Manual Version 2.1

2012-05-18T07:33:55Z

Editing definition files:

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	bga Antigen b1D-Gal,p(--2a1L-Fuc,p)--3a1D-GalNAc,p Blood group A antigen		bga Antigen b1D-Gal,p(--2a1L-Fuc,p)--3a1D-GalNAc,p Blood group A antigen
		+
		+	== Loading custom dictionary files (Developer API) ==
		+	When you are designing software that uses the GlycanBuilder software library you can easily load custom dictionaries by providing a configuration file to the BuilderWorkspace constructor that you have previously configured to point to your custom dictionaries.
		+
		+	BuilderWorkspace workspace=new BuilderWorkspace("/home/david/glycoworkbench_test.xml", true, new GlycanRendererAWT());
		+
		+	Note that when the second argument to the constructor is set to true and the supplied configuration file doesn't yet exist, the constructor will create a file of the same name, with the default configuration. The default configuration is shown below. To change the file used to load residue definitions you would change the text value "/conf/residue_types" in the "residueTypesFile" element (<residueTypesFile>/conf/residue_types</residueTypesFile>) to the location of your custom residues types file.
		+	<pre>
		+	<Configuration>
		+	<dictionaries>
		+	<uoxf_residueStylesFile>/conf/residue_styles_uoxf</uoxf_residueStylesFile>
		+	<uoxfcol_residuePlacementsFile>/conf/residue_placements_uoxf</uoxfcol_residuePlacementsFile>
		+	<uoxf_linkageStylesFile>/conf/linkage_styles_uoxf</uoxf_linkageStylesFile>
		+	<crossRingFragmentTypesFile>/conf/cross_ring_fragment_types</crossRingFragmentTypesFile>
		+	<uoxf_residuePlacementsFile>/conf/residue_placements_uoxf</uoxf_residuePlacementsFile>
		+	<cfgLink_residueStylesFile>/conf/residue_styles_cfg</cfgLink_residueStylesFile>
		+	<cfgBW_linkageStylesFile>/conf/linkage_styles_cfg</cfgBW_linkageStylesFile>
		+	<residueTypesFile>/conf/residue_types</residueTypesFile>
		+	<coreTypesFile>/conf/core_types</coreTypesFile>
		+	<cfgBW_residueStylesFile>/conf/residue_styles_cfgbw</cfgBW_residueStylesFile>
		+	<cfgBW_residuePlacementsFile>/conf/residue_placements_cfg</cfgBW_residuePlacementsFile>
		+	<cfg_linkageStylesFile>/conf/linkage_styles_cfg</cfg_linkageStylesFile>
		+	<uoxfcol_linkageStylesFile>/conf/linkage_styles_uoxf</uoxfcol_linkageStylesFile>
		+	<text_residueStylesFile>/conf/residue_styles_text</text_residueStylesFile>
		+	<cfgLink_linkageStylesFile>/conf/linkage_styles_cfglink</cfgLink_linkageStylesFile>
		+	<uoxfcol_residueStylesFile>/conf/residue_styles_uoxfcol</uoxfcol_residueStylesFile>
		+	<terminalTypesFile>/conf/terminal_types</terminalTypesFile>
		+	<cfgLink_residuePlacementsFile>/conf/residue_placements_uoxf</cfgLink_residuePlacementsFile>
		+	<text_linkageStylesFile>/conf/linkage_styles_cfg</text_linkageStylesFile>
		+	<cfg_residuePlacementsFile>/conf/residue_placements_cfg</cfg_residuePlacementsFile>
		+	<text_residuePlacementsFile>/conf/residue_placements_cfg</text_residuePlacementsFile>
		+	<cfg_residueStylesFile>/conf/residue_styles_cfg</cfg_residueStylesFile>
		+	</dictionaries>
		+	<FileHistory>
		+	<file_path3/>
		+	<file_path2/>
		+	<file_path1/>
		+	<file_path0/>
		+	<file_path7/>
		+	<file_path6/>
		+	<file_path5/>
		+	<file_path4/>
		+	<file_type1/>
		+	<file_type2/>
		+	<file_type3/>
		+	<file_type4/>
		+	<file_type0/>
		+	<file_type5/>
		+	<file_type6/>
		+	<file_type7/>
		+	</FileHistory>
		+	<CompositionOptions>
		+	<dpen>0</dpen>
		+	<or1>0</or1>
		+	<dhexa>0</dhexa>
		+	<or2>0</or2>
		+	<ddhex>0</ddhex>
		+	<neu5aclac>0</neu5aclac>
		+	<pyr>0</pyr>
		+	<hexnac>0</hexnac>
		+	<hex>0</hex>
		+	<hep>0</hep>
		+	<or1_mass>0.0</or1_mass>
		+	<or3>0</or3>
		+	<neu5gc>0</neu5gc>
		+	<hexn>0</hexn>
		+	<mur>0</mur>
		+	<or3_mass>0.0</or3_mass>
		+	<or2_mass>0.0</or2_mass>
		+	<mehex>0</mehex>
		+	<pen>0</pen>
		+	<kdp>0</kdp>
		+	<kdn>0</kdn>
		+	<s>0</s>
		+	<hexa>0</hexa>
		+	<neu5ac>0</neu5ac>
		+	<pc>0</pc>
		+	<p>0</p>
		+	<neu5gclac>0</neu5gclac>
		+	<ac>0</ac>
		+	<dhex>0</dhex>
		+	</CompositionOptions>
		+	<ResidueHistory>
		+	<queue_size>0</queue_size>
		+	</ResidueHistory>
		+	<GraphicOptions>
		+	<mass_text_font_face_custom>SansSerif.plain</mass_text_font_face_custom>
		+	<collapse_multiple_antennae>true</collapse_multiple_antennae>
		+	<node_font_size_custom>14</node_font_size_custom>
		+	<mass_text_space_custom>15</mass_text_space_custom>
		+	<node_space_custom>30</node_space_custom>
		+	<show_masses>false</show_masses>
		+	<linkage_info_size_custom>12</linkage_info_size_custom>
		+	<node_size_custom>22</node_size_custom>
		+	<show_info_custom>true</show_info_custom>
		+	<node_font_face_custom>SansSerif.plain</node_font_face_custom>
		+	<show_masses_canvas>true</show_masses_canvas>
		+	<notation>cfg</notation>
		+	<composition_font_size_custom>18</composition_font_size_custom>
		+	<orientation>0</orientation>
		+	<theme>org.pushingpixels.substance.api.skin.OfficeBlue2007Skin</theme>
		+	<display>normalinfo</display>
		+	<show_info>true</show_info>
		+	<save_spectra>false</save_spectra>
		+	<scale_canvas>1.0</scale_canvas>
		+	<composition_font_face_custom>SansSerif.plain</composition_font_face_custom>
		+	<mass_text_size_custom>14</mass_text_size_custom>
		+	<node_sub_space_custom>1</node_sub_space_custom>
		+	<linkage_info_font_face_custom>Serif.plain</linkage_info_font_face_custom>
		+	<show_redend>false</show_redend>
		+	<structures_space_custom>40</structures_space_custom>
		+	</GraphicOptions>
		+	<MassOptions>
		+	<ion_cloud>Na</ion_cloud>
		+	<reducing_end_type>freeEnd</reducing_end_type>
		+	<derivatization>perMe</derivatization>
		+	<neutral_exchanges>0</neutral_exchanges>
		+	<isotope>MONO</isotope>
		+	</MassOptions>
		+	</Configuration>
		+	</pre>

	= Interface =		= Interface =

Biopolymer Mass Spectrometry - Recent changes [en]

Manual Version 2.1