diff --git a/src/include/ZMap/zmapConfigStanzaStructs.h b/src/include/ZMap/zmapConfigStanzaStructs.h index 1e0605b05082fbfef9d577583f064a8a358a189d..eb7ae4b9e638fd5d5a02ad2de5d453c0a06e283f 100755 --- a/src/include/ZMap/zmapConfigStanzaStructs.h +++ b/src/include/ZMap/zmapConfigStanzaStructs.h @@ -6,12 +6,12 @@ * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. - * + * * This program 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 General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. @@ -23,12 +23,12 @@ * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk, * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk * - * Description: + * Description: * * HISTORY: * Last edited: Nov 13 08:58 2008 (edgrif) * Created: Tue Aug 26 12:38:28 2008 (rds) - * CVS info: $Id: zmapConfigStanzaStructs.h,v 1.4 2010-03-04 15:14:54 mh17 Exp $ + * CVS info: $Id: zmapConfigStanzaStructs.h,v 1.5 2010-03-11 08:54:37 mh17 Exp $ *------------------------------------------------------------------- */ @@ -45,7 +45,7 @@ typedef struct _ZMapConfigSourceStruct char *styles_list, *stylesfile ; char *format ; int timeout ; - gboolean writeback, sequence ; + gboolean writeback, sequence, delayed ; } ZMapConfigSourceStruct, *ZMapConfigSource; diff --git a/src/include/ZMap/zmapConfigStrings.h b/src/include/ZMap/zmapConfigStrings.h index fc8dc0b67e4a9c516ebe1fa3f2405030cde143aa..d2416bd0e75894081172961fddefd1f63394b1ef 100755 --- a/src/include/ZMap/zmapConfigStrings.h +++ b/src/include/ZMap/zmapConfigStrings.h @@ -6,12 +6,12 @@ * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. - * + * * This program 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 General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. @@ -25,13 +25,13 @@ * Description: Repository for all the configuration file stanza * keywords. We don't have to do this but its good for * documentation and also good for discipline. - * + * * READ THIS BEFORE ADDING NEW KEYWORDS: - * + * * This file produces an important user documentation * page: it tells the user what they can put in the * configuration file to control zmap. - * + * * Therefore...if you add a new configuration stanza or * keyword, please be sure to add _ALL_ the relevant * text to the html table that procedes each set of @@ -40,7 +40,7 @@ * HISTORY: * Last edited: Mar 2 14:19 2010 (edgrif) * Created: Tue Apr 25 14:36:16 2006 (edgrif) - * CVS info: $Id: zmapConfigStrings.h,v 1.24 2010-03-04 15:14:55 mh17 Exp $ + * CVS info: $Id: zmapConfigStrings.h,v 1.25 2010-03-11 08:54:37 mh17 Exp $ *------------------------------------------------------------------- */ #ifndef ZMAP_CONFIG_STRINGS_H @@ -53,11 +53,11 @@ /*! @defgroup config_stanzas ZMap configuration Files * * @section Overview - * + * * ZMap uses configuration files to find its servers, files and generally * to configure aspects of its interface. Currently these files must * reside in the users $HOME/.ZMap directory. - * + * * The main configuration file is "ZMap" and this may contain references to * to other configuration files. * @@ -74,9 +74,9 @@ /*! @addtogroup config_stanzas * * @section format Configuration File Format. - * + * * All configuration files for ZMap are a series of stanzas of the form: - * + * * <PRE> * [stanza_name] e.g. [ZMap] * resource1 = value1 show_mainwindow = false @@ -88,7 +88,7 @@ * in the following formats: * * String values are spefied literally, without quotes, e.g. host = griffin - * Some string resources will accept a list of strings, in which case these + * Some string resources will accept a list of strings, in which case these * should be separated by semicolons e.g. styles = align;dna_align;pep_align * * Boolean values must be specified as either true or false, e.g. logging = false @@ -112,7 +112,7 @@ /*! @addtogroup config_stanzas * * @section app ZMap Application Options - * + * * These are options that control the fundamental way ZMap behaves. * * <table> @@ -197,7 +197,7 @@ /*! @addtogroup config_stanzas * * @section logging Logging Options - * + * * ZMap writes messages to the logfile $HOME/.ZMap/zmap.log by default, but the log filepath * and other parameters of logging can be specified in the "logging" stanza. * @@ -239,7 +239,7 @@ * </table> * * */ -#define ZMAPSTANZA_LOG_CONFIG "logging" +#define ZMAPSTANZA_LOG_CONFIG "logging" #define ZMAPSTANZA_LOG_LOGGING "logging" #define ZMAPSTANZA_LOG_FILE "file" #define ZMAPSTANZA_LOG_DIRECTORY "directory" @@ -252,21 +252,21 @@ /*! @addtogroup config_stanzas * * @section source Data Source Options - * + * * ZMap can obtain sequence data from files and servers of various kinds, source stanzas - * specify information about the source. Each source stanza should must have a unique name, + * specify information about the source. Each source stanza should must have a unique name, * and must be referenced in the 'sources' resource in the [ZMap] stanza. - * + * * Data sources are identified using urls in the following supported variants: - * + * * <PRE> * * url = "<url_identifier>" - * + * * where <url_identifier> should match ([] = optional) - * + * * <protocol>://[[<username>:<password>@]<hostname>[:<port>]]/<location>#<format> - * + * * <protocol> may be one of acedb, file, pipe or http * <username> should be a username string * <password> should be a password string @@ -274,19 +274,19 @@ * <port> should be a port number * <location> should identify the location on a particular server * <format> may be one of gff, das, das2 (default gff) - * + * * examples - * + * * file:///var/tmp/my_gff_file.gff#gff * pipe:////software/anacode/bin/get_genes?dataset=human&name=1&analysis=ccds_gene&end=161655109... * http://das1.sanger.ac.uk:8080/das/h_sapiens#das * acedb://any:any@deskpro110:23100 - * + * * N.B. <location> might include a query string too. e.g. * * http://www.sanger.ac.uk/das/h_sapiens?chromosome=1#das * Note that for file: and pipe: sources file:///file is a relative file name and file://// is absolute. - * + * * </PRE> * * <table> @@ -366,11 +366,18 @@ * <th>"styles"</th> * <td>string</td> * <td>""</td> - * <td>List of all styles to be retrieved from styles file. If not specified then all styles will be read + * <td>List of all styles to be retrieved from styles file. If not specified then all styles will be read * if a file has been specified in the [ZMap] stanza, otherwsie the source should provide the styles itself. * By default a featureset will use a style of the same name. * * </tr> + * <tr> + * <th>"delayed"</th> + * <td>Boolean</td> + * <td>true/false</td> + * <td>If true then the server will not request features automatically on ZMap startup. The default for pipeServers is true and for others false. + * </tr> + * </table> * * */ @@ -384,6 +391,7 @@ #define ZMAPSTANZA_SOURCE_SEQUENCE "sequence" #define ZMAPSTANZA_SOURCE_WRITEBACK "writeback" #define ZMAPSTANZA_SOURCE_FORMAT "format" +#define ZMAPSTANZA_SOURCE_DELAYED "delayed" @@ -391,7 +399,7 @@ /*! @addtogroup config_stanzas * * @section types Style Options - * + * * ZMap processes/displays/formats features based on a description of the characteristics of the * features given in a "style". * @@ -517,7 +525,7 @@ /*! @addtogroup config_stanzas * * @section window ZMap Feature Window Options - * + * * The ZMap feature window is where sequence features are displayed, various aspects of it * can be configured from colours to performance factors. * @@ -668,7 +676,7 @@ /*! @addtogroup config_stanzas * * @section debug Debugging Options - * + * * You should only use these if you are a developer as they can impact the performance of * ZMap significantly or cause it to write large amounts of data to stdout. * @@ -713,7 +721,7 @@ /*! @addtogroup config_stanzas * * @section align Multiple Alignment Options - * + * * ZMap can display multiple alignments, each alignment can contain multiple blocks. This * stanza specifies which blocks in which alignment match each other. Note that all parameters * are mandatory otherwise zmap will not know how to display the blocks. @@ -784,7 +792,7 @@ * </table> * * */ -#define ZMAPSTANZA_ALIGN_CONFIG "align" +#define ZMAPSTANZA_ALIGN_CONFIG "align" #define ZMAPSTANZA_ALIGN_SEQ "reference-seq" #define ZMAPSTANZA_ALIGN_START "reference-start" #define ZMAPSTANZA_ALIGN_END "reference-end" @@ -799,7 +807,7 @@ /*! @addtogroup config_stanzas * * @section blixem Blixem Options - * + * * ZMap can show multiple alignments using the blixem program, this stanza tells * zmap how to find and run blixem. *