diff --git a/doc/images/pappso.pdf b/doc/images/pappso.pdf
deleted file mode 100755
index 20bccaab0419e0b2c2ac1bf978fcba4b5281bb48..0000000000000000000000000000000000000000
Binary files a/doc/images/pappso.pdf and /dev/null differ
diff --git a/doc/images/pappso.svg b/doc/images/pappso.svg
new file mode 100755
index 0000000000000000000000000000000000000000..9328a5eb5296e3f08ba4635c34d6706b2dee0f69
--- /dev/null
+++ b/doc/images/pappso.svg
@@ -0,0 +1,189 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ width="323.38495"
+ height="176.62407"
+ id="svg3030"
+ sodipodi:version="0.32"
+ inkscape:version="0.47pre4 r22446"
+ sodipodi:docname="pappso.svg"
+ inkscape:output_extension="org.inkscape.output.svg.inkscape"
+ version="1.1">
+ <defs
+ id="defs3032">
+ <inkscape:perspective
+ sodipodi:type="inkscape:persp3d"
+ inkscape:vp_x="0 : 526.18109 : 1"
+ inkscape:vp_y="0 : 1000 : 0"
+ inkscape:vp_z="744.09448 : 526.18109 : 1"
+ inkscape:persp3d-origin="372.04724 : 350.78739 : 1"
+ id="perspective3038" />
+ </defs>
+ <sodipodi:namedview
+ id="base"
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1.0"
+ inkscape:pageopacity="0.0"
+ inkscape:pageshadow="2"
+ inkscape:zoom="1.4"
+ inkscape:cx="193.71183"
+ inkscape:cy="108.08095"
+ inkscape:document-units="px"
+ inkscape:current-layer="layer1"
+ showgrid="false"
+ inkscape:window-width="923"
+ inkscape:window-height="706"
+ inkscape:window-x="1916"
+ inkscape:window-y="91"
+ inkscape:window-maximized="0" />
+ <metadata
+ id="metadata3035">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <g
+ inkscape:label="Calque 1"
+ inkscape:groupmode="layer"
+ id="layer1"
+ transform="translate(-184.02181,-164.05015)">
+ <g
+ id="g3819"
+ transform="matrix(0.83657685,0,0,0.83657685,100.3069,-379.84775)">
+ <path
+ d="m 294.55008,817.4744 c 101.36375,0 183.5375,-26.0925 183.5375,-58.28 0,-32.18625 -82.17375,-58.28 -183.5375,-58.28 -101.36438,0 -183.53873,26.09375 -183.53873,58.28 0,32.1875 82.17435,58.28 183.53873,58.28"
+ style="fill:#c6e6b5;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2476" />
+ <path
+ d="m 376.46633,674.8469 c -6.88375,3.935 -13.89875,8.9575 -20.80125,14.9475"
+ style="fill:none;stroke:#f79210;stroke-width:1.64024997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2478" />
+ <path
+ d="m 452.27883,694.2269 c 0.4225,-14.175 -3.50125,-25.6225 -12.1675,-32.0175 -11.8275,-8.7275 -30.045,-6.24125 -49.295,4.7625"
+ style="fill:none;stroke:#f79210;stroke-width:1.64024997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2480" />
+ <path
+ d="m 268.76258,757.4719 -128.529,0 0,16.53375 119.869,0"
+ style="fill:#54b948;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2482" />
+ <path
+ d="m 330.95883,774.00565 130.34375,0 0,-16.53375 -122.865,0 c 0,0 -5.51125,14.98375 -7.47875,16.53375"
+ style="fill:#54b948;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2484" />
+ <path
+ d="m 315.25008,835.5894 c 21.71,16.01875 64.94875,-5.74125 96.575,-48.6 31.62875,-42.86 39.67125,-90.5925 17.96125,-106.61125 -21.70875,-16.02 -64.94625,5.74 -96.57375,48.59875 -31.62875,42.86 -39.67,90.59375 -17.9625,106.6125"
+ style="fill:#cce310;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2486" />
+ <path
+ d="m 315.25008,835.5894 c 21.71,16.01875 64.94875,-5.74125 96.575,-48.6 31.62875,-42.86 39.67125,-90.5925 17.96125,-106.61125 -21.70875,-16.02 -64.94625,5.74 -96.57375,48.59875 -31.62875,42.86 -39.67,90.59375 -17.9625,106.6125 z"
+ style="fill:none;stroke:#cce310;stroke-width:1.18099999;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2488" />
+ <path
+ d="m 329.18758,807.63315 -0.0138,0.0175 c 13.89375,10.2525 41.56625,-3.6725 61.80875,-31.1025 20.24125,-27.43125 25.3875,-57.98 11.495,-68.2325 -13.895,-10.25375 -41.5675,3.67375 -61.8075,31.10375 -18.74,25.3925 -24.54125,53.45625 -14.28,65.62 l 2.78375,2.61125"
+ style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2490" />
+ <path
+ d="m 329.18758,807.63315 -0.0138,0.0175 c 13.89375,10.2525 41.56625,-3.6725 61.80875,-31.1025 20.24125,-27.43125 25.3875,-57.98 11.495,-68.2325 -13.895,-10.25375 -41.5675,3.67375 -61.8075,31.10375 -18.74,25.3925 -24.54125,53.45625 -14.28,65.62 l 2.78375,2.61125"
+ style="fill:none;stroke:#cce310;stroke-width:1.18099999;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2492" />
+ <path
+ d="m 318.21633,757.4719 -69.67375,0 c 0,0 -9.84125,15.77125 -8.66,16.53375 l 70.855,0"
+ style="fill:#54b948;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2494" />
+ <path
+ d="m 401.71508,757.4719 -136.43875,0 c 0,0 -9.84125,15.77125 -8.66,16.53375 l 135.0625,0"
+ style="fill:#54b948;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2496" />
+ <path
+ d="m 359.45883,743.65565 c 4.97375,-5.56875 10.04,-9.5225 15.19625,-11.855 3.62875,-1.64125 6.575,-2.11375 8.8375,-1.4125 2.2625,0.7025 3.55625,2.54375 3.88375,5.53 0.325,2.98375 -0.305,6.93625 -1.89625,11.85625 -2.5175,7.77875 -6.23125,14.585 -11.14125,20.41875 -4.91125,5.8375 -10.10625,9.9925 -15.5875,12.47375 -5.38125,2.435 -9.1775,2.3625 -11.3875,-0.21625 -2.21,-2.5775 -2.13625,-7.5075 0.22,-14.7925 2.94125,-9.0975 6.89875,-16.43125 11.875,-22.0025 z m -21.06625,38.935 c 0.55875,3.815 2.43375,6.17625 5.62125,7.085 3.1875,0.90875 7.37125,0.19125 12.55125,-2.15375 4.77875,-2.16125 9.63625,-5.42125 14.57125,-9.78375 4.935,-4.36 9.3125,-9.47375 13.1325,-15.33875 3.82125,-5.8675 6.72375,-11.8725 8.71125,-18.01625 1.96,-6.0575 2.6425,-10.99375 2.05,-14.80625 -0.595,-3.81 -2.49625,-6.12875 -5.71,-6.95625 -3.215,-0.8275 -7.3625,-0.0912 -12.44125,2.20625 -7.75875,3.51 -15.01,9.21875 -21.7525,17.1275 -6.74375,7.90625 -11.7425,16.88625 -14.99375,26.94 -1.72,5.315 -2.30125,9.88125 -1.74,13.69625"
+ style="fill:#bd1174;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2498" />
+ <path
+ d="m 359.45883,743.65565 c 4.97375,-5.56875 10.04,-9.5225 15.19625,-11.855 3.62875,-1.64125 6.575,-2.11375 8.8375,-1.4125 2.2625,0.7025 3.55625,2.54375 3.88375,5.53 0.325,2.98375 -0.305,6.93625 -1.89625,11.85625 -2.5175,7.77875 -6.23125,14.585 -11.14125,20.41875 -4.91125,5.8375 -10.10625,9.9925 -15.5875,12.47375 -5.38125,2.435 -9.1775,2.3625 -11.3875,-0.21625 -2.21,-2.5775 -2.13625,-7.5075 0.22,-14.7925 2.94125,-9.0975 6.89875,-16.43125 11.875,-22.0025 z m -21.06625,38.935 c 0.55875,3.815 2.43375,6.17625 5.62125,7.085 3.1875,0.90875 7.37125,0.19125 12.55125,-2.15375 4.77875,-2.16125 9.63625,-5.42125 14.57125,-9.78375 4.935,-4.36 9.3125,-9.47375 13.1325,-15.33875 3.82125,-5.8675 6.72375,-11.8725 8.71125,-18.01625 1.96,-6.0575 2.6425,-10.99375 2.05,-14.80625 -0.595,-3.81 -2.49625,-6.12875 -5.71,-6.95625 -3.215,-0.8275 -7.3625,-0.0912 -12.44125,2.20625 -7.75875,3.51 -15.01,9.21875 -21.7525,17.1275 -6.74375,7.90625 -11.7425,16.88625 -14.99375,26.94 -1.72,5.315 -2.30125,9.88125 -1.74,13.69625 z"
+ style="fill:none;stroke:#231f20;stroke-width:0.205;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2500" />
+ <path
+ d="m 444.30008,737.28315 c 1.7575,-5.565 3.04625,-10.96875 3.85375,-16.12375"
+ style="fill:none;stroke:#f79210;stroke-width:1.64024997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2502" />
+ <path
+ d="m 293.73258,830.98315 c 1.29375,7.63875 4.48625,13.95375 9.7175,18.3575 17.44125,14.6875 51.96125,3.4275 82.945,-25.01"
+ style="fill:none;stroke:#f79210;stroke-width:1.64024997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2504" />
+ <path
+ d="m 297.59383,780.70815 c -3.71375,13.9875 -5.315,27.3025 -4.84,38.96125"
+ style="fill:none;stroke:#f79210;stroke-width:1.64024997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2506" />
+ <path
+ d="m 395.16008,818.05315 c 9.33125,-8.02875 18.47375,-18.71375 26.60875,-31.41875"
+ style="fill:none;stroke:#f79210;stroke-width:1.64024997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2508" />
+ <path
+ d="m 328.55008,799.27315 -0.0137,0.0188 c 9.9925,7.375 27.11875,2.23875 43.47875,-11.4375"
+ style="fill:none;stroke:#bd1174;stroke-width:1.18099999;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2510" />
+ <path
+ d="m 399.79133,712.4219 0.0137,-0.02 c -6.4925,-4.235 -15.47875,-3.44625 -25.09375,1.295"
