X-Git-Url: http://source.jalview.org/gitweb/?p=jpred.git;a=blobdiff_plain;f=sources%2Falscript%2Fexamples%2Fexample4.als;fp=sources%2Falscript%2Fexamples%2Fexample4.als;h=b9a2c77e3a638ef470669ce6b99992305e91250b;hp=0000000000000000000000000000000000000000;hb=4a806b607a11fc8a5296b11d5b863bbf8a448808;hpb=443c228bf0712d71e7fa34b5a2dc4b2b2e79f13f diff --git a/sources/alscript/examples/example4.als b/sources/alscript/examples/example4.als new file mode 100644 index 0000000..b9a2c77 --- /dev/null +++ b/sources/alscript/examples/example4.als @@ -0,0 +1,192 @@ +# Illustration of ALSCRIPT Command File +# +# Illustrates some of the MASK commands +# +# example 1 # Comment lines begin with the # symbol +# +# +# (A) Input and output files: +# +BLOCK_FILE example1.blc # Define the block file to format +OUTPUT_FILE example4.ps # Where to put the result +# +MAX_SIDE 11 # Fiddle with margins... +Y_OFFSET 50 # This is just to fill the page with the +X_OFFSET 80 # Alignment. Defaults normally work OK +# +# (B) Page Layout and overall spacing: +# +ADD_SEQ 38 1 # Make space after sequence 38 +ADD_SEQ 39 3 # Make space after sequence 39 +ADD_SEQ 69 1 +PORTRAIT # Portrait paper orientation +POINTSIZE 10 # 10 point default pointsize +#NUMBER_SEQS 1 # Set to 1 for numbers at left of plot +IDENT_WIDTH 8 +# +# (C) Font definitions: +# +DEFINE_FONT 0 Helvetica DEFAULT # Set font 0 to be Helvetica at default pointsize +DEFINE_FONT 1 Helvetica REL 0.75 # Set font 1 to be 0.75 times default Helvetica +DEFINE_FONT 3 Helvetica-Bold DEFAULT +DEFINE_FONT 4 Times-Bold DEFAULT +DEFINE_FONT 5 Helvetica-BoldOblique DEFAULT +DEFINE_FONT 6 Times-Roman DEFAULT +SETUP # Tell the program to get on with the formatting +# +# some formatting commands +# +SURROUND_CHARS LIV ALL # Surround all L and Y characters +FONT_CHARS IV ALL 5 # Use font 5 for all I and V characters +FONT_CHARS ASN ALL 1 # Show A and S and N characters in small caps +FONT_CHARS KR ALL 4 # Show K and R in Times-Bold +BOX_REGION 14 1 16 38 # Rectangular box of residues 14-16 +SHADE_CHARS + ALL 0.0 # Shade all + characters black +SURROUND_CHARS 56+789 1 40 27 40 # Box numbers and + on line 40 +LINE TOP 2 40 8 # Draw horizontal lines to +LINE BOTTOM 2 40 8 # Join up surrounded numbers +TEXT 2 42 "Helix Pattern" +TEXT 12 42 "Glycine Loop" # Add text annotations +TEXT 21 42 "Helix Pattern" +SUB_ID 49 "Helix Predictions" +SUB_ID 58 "Sheet Predictions" # Change the identifiers for prediction histograms +SUB_ID 68 "Turn Predictions" +#INVERSE_CHARS DE ALL +#SHADE_CHARS D ALL 0.5 +#SHADE_CHARS E ALL 0.0 +# +# (D) Some formatting commands: to illustrate the use of MASK +# +mask SETUP #setup the mask +sub_chars 1 1 27 38 SPACE . #substitute spaces for dots +mask ILLEGAL "." #. is not to be used in frequency calculation +mask FRE 1 1 27 38 # do the frequency calculation +mask BOX 1 1 27 38 # use the resulting mask to create boxing lines +mask SHADE 1 1 27 38 0.2 # shade +mask INVERSE 1 1 27 38 # inverse - could also alter the font +sub_chars 1 1 27 38 . SPACE # switch the dots back to spaces +# +# (E) Now make the prediction histograms nicer. +# +SURROUND_CHARS H 1 44 27 53 +SHADE_CHARS H 1 44 27 53 0.5 # Shade the Helix predictions 0.5 grey +SUB_CHARS 1 44 27 53 H SPACE # Substitute " " for "H" +# +SURROUND_CHARS E 1 54 27 63 # Surround the Beta Predictions +SHADE_CHARS E 1 54 27 63 0.7 # Shade the Beta Predictions +SUB_CHARS 1 54 27 63 E SPACE # Substitute the E for space in the beta predictions +# +SURROUND_CHARS T 1 64 27 73 # Surround the Turn Predictions +SHADE_CHARS T 1 64 27 73 0.9 # Shade the Turn Predictions +SUB_CHARS 1 64 27 73 T SPACE # Substitute the T for space in the turn predictions +# +SUB_ID 75 "Summary Prediction" # Annotate and shade the summary prediction +SHADE_CHARS HY 1 75 27 75 0.5 +SHADE_CHARS T 1 75 27 75 0.9 +# +# +# Now change the identifier codes +# +ID_FONT ALL 6 +SUB_ID 1 "Annexin I H4" +SUB_ID 2 "Annexin I M4" +SUB_ID 3 "Annexin I R4" +SUB_ID 4 "Annexin V R4" +SUB_ID 5 "Annexin V H4" +SUB_ID 6 "Annexin V C4" +SUB_ID 7 "Annexin II H4" +SUB_ID 8 "Annexin II B4" +SUB_ID 9 "Annexin II M4" +SUB_ID 10 "Annexin IV P4" +SUB_ID 11 "Annexin IV B4" +SUB_ID 12 "Annexin IV H4" +SUB_ID 13 "Annexin VI H4" +SUB_ID 14 "Annexin VI M4" +SUB_ID 15 "Annexin VI H8" +SUB_ID 16 "Annexin VI M8" +SUB_ID 17 "Annexin V BH4" +SUB_ID 18 "Annexin VII 4" +SUB_ID 19 "Annexin III H4" +SUB_ID 20 "Annexin III R4" +SUB_ID 21 "Annexin II M3" +SUB_ID 22 "Annexin II H3" +SUB_ID 23 "Annexin II B3" +SUB_ID 24 "Annexin I H3" +SUB_ID 25 "Annexin I M3" +SUB_ID 26 "Annexin I R3" +SUB_ID 27 "Annexin V C3" +SUB_ID 28 "Annexin V H3" +SUB_ID 29 "Annexin V R3" +SUB_ID 30 "Annexin VI H3" +SUB_ID 31 "Annexin VI M3" +SUB_ID 32 "Annexin IV H3" +SUB_ID 33 "Annexin IV B3" +SUB_ID 34 "Annexin IV P3" +SUB_ID 35 "Annexin V BH3" +SUB_ID 36 "Annexin III H3" +SUB_ID 37 "Annexin III R3" +SUB_ID 38 "Annexin VII 3" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +