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/* @source ajobowrite *********************************************************
**
** AJAX OBO writing functions
**
** @author Copyright (C) 2010 Peter Rice
** @version $Revision: 1.15 $
** @modified May 5 pmr 2010 First AJAX version
** @modified Sep 8 2010 pmr Added output formats
** @modified $Date: 2012/08/21 10:54:04 $ by $Author: rice $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
#include "ajlib.h"
#include "ajobowrite.h"
#include "ajobo.h"
#include "ajfileio.h"
static AjBool oboWriteExcel(AjPFile outf, const AjPObo obo);
static AjBool oboWriteHtml(AjPFile outf, const AjPObo obo);
static AjBool oboWriteJson(AjPFile outf, const AjPObo obo);
static AjBool oboWriteList(AjPFile outf, const AjPObo obo);
static AjBool oboWriteObo(AjPFile outf, const AjPObo obo);
static AjBool oboWriteObobrief(AjPFile outf, const AjPObo obo);
static AjBool oboWriteXml(AjPFile outf, const AjPObo obo);
/* @datastatic OboPOutFormat **************************************************
**
** Obo output formats data structure
**
** @alias OboSoutFormat
** @alias OboOOutFormat
**
** @attr Name [const char*] Format name
** @attr Obo [const char*] Ontology term id from EDAM
** @attr Desc [const char*] Format description
** @attr Write [AjBool function] Output function, returns ajTrue on success
** @@
******************************************************************************/
typedef struct OboSOutFormat
{
const char *Name;
const char *Obo;
const char *Desc;
AjBool (*Write) (AjPFile outf, const AjPObo obo);
} OboOOutFormat;
#define OboPOutFormat OboOOutFormat*
static OboOOutFormat obooutFormatDef[] =
{
/* "Name", OBO "Description" */
/* WriteFunction */
{"obo", "2196", "OBO format",
&oboWriteObo},
{"brief", "0000", "OBO format id, name and namespace only",
&oboWriteObobrief},
{"list", "0000", "Identifier only",
&oboWriteList},
{"html", "2331", "HTML with markup",
&oboWriteHtml},
{"xml", "2332", "XML format",
&oboWriteXml},
{"json", "0000", "JSON format",
&oboWriteJson},
{"excel", "0000", "Tab-delimited file for import to Microsoft Excel",
&oboWriteExcel},
{NULL, NULL, NULL, NULL}
};
/* @filesection ajobo ********************************************************
**
** @nam1rule aj Function belongs to the AJAX library.
**
******************************************************************************/
/* @datasection [AjPFile] Obo Term output *************************************
**
** Function is for manipulating obo term objects
**
** @nam2rule Oboout Obo term output
**
******************************************************************************/
/* @section obo term outputs **********************************************
**
** These functions write the obo term provided by the first argument
**
** @fdata [AjPFile]
**
** @nam3rule Write Write an obo term
** @nam4rule Format Use a nmaed format
** @nam4rule Html Write as HTML with markup
** @nam4rule Obo Write as standard OBO format
**
** @argrule Write outf [AjPOutfile] Output file
** @argrule Write obo [const AjPObo] Obo term
** @argrule Format fmt [const AjPStr] Format name
**
** @valrule * [AjBool] true on success
**
** @fcategory output
**
******************************************************************************/
/* @func ajObooutWrite ********************************************************
**
** Write an OBO term in a named format
**
** @param [u] outf [AjPOutfile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
AjBool ajObooutWrite(AjPOutfile outf, const AjPObo obo)
{
ajuint i = ajOutfileGetFormatindex(outf);
AjPFile outfile = ajOutfileGetFile(outf);
return (*obooutFormatDef[i].Write)(outfile, obo);
}
/* @funcstatic oboWriteExcel **************************************************