+ style="fill:none;stroke:#bd1174;stroke-width:1.18099999;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2512" />
+ <path
+ d="m 364.06633,757.66565 -28.25625,0 c 0,0 -9.84125,15.77125 -8.66125,16.53375 l 26.53,0"
+ style="fill:#54b948;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2514" />
+ <path
+ d="m 291.40508,730.2269 10.44,0.025 c 2.45,0.005 4.02625,0.21375 4.73375,0.625 1.08125,0.66375 1.54,2.0275 1.38125,4.08875 -0.16125,2.06375 -0.96,4.5425 -2.3975,7.43625 -1.98625,3.9975 -4.26,7.09625 -6.82,9.29375 -2.56,2.19875 -5.58375,3.2925 -9.0725,3.285 l -10.55,-0.0237 12.285,-24.73 z m -30.41375,61.22125 14.01125,-28.205 10.47125,0.025 c 5.7725,0.0125 10.7825,-2.0275 15.02625,-6.11875 4.245,-4.09375 7.83875,-9.10125 10.78,-15.02125 1.71375,-3.44875 2.8725,-6.615 3.47625,-9.49625 0.60375,-2.8825 0.625,-5.12375 0.065,-6.7275 -0.5625,-1.6 -1.705,-2.6875 -3.42625,-3.2625 -1.21125,-0.44625 -3.1725,-0.67375 -5.88375,-0.67875 l -15.4075,-0.0362 -34.53125,69.50875 5.41875,0.0125"
+ style="fill:#bd1174;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2516" />
+ <path
+ d="m 291.40508,730.2269 10.44,0.025 c 2.45,0.005 4.02625,0.21375 4.73375,0.625 1.08125,0.66375 1.54,2.0275 1.38125,4.08875 -0.16125,2.06375 -0.96,4.5425 -2.3975,7.43625 -1.98625,3.9975 -4.26,7.09625 -6.82,9.29375 -2.56,2.19875 -5.58375,3.2925 -9.0725,3.285 l -10.55,-0.0237 12.285,-24.73 z m -30.41375,61.22125 14.01125,-28.205 10.47125,0.025 c 5.7725,0.0125 10.7825,-2.0275 15.02625,-6.11875 4.245,-4.09375 7.83875,-9.10125 10.78,-15.02125 1.71375,-3.44875 2.8725,-6.615 3.47625,-9.49625 0.60375,-2.8825 0.625,-5.12375 0.065,-6.7275 -0.5625,-1.6 -1.705,-2.6875 -3.42625,-3.2625 -1.21125,-0.44625 -3.1725,-0.67375 -5.88375,-0.67875 l -15.4075,-0.0362 -34.53125,69.50875 5.41875,0.0125 z"
+ style="fill:none;stroke:#231f20;stroke-width:0.205;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2518" />
+ <path
+ d="m 257.18133,730.3619 10.43875,0.025 c 2.45,0.006 4.02625,0.21375 4.7325,0.625 1.0825,0.66375 1.5425,2.0275 1.38375,4.09 -0.1625,2.0625 -0.96125,4.54 -2.39875,7.435 -1.98625,3.9975 -4.25875,7.09625 -6.82,9.29375 -2.55875,2.1975 -5.58375,3.2925 -9.0725,3.285 l -10.55,-0.025 12.28625,-24.72875 z m -30.41462,61.22125 14.01212,-28.205 10.47,0.025 c 5.77375,0.0138 10.7825,-2.02625 15.02625,-6.11875 4.245,-4.09375 7.84,-9.10125 10.78,-15.02125 1.71375,-3.45 2.8725,-6.61375 3.47625,-9.49625 0.605,-2.88125 0.625,-5.12375 0.065,-6.7275 -0.5625,-1.6 -1.705,-2.6875 -3.42625,-3.2625 -1.21125,-0.44625 -3.1725,-0.6725 -5.88375,-0.67875 l -15.40625,-0.035 -34.53138,69.50625 5.41801,0.0138"
+ style="fill:#bd1174;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2520" />
