<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<br><br>This is in 1.997.<br><br>Thanks<div><br></div><div>BTW, I got an undeliverable notification from help@gmod.org when I first sent this.<br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-interchange-newline"><br></div><div>Keiran Raine</div><div>Senior Computer Biologist</div><div>The Cancer Genome Project</div><div>Ext: 2100</div><div><a href="mailto:kr2@sanger.ac.uk">kr2@sanger.ac.uk</a></div><div><br></div></div></span>The Wellcome Trust Sanger Institute is operated by Genome Research <br>Limited, a charity registered in England with number 1021457 and a <br>company registered in England with number 2742969, whose registered <br>office is 215 Euston Road, London, NW1 2BE. </div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span></div></span> </div><br><div><div>On 17 Dec 2009, at 23:28, Dave Clements, GMOD Help Desk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Keiran,<br></div><div><br></div><div>This definitely sounds like a bug to me. What specific version of GBrowse are you seeing this in?</div><div><br></div><div>I'll create a bug report for it.</div><div><br></div> <div>Dave C</div><br><div class="gmail_quote">On Thu, Dec 10, 2009 at 3:38 AM, Keiran Raine <span dir="ltr"><<a href="mailto:kr2@sanger.ac.uk">kr2@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> <div style="word-wrap:break-word">Hi,<div><br></div><div>When I use the bicolor_pivoit option on the box form of xyplot I am finding that the elements below the threshold, although the correct outline colour, have no fill:</div> <div><br></div><div><span><Picture 1.png></span><br><div><br></div><div>Has anyone else had this problem?</div><div><br></div><div><div><font face="Courier" size="3"><span style="font-size:12px">[segmentXyplot]</span></font></div> <div><font face="Courier" size="3"><span style="font-size:12px">feature = parent_segment</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">glyph = xyplot</span></font></div> <div><font face="Courier" size="3"><span style="font-size:12px">graph_type<span style="white-space:pre"> </span></span></font><font face="Courier" size="3"><span style="font-size:12px"> = boxes</span></font></div><div> <font face="Courier" size="3"><span style="font-size:12px">fgcolor = black</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">bicolor_pivot = 2</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">pos_color = blue</span></font></div> <div><font face="Courier" size="3"><span style="font-size:12px">neg_color = red</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">database = GRC37_56</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">max_score </span></font><font face="Courier" size="3"><span style="font-size:12px"> = 5</span></font></div> <div><font face="Courier" size="3"><span style="font-size:12px">min_score <span style="white-space:pre"> </span></span></font><font face="Courier" size="3"><span style="font-size:12px">= 0</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">height = 50</span></font></div> <div><font face="Courier" size="3"><span style="font-size:12px">key = Segmentation</span></font></div><div><font face="Courier" size="3"><span style="font-size:12px">category = Copy number</span></font></div> <div><font face="Courier" size="3"><span style="font-size:12px">label = 0</span></font></div></div><div><br></div><div> <span style="font-size:12px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"> <span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"> <span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"> <div>The perldoc for this element indicates that the fill should be taken from the neg_color.</div><div><br></div><div>Thanks,<br><br></div><div>Keiran Raine</div><div>Senior Computer Biologist</div><div>The Cancer Genome Project</div> <div>Ext: 2100</div><div><a href="mailto:kr2@sanger.ac.uk" target="_blank">kr2@sanger.ac.uk</a></div><div><br></div></div></span>The Wellcome Trust Sanger Institute is operated by Genome Research <br>Limited, a charity registered in England with number 1021457 and a <br> company registered in England with number 2742969, whose registered <br>office is 215 Euston Road, London, NW1 2BE. </div></span><br></span><br></div></span></div></span> </div><br></div> <br> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. <br> </div><br>------------------------------------------------------------------------------<br> Return on Information:<br> Google 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The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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