**
** Write an OBO term in an tab-delimited format
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteExcel(AjPFile outf, const AjPObo obo)
{
if(!outf) return ajFalse;
if(!obo) return ajFalse;
/*ajFmtPrintF(outf, "id\tnamespace\tname\n");*/
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "%S\t", obo->Trueid);
else
ajFmtPrintF(outf, "%S\t", obo->Id);
ajFmtPrintF(outf, "%S\t%S\n", obo->Namespace, obo->Name);
return ajTrue;
}
/* @funcstatic oboWriteHtml ***************************************************
**
** Write an OBO term in an HTML format
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteHtml(AjPFile outf, const AjPObo obo)
{
AjIList iter = NULL;
AjPObotag obotag;
if(!outf) return ajFalse;
if(!obo) return ajFalse;
ajFmtPrintF(outf, "[Term]\n");
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "id: %S\n", obo->Trueid);
else
ajFmtPrintF(outf, "id: %S\n", obo->Id);
if(ajStrGetLen(obo->Name))
ajFmtPrintF(outf, "name: %S\n", obo->Name);
if(ajStrGetLen(obo->Namespace))
ajFmtPrintF(outf, "namespace: %S\n", obo->Namespace);
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "alt_id: %S\n", obo->Id);
if(ajStrGetLen(obo->Def))
ajFmtPrintF(outf, "def: %S\n", obo->Def);
if(ajStrGetLen(obo->Comment))
ajFmtPrintF(outf, "comment: %S\n", obo->Comment);
iter = ajListIterNewread(obo->Taglist);
while(!ajListIterDone(iter))
{
obotag = (AjPObotag) ajListIterGet(iter);
/* pick out ONTO:id for markup - based on each ontology */
/* EDAM: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[edam-ID:0000346]+-e */
ajFmtPrintF(outf, "%S: %S", obotag->Name, obotag->Value);
if(ajStrGetLen(obotag->Modifier))
ajFmtPrintF(outf, " %S",
obotag->Modifier);
if(ajStrGetLen(obotag->Comment))
ajFmtPrintF(outf, " ! %S",
obotag->Comment);
ajFmtPrintF(outf, "\n");
}
ajListIterDel(&iter);
return ajTrue;
}
/* @funcstatic oboWriteJson ***************************************************
**
** Write an OBO term in JSON format
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteJson(AjPFile outf, const AjPObo obo)
{
AjIList iter = NULL;
AjPObotag obotag;
AjPStr defstr = NULL;
AjPStr xrefacc = NULL;
AjPStr xrefdb = NULL;
AjPStr synscope = NULL;
AjPStr synstr = NULL;
AjPStr reltype = NULL;
AjPStr relto = NULL;
if(!outf) return ajFalse;
if(!obo) return ajFalse;
ajFmtPrintF(outf, "{\n");
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, " \"id\": \"%S\",\n", obo->Trueid);
else
ajFmtPrintF(outf, " \"id\": \"%S\",\n", obo->Id);
if(ajStrGetLen(obo->Name))
ajFmtPrintF(outf, " \"name\": \"%S\"\n", obo->Name);
if(ajStrGetLen(obo->Namespace))
ajFmtPrintF(outf, " \"namespace\": \"%S\",\n", obo->Namespace);
/*
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "alt_id: %S\n", obo->Id);
*/
if(ajStrGetLen(obo->Def))
{
ajFmtPrintF(outf, " \"def\":\n {\n");
ajFmtPrintF(outf, " \"defstr\": \"%S\",\n", defstr);
ajFmtPrintF(outf, " \"dbxref\":\n");
ajFmtPrintF(outf, " [\n");
ajFmtPrintF(outf, " {\n");
ajFmtPrintF(outf, " \"acc\": \"%S\",\n", xrefacc);
ajFmtPrintF(outf, " \"dbname\": \"%S\",\n", xrefdb);
ajFmtPrintF(outf, " }\n"); /* comma if there are more */
ajFmtPrintF(outf, " ]\n");
ajFmtPrintF(outf, " },\n");
}
if(ajStrGetLen(obo->Comment))
ajFmtPrintF(outf, " \"comment\": \"%S\",\n", obo->Comment);
iter = ajListIterNewread(obo->Taglist);
while(!ajListIterDone(iter))
{
obotag = (AjPObotag) ajListIterGet(iter);
if(ajStrMatchC(obotag->Name, "is_obsolete") ||
ajStrMatchC(obotag->Name, "built_in") ||
ajStrMatchC(obotag->Name, "is_anonymous"))
{
if(ajStrMatchC(obotag->Name, "true"))
ajFmtPrintF(outf, " \"%S\": 1,\n",
obotag->Name);
}
else if (ajStrMatchC(obotag->Name, "consider") ||
ajStrMatchC(obotag->Name, "is_a") ||
ajStrMatchC(obotag->Name, "intersection_of") ||
ajStrMatchC(obotag->Name, "union_of") ||
