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+<HEAD>
+<TITLE> OPTIONAL STEP 1 COMMANDS</TITLE>
+</HEAD>
+<BODY><P>
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+<B> Next:</B> <A NAME=tex2html385 HREF=subsubsection3_16_1_4.html> STEP 2 COMMANDS</A>
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+<HR> <P>
+<H3><A NAME=SECTION00016130000000000000> OPTIONAL STEP 1 COMMANDS</A></H3>
+<P>
+ADD_SEQ <int> <int>
+<P>
+Allows extra sequence positions to be created in an existing alignment. This
+permits additional annotations to be interspaced either above, below, or
+anywhere in the middle of an alignment. For example:
+<P>
+ADD_SEQ 0 10
+<P>
+would create an additional 10 sequences - all set to the blank character
+before the first sequence in the block file that has been read in.
+<P>
+ADD_SEQ 3 1
+<P>
+would add an extra sequence after sequence 3.
+<P>
+IMPORTANT: If you use the ADD_SEQ facility to add sequences anywhere except
+after the last sequence, then remember that the sequence
+numbers will alter. All formatting commands that follow this command
+must use the new sequence numbering. Thus in the first example:
+<P>
+ADD_SEQ 0 10
+<P>
+what was sequence number 1 becomes sequence 11. Sequences 1-10 are
+the new blank sequences to be used for annotation. Note that the
+sequence numbers only change for commands AFTER the SETUP command,
+thus, multiple add_seq commands refer to the sequence number as
+implied by the block file.
+<P>
+POINTSIZE <int>
+<P>
+Defines the pointsize to be used to scale the plot and space the characters.
+Default is 10 point.
+<P>
+NUMBER_SEQSIf present, then the sequence number is output with the identifier
+code. This is useful for finding the coordinates of residues to box
+or otherwise highlight.
+<P>
+LANDSCAPE
+<P>
+Specifies that alignments will be plotted with the longest paper axis
+horizontal. (Can get longer alignments on a page this way).
+<P>
+PORTRAIT
+<P>
+Specifies that alignments will be plotted with the longest paper axis vertical
+(can get more sequences on a page this way).
+<P>
+IDENT_WIDTH <int>
+<P>
+Units are characters.
+<P>
+Reserves <int> characters at left of every page for plotting
+identifiers. Note that not all this space need be used, if a smaller
+pointsize is used to plot out the identifier codes, than is used for
+the main alignment.
+<P>
+LINE_WIDTH_FACTOR <float>
+<P>
+Value greater than 0 that scales the default line width. The linewidth
+is obtained by multiplying the pointsize by this factor.
+<P>
+X_SPACE_FACTOR <float>
+<P>
+Y_SPACE_FACTOR <float>
+<P>
+This determines the spacing between adjacent residues in the X and Y
+directions. The spacing is calculated as: POINTSIZE + POINTSIZE *
+X_SPACE_FACTORor POINTSIZE + POINTSIZE * Y_SPACE_FACTOR as
+appropriate. Defaults are 0.2 and 0.0 respectively.
+<P>
+X_SHIFT_FACTOR <float>
+<P>
+Y_SHIFT_FACTOR <float>
+<P>
+These determine the shift relative to the residue drawing position
+that is given to the boxing lines. The shift is calculated as
+follows
+<P>
+(POINTSIZE + POINTSIZE * X_SPACE_FACTOR) * X_SHIFT_FACTOR
+similarly for Y_SHIFT_FACTOR.
+<P>
+The defaults are 0.3 and 0.0 respectively.
+<P>
+Fiddling with the X_SPACE/SHIFT values is useful to fine tune the
+appearance of the alignment.
+<P>
+MAX_INPUT_LEN <int>
+<P>
+Units are characters.
+Defines the maximum number of characters possible in the input line
+length. This must be greater than the maximum number of sequences
+(MAX_NSEQ).
+<P>
+e.g. MAX_INPUT_LEN 600
+<P>
+Increases the default value of 500 characters to 600 characters.
+<P>
+MAX_NSEQ <int>
+<P>
+Units are characters. Defines the maximum number of sequences that
+may be read by the program. This parameter has a large default (500).
+You may need to reduce it on computers with small memories.
+<P>
+MAX_ILEN <int>
+<P>
+Units are characters.
+The maximum length allowed for a sequence identifier code.
+<P>
+MAX_SEQ_LEN <int>
+<P>
+Defines the maximum length allowed for a sequence alignment - this may
+need to be reduced from the 8000 default value on smaller computers.
+<P>
+X_OFFSET <int>
+Units of points (1/72 inch).
+<P>
+Defines the offset along the X-axis that the alignments will be shifted prior
+to printing. Fiddle with this value to get a nice offset from the bottom left
+hand corner of the page if your page size is not A4.
+<P>
+Y_OFFSET <int>
+Units of points (1/72 inch).
+<P>
+As for X_OFFSET, only Y axis.
+<P>
+MAX_SIDE <int>
+Units of inches.
+<P>
+Defines the length of the longest side of the printer page.
+<P>
+MIN_SIDE <int>
+Units of inches.
+<P>
+Defines the length of the shortest side of the printer page.
+<P>
+VERTICAL_SPACING <int>
+<P>
+Defines the vertical spacing in character units between blocks of sequences
+when more than one block will fit on a page - default is 0.
+<P>
+DEFINE_COLOUR <int> <float> <float> <float>
+<P>
+DEFINE_COLORDefines a colour - the first number is a number by which the colour will
+be referred. The following three numbers are the intensities of red,
+green and blue respectively. Thus:
+<P>
+DEFINE_COLOUR 1 0 0.2 0.8
+<P>
+sets colour number 1 to be a colour with no red, 0.2 green and 0.8 blue.
+The exact appearance of this colour will depend on the output device.
+If you find suitable combinations of colours for your printer, then
+please let me know and I shall distribute your suggestions with the
+program.
+<P>
+DO_TICKSIf present, then tick marks are drawn below the numbers at the top of the page.
+Otherwise no ticks are shown.
+<P>
+NUMBER_INT <int>
+<P>
+Specifies the interval for writing residue position numbers. Default is 10
+<P>
+NO_NUMBERSSwitches all residue numbering off.
+<P>
+<HR> <A NAME=tex2html384 HREF=subsubsection3_16_1_4.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <A NAME=tex2html382 HREF=subsection3_16_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif.gif"></A> <A NAME=tex2html376 HREF=subsubsection3_16_1_2.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif.gif"></A> <A NAME=tex2html386 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/contents_motif.gif"></A> <BR>
+<B> Next:</B> <A NAME=tex2html385 HREF=subsubsection3_16_1_4.html> STEP 2 COMMANDS</A>
+<B>Up:</B> <A NAME=tex2html383 HREF=subsection3_16_1.html> ALSCRIPT Command Summary</A>
+<B> Previous:</B> <A NAME=tex2html377 HREF=subsubsection3_16_1_2.html> REQUIRED STEP 1 </A>
+<HR> <P>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
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