PK W~U; META-INF/PK V~U;;әMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.7.1 Created-By: 11.3-b02 (Sun Microsystems Inc.) Main-Class: Recom.Recom Class-Path: X-COMMENT: Main-Class will be added automatically by build PK V~U;RATUtil/PK V~U; ReadMeFiles/PK V~U;Recom/PK V~U; ORATUtil/BioUtil.class2 @}~ }                ?   }      $  ( (   .    ? 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Y**+*,    /* 7=+=*>$*+*2=" -/5*%775 ! * PK V~U;F##RATUtil/RATUtil.class2 8r st su svw x syz {|}~ r @$     ' & * &      FileFilterExt InnerClasses()VCodeLineNumberTableLocalVariableTablethisLRATUtil/RATUtil;createComponentImage4(Ljava/awt/Component;)Ljava/awt/image/BufferedImage; componentLjava/awt/Component;imageLjava/awt/image/BufferedImage;graphicsLjava/awt/Graphics; StackMapTablew encodeImage/(Ljava/awt/image/BufferedImage;Ljava/io/File;)VeLjava/io/IOException; bufferedImagefileLjava/io/File;}getFileExtension"(Ljava/io/File;)Ljava/lang/String;nameLjava/lang/String;iI roundDouble(DI)DdDplaceschooseSequenceTypeM(Ljava/lang/String;Ljava/io/File;Ljava/util/ArrayList;Ljava/util/ArrayList;)VnameIndicatorCharLjava/io/FileNotFoundException;bfLjava/io/BufferedReader;s fileExtensionLjava/util/ArrayList;seq SourceFile RATUtil.java <= java/awt/image/BufferedImage jpg java/io/IOExceptionjava/lang/StringBuilderSorry, an error has occured :     aln  fas> fsafastafstgde java/io/BufferedReaderjava/io/FileReader < <java/io/FileNotFoundException = % # phy )Can't recognise that as an alignment file RATUtil/RATUtiljava/lang/ObjectRATUtil/RATUtil$FileFilterExtjava/awt/Graphicsjava/lang/String java/io/Filejava/util/ArrayListjava/awt/ComponentgetWidth()I getHeight createImage(II)Ljava/awt/Image; getGraphics()Ljava/awt/Graphics;paintAll(Ljava/awt/Graphics;)Vjavax/imageio/ImageIOwriteA(Ljava/awt/image/RenderedImage;Ljava/lang/String;Ljava/io/File;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;javax/swing/JOptionPaneshowMessageDialog)(Ljava/awt/Component;Ljava/lang/Object;)VgetName lastIndexOf(I)Ilength substring(I)Ljava/lang/String; toLowerCasejava/lang/Mathpow(DD)Dround(D)Jequals(Ljava/lang/Object;)ZRATUtil/BioUtilreadClustalwFileToArray;(Ljava/io/File;Ljava/util/ArrayList;Ljava/util/ArrayList;)ZreadFastaFileToArrayM(Ljava/io/File;Ljava/lang/String;Ljava/util/ArrayList;Ljava/util/ArrayList;)ZcanRead()Z(Ljava/io/File;)V(Ljava/io/Reader;)VprintStackTracereadLine startsWith(Ljava/lang/String;)ZreadFileGdePercentreadFileGdeHashreadPhylipFileToArrayjava/lang/Systemexit(I)V!78<=>3*? *@ AB CD> ***L+M,*,+?4569;@  EFGH IJK LM NO>$*+ WM Y  , ?QV S U#Y@  PQ$RH$STKKU VW>+*(*L+.=+d+`?cf hil)o@  XYZ[+STK) \]>L&ko?z@^_`[ ab>* +,-W*:+,- W*!:+,- W*":+,- W*#:+,- W*$d+%z:&Y'Y+(): :+:,: :-./ +,-0W1/ +,-2W *3 +,-4W 56* ?(  ),59BENR[^gktw@z cY9 cYR cYk cYPdPQTef6gYhYSTXijiKE&klmmno klmmnkU pq; 97: PK V~U;&QAFFReadMeFiles/AutoSearch.txt Auto search looks for sequences that fit the parameters supplied in the 3 boxes. It looks at EVERY sequence in the alignment in turn and compares it to all the other sequences. There are 3 fields involved: Field 1. Find sequences that start below the following similarity (%): Field 2. then jumps to over(%): RAT, using its sliding window technique, searches each sequence and looks for a window that has a sequence similarity less than, or equal to, that in Field 1, which then jumps to that set in Field 2 (equal to, or greater than). Field 3. Maximum number of contributing sequences: You can restrict the number of sequences that you want to include as contributing to recombination. The default number is the number of sequences (so, no restriction) Tip: If you are examining closely related sequences that may share many similar motifs, reduce the number of sequences. This will reduce the chance of getting hits on conserved regions. HINT: Hit 'Execute' to examine how similar your sequences are. That way, you should have an idea of what parameters to use in the relevant fields. PK V~U;q~kkReadMeFiles/EndAt.txt End at position: This is the position on the sequence where analysis finishes. The default position is that of sequence length, namely the last position in the sequence. If you wish only to analyse a particular area within your sequence, you can change this parameter to reflect the area of interest. This parameter must be higher than Start at position. PK V~U;9B11ReadMeFiles/IncrementSize.txt Increment size: The sliding window of RAT moves along the sequences in short increments and then examines an area the size of the given window size. After each