+ <path
+ d="m 257.18133,730.3619 10.43875,0.025 c 2.45,0.006 4.02625,0.21375 4.7325,0.625 1.0825,0.66375 1.5425,2.0275 1.38375,4.09 -0.1625,2.0625 -0.96125,4.54 -2.39875,7.435 -1.98625,3.9975 -4.25875,7.09625 -6.82,9.29375 -2.55875,2.1975 -5.58375,3.2925 -9.0725,3.285 l -10.55,-0.025 12.28625,-24.72875 z m -30.41462,61.22125 14.01212,-28.205 10.47,0.025 c 5.77375,0.0138 10.7825,-2.02625 15.02625,-6.11875 4.245,-4.09375 7.84,-9.10125 10.78,-15.02125 1.71375,-3.45 2.8725,-6.61375 3.47625,-9.49625 0.605,-2.88125 0.625,-5.12375 0.065,-6.7275 -0.5625,-1.6 -1.705,-2.6875 -3.42625,-3.2625 -1.21125,-0.44625 -3.1725,-0.6725 -5.88375,-0.67875 l -15.40625,-0.035 -34.53138,69.50625 5.41801,0.0138 z"
+ style="fill:none;stroke:#231f20;stroke-width:0.205;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2522" />
+ <path
+ d="m 188.0397,729.5794 10.43888,0.0238 c 2.44875,0.006 4.02588,0.215 4.733,0.62625 1.082,0.6625 1.542,2.0275 1.38225,4.08875 -0.16113,2.06375 -0.95987,4.54125 -2.39788,7.435 -1.98587,3.99875 -4.25974,7.09625 -6.81937,9.29375 -2.56,2.19875 -5.5845,3.29375 -9.07225,3.285 l -10.55075,-0.025 12.28612,-24.7275 z m -30.41462,61.22 14.01175,-28.20375 10.47025,0.0238 c 5.77287,0.0137 10.78225,-2.02625 15.02688,-6.12 4.24412,-4.09125 7.83887,-9.1 10.77974,-15.01875 1.71388,-3.45 2.87201,-6.615 3.4765,-9.4975 0.60363,-2.88125 0.625,-5.1225 0.064,-6.72625 -0.56201,-1.60125 -1.70463,-2.68875 -3.42625,-3.26375 -1.21051,-0.445 -3.17188,-0.6725 -5.88326,-0.6775 l -15.40675,-0.0362 -34.53174,69.5075 5.41887,0.0125"
+ style="fill:#bd1174;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2524" />
+ <path
+ d="m 188.0397,729.5794 10.43888,0.0238 c 2.44875,0.006 4.02588,0.215 4.733,0.62625 1.082,0.6625 1.542,2.0275 1.38225,4.08875 -0.16113,2.06375 -0.95987,4.54125 -2.39788,7.435 -1.98587,3.99875 -4.25974,7.09625 -6.81937,9.29375 -2.56,2.19875 -5.5845,3.29375 -9.07225,3.285 l -10.55075,-0.025 12.28612,-24.7275 z m -30.41462,61.22 14.01175,-28.20375 10.47025,0.0238 c 5.77287,0.0137 10.78225,-2.02625 15.02688,-6.12 4.24412,-4.09125 7.83887,-9.1 10.77974,-15.01875 1.71388,-3.45 2.87201,-6.615 3.4765,-9.4975 0.60363,-2.88125 0.625,-5.1225 0.064,-6.72625 -0.56201,-1.60125 -1.70463,-2.68875 -3.42625,-3.26375 -1.21051,-0.445 -3.17188,-0.6725 -5.88326,-0.6775 l -15.40675,-0.0362 -34.53174,69.5075 5.41887,0.0125 z"
+ style="fill:none;stroke:#231f20;stroke-width:0.205;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2526" />
+ <path
+ d="m 219.14908,742.5219 c 3.13225,-4.38375 6.09663,-8.845 8.8945,-13.38375 -1.22563,3.8025 -2.65138,8.6325 -4.27975,14.4925 l -5.291,19.34125 -13.99175,-0.0312 14.668,-20.41875 z m -34.8115,48.875 14.892,-20.975 17.24463,0.04 -5.75051,20.99625 6.15238,0.0137 17.81737,-69.54625 -5.90274,-0.0138 -50.18663,69.4725 5.7335,0.0125"