ajStrMatchC(obotag->Name, "disjoint_from") ||
ajStrMatchC(obotag->Name, "subset") ||
ajStrMatchC(obotag->Name, "replaced_by") ||
ajStrMatchC(obotag->Name, "alt_id"))
{
ajFmtPrintF(outf, " \"%S\": \"%S\",\n",
obotag->Name, obotag->Value);
}
else if(ajStrMatchC(obotag->Name, "synonym"))
{
ajFmtPrintF(outf, " \"synonym\":\n");
ajFmtPrintF(outf, " {\n");
ajFmtPrintF(outf, " \"scope\": \"%S\",\n", synscope);
ajFmtPrintF(outf, " \"synonym_text\": \"%S\",\n", synstr);
ajFmtPrintF(outf, " },\n>");
}
else if(ajStrMatchC(obotag->Name, "relationship"))
{
ajFmtPrintF(outf, " \"relationship\":\n");
ajFmtPrintF(outf, " [\n");
ajFmtPrintF(outf, " {\n");
ajFmtPrintF(outf, " \"type\": \"%S\",\n", reltype);
ajFmtPrintF(outf, " \"to\": \"%S\",\n", relto);
ajFmtPrintF(outf, " }\n"); /* comma if there are more */
ajFmtPrintF(outf, " ]\n");
}
else
{
ajFmtPrintF(outf, " \"%S\": \"%S\",\n",
obotag->Name, obotag->Value);
ajWarn("ontology term '%S' has tag '%S:' unknown in JSON output",
obo->Id, obotag->Name);
}
}
ajFmtPrintF(outf, "}\n");
ajListIterDel(&iter);
ajStrDel(&defstr);
ajStrDel(&xrefacc);
ajStrDel(&xrefdb);
ajStrDel(&synscope);
ajStrDel(&synstr);
ajStrDel(&reltype);
ajStrDel(&relto);
return ajTrue;
}
/* @funcstatic oboWriteList ***************************************************
**
** Write an OBO term as the simple id with the ontology name prefix
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteList(AjPFile outf, const AjPObo obo)
{
if(!outf) return ajFalse;
if(!obo) return ajFalse;
ajWritelineNewline(outf, obo->Fullid);
return ajTrue;
}
/* @funcstatic oboWriteObo ****************************************************
**
** Write an OBO term in OBO format
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteObo(AjPFile outf, const AjPObo obo)
{
AjIList iter = NULL;
AjPObotag obotag;
if(!outf) return ajFalse;
if(!obo) return ajFalse;
ajFmtPrintF(outf, "[Term]\n");
if(ajStrGetLen(obo->Db))
{
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "id: %S:%S\n", obo->Db, obo->Trueid);
else
ajFmtPrintF(outf, "id: %S:%S\n", obo->Db, obo->Id);
}
else
{
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "id: %S\n", obo->Trueid);
else
ajFmtPrintF(outf, "id: %S\n", obo->Id);
}
if(ajStrGetLen(obo->Name))
ajFmtPrintF(outf, "name: %S\n", obo->Name);
if(ajStrGetLen(obo->Namespace))
ajFmtPrintF(outf, "namespace: %S\n", obo->Namespace);
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "alt_id: %S\n", obo->Id);
if(ajStrGetLen(obo->Def))
ajFmtPrintF(outf, "def: %S\n", obo->Def);
if(ajStrGetLen(obo->Comment))
ajFmtPrintF(outf, "comment: %S\n", obo->Comment);
iter = ajListIterNewread(obo->Taglist);
while(!ajListIterDone(iter))
{
obotag = (AjPObotag) ajListIterGet(iter);
ajFmtPrintF(outf, "%S: %S", obotag->Name, obotag->Value);
if(ajStrGetLen(obotag->Modifier))
ajFmtPrintF(outf, " %S",
obotag->Modifier);
if(ajStrGetLen(obotag->Comment))
ajFmtPrintF(outf, " ! %S",
obotag->Comment);
ajFmtPrintF(outf, "\n");
}
ajListIterDel(&iter);
ajFmtPrintF(outf, "\n");
return ajTrue;
}
/* @funcstatic oboWriteObobrief ***********************************************
**
** Write an OBO term in brief OBO format (id, name and namespace only)
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteObobrief(AjPFile outf, const AjPObo obo)
{
if(!outf) return ajFalse;
if(!obo) return ajFalse;
ajFmtPrintF(outf, "[Term]\n");
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "id: %S\n", obo->Trueid);
else
ajFmtPrintF(outf, "id: %S\n", obo->Id);
if(ajStrGetLen(obo->Name))
ajFmtPrintF(outf, "name: %S\n", obo->Name);
if(ajStrGetLen(obo->Namespace))
ajFmtPrintF(outf, "namespace: %S\n", obo->Namespace);
return ajFalse;
}
/* @funcstatic oboWriteXml ****************************************************