increment the sequences is re-evaluated. The default increment size is half that of the default window size (i.e. 5% of the sequence size). PK V~U;JA^ReadMeFiles/OutOfMemory.txt Out of memory: Throughout RAT, checks are made on available memory. If the file is too big for the Java Virtual Machine's it will give an error and fail. This is due to the JVM not having enough memory allocation pool to carry out the task. The default value is 65Mb To correct this, try the following steps: 1. Open a command-line prompt 2. Navigate to the folder containing RAT.jar 3. Type the following (case sensitive, space sensitive, parameters in <>) "java -Xms -Xmx -jar Rat.jar" Parameters: - how much memory to allocate to the task - specify what units of memory we are using - bytes(b), kilobytes(k), or megabytes(m) -Xmsn Specify the initial size of the memory allocation pool. This value must greather than 1000b. The default value is 1m -Xmxn Specify the maximum size of the memory allocation pool. This value must greather than 1000b. The default value is 64m. example: C:\Java\dist\lib>java -Xms20m -Xmx100m -jar Rat.jar PK V~U;\ppReadMeFiles/ParameterInput.txtThere are 4 inputs that vary the way the data is displayed and analysed. Window size: RAT uses a sliding window, which moves down the sequences and makes comparisons between areas of nucleotides (nts)/amino acids (aas) at the same position. The window size parameter is the amount of nts/aas that the window examines at one time. The default value is 10% of the sequence. You can increase or decrease this value. Increment size: The sliding window of RAT moves along the sequences in short increments and then examines an area the size of the given window size. After each increment the sequences is re-evaluated. The default increment size is half that of the default window size (i.e. 5% of the sequence size). Start at position: This is the position on the sequence where analysis starts. The default position is position 1. If you wish only to analyse a particular area within your sequence, you can change this parameter to reflect the area of interest. This parameter must be lower than End at position. End at position: This is the position on the sequence where analysis finishes. The default position is that of sequence length, namely the last position in the sequence. If you wish only to analyse a particular area within your sequence, you can change this parameter to reflect the area of interest. This parameter must be higher than Start at position. PK V~U;ɌO//ReadMeFiles/StartAt.txt Start at position: This is the position on the sequence where analysis starts. The default position is position 1. If you wish only to analyse a particular area within your sequence, you can change this parameter to reflect the area of interest. This parameter must be lower than End at position. PK V~U;L\\ReadMeFiles/WindowSize.txt Window size: RAT uses a sliding window, which moves down the sequences and makes comparisons between areas of nucleotides (nts)/amino acids (aas) at the same position. The window size parameter is the amount of nts/aas that the window examines at one time. The default value is 10% of the sequence. You can increase or decrease this value. PK V~U;XD ѓReadMeFiles/fileSelection.txt RAT accepts the following file extensions for use .aln .fas .fsa .fasta .fst .gde (must have % as the sequence identifier - # will not work) .phyPK V~U;[!! ReadMeFiles/testSequenceName.txt The test sequence is the sequence you wish to examine. If you want, for example, to see how sequence gi|9630804|ref|NP_056820.1|Norwalk polyprotein, compares to the other sequences in the alignment, then select this sequence and hit 'execute' to see the graphical representation of it. 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Cancel Execute =Find sequences that start below the following similarity (%): 82 then jump to over (%): 92 (Maximum number of contributing sequences  Search java/util/Vector  javax/swing/JMenuBar   javax/swing/JMenuHelp   javax/swing/JMenuItemHelp on file selection  Test sequence Input Parameters  All input parameters  Window size Increment size Start at position End at position Auto Search Parameters Memory allocation  Auto Search  Auto Search  :Click here to choose alignment file (Fasta files are best) Choose sequence to examine9Choose lenght of window. Default = 0.1 of sequence length9Choose length of window. Default = 0.1 of sequence length:Choose window increment size. 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