+ style="fill:#bd1174;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2528" />
+ <path
+ d="m 219.14908,742.5219 c 3.13225,-4.38375 6.09663,-8.845 8.8945,-13.38375 -1.22563,3.8025 -2.65138,8.6325 -4.27975,14.4925 l -5.291,19.34125 -13.99175,-0.0312 14.668,-20.41875 z m -34.8115,48.875 14.892,-20.975 17.24463,0.04 -5.75051,20.99625 6.15238,0.0137 17.81737,-69.54625 -5.90274,-0.0138 -50.18663,69.4725 5.7335,0.0125 z"
+ style="fill:none;stroke:#231f20;stroke-width:0.205;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2530" />
+ <path
+ d="m 300.83508,767.55565 5.5025,-0.79 c -1.49,3.48125 -2.35125,6.3375 -2.58625,8.57 -0.235,2.2325 0.225,4.03875 1.38125,5.42 1.155,1.38 2.88375,2.0725 5.1825,2.07875 2.04,0.004 4.1025,-0.51375 6.185,-1.55375 2.0825,-1.04125 3.9575,-2.47 5.6225,-4.2875 1.6675,-1.81625 3.03125,-3.79375 4.09375,-5.93 1.075,-2.16625 1.64875,-4.06 1.71875,-5.6775 0.07,-1.61875 -0.46625,-2.9825 -1.6125,-4.09 -0.72625,-0.725 -2.57,-1.85625 -5.5275,-3.3925 -2.95875,-1.53875 -4.855,-2.98875 -5.68625,-4.3575 -1.09125,-1.745 -1.475,-3.91125 -1.1525,-6.49375 0.3225,-2.58375 1.28125,-5.4775 2.87,-8.68 1.74875,-3.5175 3.9625,-6.80125 6.6475,-9.855 2.68375,-3.055 5.53875,-5.3725 8.565,-6.9525 3.02375,-1.5775 5.9075,-2.365 8.64375,-2.36 3.015,0.008 5.26,0.84625 6.73625,2.51875 1.47375,1.6725 2.0275,4.12875 1.65875,7.36875 -0.37,3.24 -1.525,6.90625 -3.46625,11 l -5.515,0.65625 c 1.89125,-4.3625 2.595,-7.66125 2.11125,-9.89625 -0.48625,-2.23125 -2.2825,-3.3525 -5.3925,-3.35875 -3.23875,-0.008 -6.105,1.00375 -8.59875,3.0325 -2.49125,2.02875 -4.4475,4.4775 -5.87125,7.3425 -1.2375,2.48875 -1.72875,4.5375 -1.47625,6.14625 0.23125,1.61 2.10375,3.26125 5.62,4.9575 3.51625,1.695 5.77875,3.1775 6.78625,4.4425 1.4525,1.86875 2.03625,4.23 1.7525,7.08875 -0.28625,2.86 -1.3525,6.15 -3.2025,9.87125 -1.83375,3.6925 -4.1825,7.17125 -7.04375,10.435 -2.86125,3.26375 -5.9025,5.80125 -9.1225,7.61 -3.22125,1.80625 -6.2825,2.70875 -9.18375,2.7025 -3.6775,-0.009 -6.305,-0.9325 -7.88,-2.7725 -1.575,-1.84 -2.155,-4.6025 -1.73875,-8.29 0.4175,-3.6875 1.7425,-7.85375 3.97875,-12.50375"
+ style="fill:#bd1174;fill-opacity:1;fill-rule:nonzero;stroke:none"
+ id="path2532" />
+ <path
