  +!/"5#9$=%> >%&'()*),N+ + +Y- + + 6-&+Y  + -:6*+2 + + F()* +&,*-00<1Y0_4c6i8u9~:8=?> %&+,-,3Z.i$/0'(12PK |4 AMETA-INF/PK |4]p'META-INF/MANIFEST.MFPK |4 Acositoms/PK |4pEcositoms/CosiSample.classPK |42cositoms/CosiToMs.classPK |4\\cositoms/NewMsOutputFile.classPK