--- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000 +++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000 @@ -1,6 +1,6 @@ #!@WHICHPERL@ ## -## $Id: process_request.pl 1339 2006-09-21 19:46:28Z tbailey $ +## $Id: process_request.pl 1807 2007-05-30 01:34:31Z tbailey $ ## ## $Log: process_request.pl,v $ ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya @@ -55,7 +55,8 @@ $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl"; # # You can change this if you wish to use a different JASPAR server -$jaspar_root = "http://mordor.cgb.ki.se"; +#$jaspar_root = "http://mordor.cgb.ki.se"; +$jaspar_root = "http://asp.ii.uib.no:8090"; $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl"; # # You can change this if you wish to use a different Meta-MEME server @@ -221,7 +222,7 @@ $fasta = ""; # return value @lines = split(/\n/, $block); # split block into lines - for ($i = 1; $i<$#lines; $i++) { + for ($i = 2; $i<$#lines; $i++) { last if $lines[$i] =~ /^\/\//; @words = split(/\s+/, $lines[$i]); # split line into words # get sequence line @@ -239,7 +240,7 @@ $fasta = ""; # return value @lines = split(/\n/, $block); # split block into lines - for ($i = 1; $i<$#lines; $i++) { + for ($i = 2; $i<$#lines; $i++) { last if $lines[$i] =~ /^\/\//; @words = split(/\s+/, $lines[$i]); # split line into words # get id line and sequence line @@ -311,7 +312,8 @@ $content = $request->content; # fix bug in JASPAR output; add database field to view buttons - $content =~ s/rm=present/rm=present&db=$sub_db/g; + # remove fix: JASPAR fixed the bug + # $content =~ s/rm=present/rm=present&db=$sub_db/g; # display the page print $content; --- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000 +++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000 @@ -1,5 +1,5 @@ /* - * $Id: ureadseq.c 1339 2006-09-21 19:46:28Z tbailey $ + * $Id: ureadseq.c 1787 2007-05-18 08:17:28Z tbailey $ * * $Log$ * Revision 1.2 2006/03/08 20:50:11 nadya @@ -206,10 +206,9 @@ Local void addinfo(char *s, struct ReadSeqVars *V) { - char s2[256], *si; + char *si = (char *) malloc((strlen(s) + 40) * sizeof(char)); boolean saveadd; - si = s2; while (*s == ' ') s++; sprintf(si, " %d) %s\n", V->nseq, s); @@ -217,6 +216,7 @@ V->addit = true; V->isseqchar = isAnyChar; addseq( si, V); + free(si); V->addit = saveadd; V->isseqchar = isSeqChar; } @@ -966,7 +966,6 @@ } while ((l == 0) && !feof(V->f)); if (feof(V->f)) V->err = eNoData; - else switch (format_) { case kPlain : readPlain(V); break; case kIG : readIG(V); break; @@ -1181,7 +1180,7 @@ int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0; char sp[MAXLINE]; long linestart=0; - int maxlines2check=500; + int maxlines2check=5000; #define ReadOneLine(sp) \ { done |= (feof(fseq)); \ --- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000 +++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000 @@ -1,5 +1,5 @@ /* - * $Id: ureadseq.h 1339 2006-09-21 19:46:28Z tbailey $ + * $Id: ureadseq.h 1048 2006-07-06 20:07:44Z cegrant $ * * $Log$ * Revision 1.1 2005/07/29 19:12:07 nadya @@ -15,7 +15,7 @@ #include "config.h" #include "macros.h" -#define MAXLINE 1024 +#define MAXLINE 10240 typedef char boolean; #define NEWLINE '\n' --- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000 +++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000 @@ -433,6 +433,7 @@ name[i++] = c; /* non-blank: add to name */ } } + Resize(name, i+1, char); name[i] = '\0'; /* read in description */ --- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000 +++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000 @@ -208,42 +208,39 @@ <h2><a name="patch">Getting and installing the patches</a></h2> <p>The distribution may have patches associated with it. They are available from <a href="http://meme.nbcr.net/downloads/">http://meme.nbcr.net/downloads/</a>. -The patch file name is <span class="command">filename.VERSION.patch</span>. In addition, a -patched file is distributed as well and can be used as a drop-in substitute -for the original file. The drop-in file is <span class="command">filename.VERSION</span>. -It is necessary to download only one of the two files depending on the method used for -patching. All patches for a specific version should be installed. The list -below provides instructions for installation of availble patches for specific -version. +Patch files are located in a directory named +<span class="command">VERSION.patches</span>, +for example, <span class="command">meme_3.5.4.patches</span>. +Patch file have names like: +<span class="command">VERSION.patch_SERIAL_NO</span>, for example, <span class="command">meme_3.5.4.patch_3</span>. +</p> <p> To install a patch, download the patch file from the URL given above. +Then perform the following commands to install it: + <br><span class="command">$ cp PATCH_FILE VERSION </span> <br><span class="command">$ cd VERSION </span> + <br><span class="command">$ patch -p1 < PATCH_FILE </span> + <br><span class="command">$ make install </span> + <br><span class="command">$ make test </span> +</p> +<p> +For example, to install the first patch to version meme_3.5.4, you would perform the following commands: + <br><span class="command">$ cp meme_3.5.4.patch_1 meme_3.5.4 </span> + <br><span class="command">$ cd meme_3.5.4 </span> + <br><span class="command">$ patch -p1 < meme_3.5.4.patch_1 </span> + <br><span class="command">$ make install </span> + <br><span class="command">$ make test </span> +</p> +<p> +You must install all of the patches for a specific version in serial +number order. For example, if you wish to install patch number 3, +you must first have installed patches number 1 and 2 for that version. +This is easy to do. Just download all the patches for your current +version, copy them to your current versions's directory, and then +install them in order by repeating the <span class="command">patch</span>, +command above, with each patch file. You only need to run the +<span class="command">install</span> and +<span class="command">make test</span> commands once, after +the last <span class="command">patch</patch> command. </p> -<center> -<table class="large" border=1 cellspacing=0> -<tr> - <th width=7% class="head">Version</th> - <th width=25% class="head">Patch list</th> - <th class="head">Installation</th> -</tr> -<tr> - <td align=center>3.5.0</td> - <td align=center>mast-client.txt</td> - <td> - <ol> - <li>If downloaded a patch file <code>mast-client.txt.3.5.0.patch</code>: - <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/</span> - <br><span class="command"># cd meme_3.5.0/scripts/</span> - <br><span class="command"># patch -p0 < mast-client.txt.3.5.0.patch </span> - <br> - </li> - <li>If downloaded a patched file <code>mast-client.txt.3.5.0</code>: - <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt</span> - </li> - </ol> - </td> -</tr> -</table> -</center> - <p> <p>[<a href="#top"> Top </a>]</p>