+ d="m 300.83508,767.55565 5.5025,-0.79 c -1.49,3.48125 -2.35125,6.3375 -2.58625,8.57 -0.235,2.2325 0.225,4.03875 1.38125,5.42 1.155,1.38 2.88375,2.0725 5.1825,2.07875 2.04,0.004 4.1025,-0.51375 6.185,-1.55375 2.0825,-1.04125 3.9575,-2.47 5.6225,-4.2875 1.6675,-1.81625 3.03125,-3.79375 4.09375,-5.93 1.075,-2.16625 1.64875,-4.06 1.71875,-5.6775 0.07,-1.61875 -0.46625,-2.9825 -1.6125,-4.09 -0.72625,-0.725 -2.57,-1.85625 -5.5275,-3.3925 -2.95875,-1.53875 -4.855,-2.98875 -5.68625,-4.3575 -1.09125,-1.745 -1.475,-3.91125 -1.1525,-6.49375 0.3225,-2.58375 1.28125,-5.4775 2.87,-8.68 1.74875,-3.5175 3.9625,-6.80125 6.6475,-9.855 2.68375,-3.055 5.53875,-5.3725 8.565,-6.9525 3.02375,-1.5775 5.9075,-2.365 8.64375,-2.36 3.015,0.008 5.26,0.84625 6.73625,2.51875 1.47375,1.6725 2.0275,4.12875 1.65875,7.36875 -0.37,3.24 -1.525,6.90625 -3.46625,11 l -5.515,0.65625 c 1.89125,-4.3625 2.595,-7.66125 2.11125,-9.89625 -0.48625,-2.23125 -2.2825,-3.3525 -5.3925,-3.35875 -3.23875,-0.008 -6.105,1.00375 -8.59875,3.0325 -2.49125,2.02875 -4.4475,4.4775 -5.87125,7.3425 -1.2375,2.48875 -1.72875,4.5375 -1.47625,6.14625 0.23125,1.61 2.10375,3.26125 5.62,4.9575 3.51625,1.695 5.77875,3.1775 6.78625,4.4425 1.4525,1.86875 2.03625,4.23 1.7525,7.08875 -0.28625,2.86 -1.3525,6.15 -3.2025,9.87125 -1.83375,3.6925 -4.1825,7.17125 -7.04375,10.435 -2.86125,3.26375 -5.9025,5.80125 -9.1225,7.61 -3.22125,1.80625 -6.2825,2.70875 -9.18375,2.7025 -3.6775,-0.009 -6.305,-0.9325 -7.88,-2.7725 -1.575,-1.84 -2.155,-4.6025 -1.73875,-8.29 0.4175,-3.6875 1.7425,-7.85375 3.97875,-12.50375 z"
+ style="fill:none;stroke:#231f20;stroke-width:0.205;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ id="path2534" />
+ </g>
+ </g>
+</svg>
diff --git a/doc/xtandem_pipeline.tex b/doc/xtandem_pipeline.tex
index f45bf4cca2f1a61f7af653765766cf6c271350a6..915344a7f971323b1437f7c3de6e0df8a0dff2e0 100644
--- a/doc/xtandem_pipeline.tex
+++ b/doc/xtandem_pipeline.tex
@@ -17,7 +17,7 @@
\author{Benoit Valot and Olivier Langella\\
\texttt{valot@moulon.inra.fr; langella@moulon.inra.fr}\\
PAPPSO - \url{http://pappso.inra.fr/}\\
-\includegraphics[width=1cm]{images/pappso.pdf}
+\includegraphics[width=1cm]{images/pappso}
}
\title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results}
\date{22 June 2012}
@@ -29,7 +29,7 @@ PAPPSO - \url{http://pappso.inra.fr/}\\
%\fancyhead{}
\fancyfoot{}
\rfoot{\thepage}
-\lfoot{\includegraphics[width=1cm]{images/pappso.pdf}}
+\lfoot{\includegraphics[width=1cm]{images/pappso}}
\begin{document}
@@ -106,7 +106,7 @@ At the firt start, the application open the configuration path window:
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_configuration.png}
+\center \includegraphics[scale=0.5]{images/tandem_configuration}
\caption{Configuration window}
\label{configuration}
\end{figure}
@@ -124,7 +124,7 @@ Three successive graphical boxes help you select first the mzXML files or other
To perform database searching, you must create or edit a model XML file (stored in the xtandem models folder). Open the menu \textit{Option $\rightarrow$ X!Tandem preset} (Fig~\ref{xtandem_parameter}).