**
** Write an OBO term in OBO-XML format
**
** @param [u] outf [AjPFile] Output file
** @param [r] obo [const AjPObo] Obo term object
**
** @return [AjBool] True on success
**
**
** @release 6.4.0
******************************************************************************/
static AjBool oboWriteXml(AjPFile outf, const AjPObo obo)
{
AjIList iter = NULL;
AjPObotag obotag;
AjPStr defstr = NULL;
AjPStr xrefacc = NULL;
AjPStr xrefdb = NULL;
AjPStr synscope = NULL;
AjPStr synstr = NULL;
AjPStr reltype = NULL;
AjPStr relto = NULL;
ajuint nrefs = 0;
ajuint i;
if(!outf) return ajFalse;
if(!obo) return ajFalse;
ajFmtPrintF(outf, "<term>\n");
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, " <id>%S</id>\n", obo->Trueid);
else
ajFmtPrintF(outf, " <id>%S</id>\n", obo->Id);
if(ajStrGetLen(obo->Name))
ajFmtPrintF(outf, " <name>%S</name>\n", obo->Name);
if(ajStrGetLen(obo->Namespace))
ajFmtPrintF(outf, " <namespace>%S</namespace>\n", obo->Namespace);
/*
if(ajStrGetLen(obo->Trueid))
ajFmtPrintF(outf, "alt_id: %S\n", obo->Id);
*/
if(ajStrGetLen(obo->Def))
{
ajOboGetDef(obo, &defstr, &nrefs);
ajFmtPrintF(outf, " <def>\n");
ajFmtPrintF(outf, " <defstr>%S</defstr>\n", defstr);
for(i=1; i<= nrefs; i++)
{
/*ajOboGetDefXref(obo, i, &xrefdb, &xrefacc);*/
ajFmtPrintF(outf, " <dbxref>\n");
ajFmtPrintF(outf, " <acc>%S</acc>\n", xrefacc);
ajFmtPrintF(outf, " <dbname>%S</dbname>\n", xrefdb);
ajFmtPrintF(outf, " </dbxref>\n");
}
ajFmtPrintF(outf, " </def>\n");
}
if(ajStrGetLen(obo->Comment))
ajFmtPrintF(outf, " <comment>%S</comment>\n", obo->Comment);
iter = ajListIterNewread(obo->Taglist);
while(!ajListIterDone(iter))
{
obotag = (AjPObotag) ajListIterGet(iter);
if(ajStrMatchC(obotag->Name, "is_obsolete") ||
ajStrMatchC(obotag->Name, "built_in") ||
ajStrMatchC(obotag->Name, "is_anonymous"))
{
if(ajStrMatchC(obotag->Name, "true"))
ajFmtPrintF(outf, " <%S>1</%S>\n",
obotag->Name, obotag->Name);
}
else if (ajStrMatchC(obotag->Name, "consider") ||
ajStrMatchC(obotag->Name, "is_a") ||
ajStrMatchC(obotag->Name, "intersection_of") ||
ajStrMatchC(obotag->Name, "union_of") ||
ajStrMatchC(obotag->Name, "disjoint_from") ||
ajStrMatchC(obotag->Name, "subset") ||
ajStrMatchC(obotag->Name, "replaced_by") ||
ajStrMatchC(obotag->Name, "alt_id"))
{
ajFmtPrintF(outf, " <%S>%S</%S>\n",
obotag->Name, obotag->Value, obotag->Name);
}
else if(ajStrMatchC(obotag->Name, "synonym"))
{
ajFmtPrintF(outf, " <synonym score=\"%S\">\n", synscope);
ajFmtPrintF(outf, " <synonym_text>%S</synonym_text>\n",
synstr);
ajFmtPrintF(outf, " </synonym\n>");
}
else if(ajStrMatchC(obotag->Name, "relationship"))
{
ajFmtPrintF(outf, " <relationship>\n");
ajFmtPrintF(outf, " <type>%S</type>\n", reltype);
ajFmtPrintF(outf, " <to>%S</to>\n", relto);
ajFmtPrintF(outf, " </relationship>\n");
}
else
{
ajFmtPrintF(outf, " <%S>%S</%S>\n",
obotag->Name, obotag->Value, obotag->Name);
ajWarn("ontology term '%S' has tag '%S:' unknown in OBO-XML output",
obo->Id, obotag->Name);
}
}
ajListIterDel(&iter);
ajStrDel(&defstr);
ajStrDel(&xrefacc);
ajStrDel(&xrefdb);
ajStrDel(&synscope);
ajStrDel(&synstr);
ajStrDel(&reltype);
ajStrDel(&relto);
return ajTrue;
}
/* @datasection [none] Miscellaneous functions ********************************
**
** Functions to initialise and clean up internals
**
** @nam2rule Oboout Obo term output internals
**
******************************************************************************/
/* @section Printing **********************************************************
**
** Printing details of the internals to a file
**
** @fdata [none]
**
** @nam2rule Obooutprint
**
** @fcategory output
**
******************************************************************************/
/* @section Print *************************************************************