\begin{figure}[!ht]
-\center \includegraphics[scale=0.4]{images/tandem_parameter.png}
+\center \includegraphics[scale=0.4]{images/tandem_parameter}
\caption{X!Tandem preset window}
\label{xtandem_parameter}
\end{figure}
@@ -153,7 +153,7 @@ X!Tandem works with open peak-list files like mzXML, mgf, mzData, mzML or pkl fi
X!Tandem software uses only protein databases in fasta format. It doesn't work with EST\footnote{Expressed Sequenced tag} sequences. You can transform your database using our application \textit{Protein database manager}, available \href{http://pappso.inra.fr/bioinformatique.html}{here}, or you can directly run it \href{http://pappso.inra.fr/documents/bioinformatique/database_manager.jnlp}{here}.
\begin{figure}[!ht]
-\center \includegraphics[scale=0.4]{images/tandem_analysis.png}
+\center \includegraphics[scale=0.4]{images/tandem_analysis}
\caption{X!Tandem parameter window}
\label{xtandem_analysis}
\end{figure}
@@ -204,7 +204,7 @@ Interesting because it allows you to always include the same contaminant protein
\end{description}
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_filter.png}
+\center \includegraphics[scale=0.5]{images/tandem_filter}
\caption{Filter window}
\label{filter}
\end{figure}
@@ -229,7 +229,7 @@ After loading the results, you can select the result to view in the main window
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_principal.png}
+\center \includegraphics[scale=0.5]{images/tandem_principal}
\caption{Main window}
\label{principal}
\end{figure}
@@ -245,7 +245,7 @@ View the list of protein identified on the result. For more details on column se
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_protein.png}
+\center \includegraphics[scale=0.5]{images/window_protein}
\caption{Proteins List}
\end{figure}
@@ -254,7 +254,7 @@ View the list of protein identified on the result. For more details on column se
View the protein sequence and coverage on a identified protein. To view this window, you must open it in the menu \textit{Windows $\rightarrow$ Protein details}.
\begin{figure}[!ht]
-\center \includegraphics[scale=0.7]{images/window_protein_detail.png}
+\center \includegraphics[scale=0.7]{images/window_protein_detail}
\caption{Protein details}
\end{figure}
@@ -269,7 +269,7 @@ View the peptides identified a protein. For more details on column see Fig~\ref{
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_peptide.png}
+\center \includegraphics[scale=0.5]{images/window_peptide}
\caption{Peptides List}
\end{figure}
@@ -283,7 +283,7 @@ View the MS/MS spectra of an identified peptide.
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_peptide_detail.png}
+\center \includegraphics[scale=0.5]{images/window_peptide_detail}
\caption{Peptides Details}
\end{figure}
@@ -310,7 +310,7 @@ The export window (Fig~\ref{export}) shows the different types of available expo
\end{description}
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_export.png}
+\center \includegraphics[scale=0.5]{images/tandem_export}
\caption{Export window}
\label{export}
\end{figure}
@@ -344,7 +344,7 @@ The identified proteins are represented by sample (individual mode) or for all s
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_prot.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_prot}
\caption{Protein results}
\label{prot}
\end{figure}
@@ -381,7 +381,7 @@ Identified peptides are grouped by group (Fig~\ref{pep}). One line corresponds t
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide}
\caption{Peptide results}
\label{pep}
\end{figure}
@@ -412,7 +412,7 @@ The list of proteins is repeated 4 times, corresponding to the 4 parameters that
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison}
\caption{Comparison results}
\label{compar}
\end{figure}
@@ -427,7 +427,7 @@ In this case, the column corresponding to the normal and reverse search are indi
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_fdr.png}
+\center \includegraphics[scale=0.5]{images/tandem_fdr}
\caption{FDR results}
\label{fdr2}
\end{figure}