**
** Printing to a file
**
** @fdata [none]
**
** @nam3rule Book Print as docbook table
** @nam3rule Html Print as html table
** @nam3rule Wiki Print as wiki table
** @nam3rule Text Print as text
**
** @argrule * outf [AjPFile] output file
** @argrule Text full [AjBool] Print all details
**
** @valrule * [void]
**
** @fcategory cast
**
******************************************************************************/
/* @func ajObooutprintBook ****************************************************
**
** Reports the obo term format internals as Docbook text
**
** @param [u] outf [AjPFile] Output file
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObooutprintBook(AjPFile outf)
{
ajint i = 0;
ajFmtPrintF(outf, "<para>The supported obo term output "
"formats are summarised "
"in the table below. The columns are as follows: "
"<emphasis>Output format</emphasis> (format name), "
"<emphasis>Description</emphasis> (short description of "
"the format).</para> \n\n");
ajFmtPrintF(outf, "<table frame=\"box\" rules=\"cols\">\n");
ajFmtPrintF(outf, " <caption>Obo term output formats</caption>\n");
ajFmtPrintF(outf, " <thead>\n");
ajFmtPrintF(outf, " <tr align=\"center\">\n");
ajFmtPrintF(outf, " <th>Output Format</th>\n");
ajFmtPrintF(outf, " <th>Description</th>\n");
ajFmtPrintF(outf, " </tr>\n");
ajFmtPrintF(outf, " </thead>\n");
ajFmtPrintF(outf, " <tbody>\n");
for(i=0; obooutFormatDef[i].Name; i++)
{
ajFmtPrintF(outf, " <tr>\n");
ajFmtPrintF(outf, " <td>%s</td>\n",
obooutFormatDef[i].Name);
ajFmtPrintF(outf, " <td>%s</td>\n",
obooutFormatDef[i].Desc);
}
ajFmtPrintF(outf, " </tbody>\n");
ajFmtPrintF(outf, "</table>\n");
return;
}
/* @func ajObooutprintHtml ****************************************************
**
** Reports the internal data structures
**
** @param [u] outf [AjPFile] Output file
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObooutprintHtml(AjPFile outf)
{
ajint i = 0;
ajFmtPrintF(outf, "<table border=3>");
ajFmtPrintF(outf, "<tr><th>Obo term Format</th>\n");
ajFmtPrintF(outf, "<th>Description</th></tr>\n");
ajFmtPrintF(outf, "\n");
ajFmtPrintF(outf, "# Obo term output formats\n");
ajFmtPrintF(outf, "# Name Format name (or alias)\n");
ajFmtPrintF(outf, "# Desc Format description\n");
ajFmtPrintF(outf, "# Name Description\n");
ajFmtPrintF(outf, "\n");
ajFmtPrintF(outf, "OboFormat {\n");
for(i=0; obooutFormatDef[i].Name; i++)
{
ajFmtPrintF(outf, "<tr><td>\n%-12s\n"
"<td>\"%s\"</td></tr>\n",
obooutFormatDef[i].Name,
obooutFormatDef[i].Desc);
}
ajFmtPrintF(outf, "}\n\n");
return;
}
/* @func ajObooutprintText ****************************************************
**
** Reports the internal data structures
**
** @param [u] outf [AjPFile] Output file
** @param [r] full [AjBool] Full report (usually ajFalse)
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObooutprintText(AjPFile outf, AjBool full)
{
ajint i = 0;
ajFmtPrintF(outf, "\n");
ajFmtPrintF(outf, "# Obo term output formats\n");
ajFmtPrintF(outf, "# Name Format name (or alias)\n");
ajFmtPrintF(outf, "# Desc Format description\n");
ajFmtPrintF(outf, "# Name Description\n");
ajFmtPrintF(outf, "\n");
ajFmtPrintF(outf, "OboFormat {\n");
for(i=0; obooutFormatDef[i].Name; i++)
{
if(full)
ajFmtPrintF(outf, " %-12s \"%s\"\n",
obooutFormatDef[i].Name,
obooutFormatDef[i].Desc);
}
ajFmtPrintF(outf, "}\n\n");
return;
}
/* @func ajObooutprintWiki ****************************************************
**
** Reports the obo term output format internals as wikitext
**
** @param [u] outf [AjPFile] Output file
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObooutprintWiki(AjPFile outf)
{
ajint i = 0;
ajint j = 0;
AjPStr namestr = NULL;
ajFmtPrintF(outf, "{| class=\"wikitable sortable\" border=\"2\"\n");
ajFmtPrintF(outf, "|-\n");
ajFmtPrintF(outf, "!Format!!"
"class=\"unsortable\"|Description\n");
for(i=0; obooutFormatDef[i].Name; i++)
{
ajFmtPrintF(outf, "|-\n");
ajStrAssignC(&namestr, obooutFormatDef[i].Name);
for(j=i+1; obooutFormatDef[j].Name; j++)
{
if(obooutFormatDef[j].Write == obooutFormatDef[i].Write)
{
ajFmtPrintAppS(&namestr, "<br>%s",
obooutFormatDef[j].Name);
ajWarn("Obo term output format '%s' same as '%s' "
"but not alias",
obooutFormatDef[j].Name,
obooutFormatDef[i].Name);
}
}
ajFmtPrintF(outf, "|%S||%s\n",
namestr,
obooutFormatDef[i].Desc);
}
ajFmtPrintF(outf, "|}\n");
ajStrDel(&namestr);
return;
}
/* @datasection [none] Output formats *****************************************
**
** Output formats internals
**
** @nam2rule Obooutformat Obo term output format specific
**
******************************************************************************/
/* @section cast **************************************************************
**
** Values for output formats
**
** @fdata [none]
**
** @nam3rule Find Return index to named format
** @nam3rule Test Test format value
**
** @argrule * format [const AjPStr] Format name
** @argrule Find iformat [ajint*] Index matching format name
**
** @valrule * [AjBool] True if found
**
** @fcategory cast
**
******************************************************************************/
/* @func ajObooutformatFind ***************************************************
**
** Looks for the specified format(s) in the internal definitions and
** returns the index.
**
** Sets iformat as the recognised format, and returns ajTrue.
**
** @param [r] format [const AjPStr] Format required.
** @param [w] iformat [ajint*] Index
** @return [AjBool] ajTrue on success.
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ajObooutformatFind(const AjPStr format, ajint* iformat)
{
AjPStr tmpformat = NULL;
ajuint i = 0;
/* ajDebug("obooutformatFind '%S'\n", format); */
if(!ajStrGetLen(format))
return ajFalse;
ajStrAssignS(&tmpformat, format);
ajStrFmtLower(&tmpformat);
for(i=0; obooutFormatDef[i].Name; i++)
{
/* ajDebug("test %d '%s' \n", i, obooutFormatDef[i].Name); */
if(ajStrMatchCaseC(tmpformat, obooutFormatDef[i].Name))
{
*iformat = i;
ajStrDel(&tmpformat);
/* ajDebug("found '%s' at %d\n", obooutFormatDef[i].Name, i); */
return ajTrue;
}
}
ajErr("Unknown output format '%S'", format);
ajStrDel(&tmpformat);
*iformat = 0;
return ajFalse;
}
/* @func ajObooutformatTest ***************************************************
**
** Tests whether a named OBO output format is known
**
** @param [r] format [const AjPStr] Format
** @return [AjBool] ajTrue if formats was accepted
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ajObooutformatTest(const AjPStr format)
{
ajint i;
for (i=0; obooutFormatDef[i].Name; i++)
if(ajStrMatchCaseC(format, obooutFormatDef[i].Name))
return ajTrue;
return ajFalse;
}
/* @datasection [none] Miscellaneous functions ********************************
**
** Functions to initialise and clean up internals
**
** @nam2rule Oboout Obo output internals
**
******************************************************************************/
/* @section Miscellaneous *****************************************************
**
** Functions to initialise and clean up internals
**
** @fdata [none]
**
** @nam3rule Exit Clean up and exit
**
** @valrule * [void]
**
** @fcategory misc
**
******************************************************************************/
/* @func ajObooutExit *********************************************************
**
** Cleans up obo term outputinternal memory
**
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObooutExit(void)
{
return;
}
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