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From: <nl...@us...> - 2007-05-30 18:50:14
|
Revision: 651
http://svn.sourceforge.net/obo/?rev=651&view=rev
Author: nlw
Date: 2007-05-30 11:50:02 -0700 (Wed, 30 May 2007)
Log Message:
-----------
phenote web help: changing < and > to escaped on pages
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/help/Phenote.jhm
phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm
Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm 2007-05-30 18:50:02 UTC (rev 651)
@@ -42,13 +42,13 @@
<mapID target="Sample_Configuration_1" url="html/Sample_Configuration_1.htm"/>
<mapID target="Sample_Configuration_2" url="html/Sample_Configuration_2.htm"/>
<mapID target="Term_Info" url="html/Term_Info.htm"/>
- <mapID target="The__field__Tag" url="html/The__field__Tag.htm"/>
- <mapID target="The__dataadapter__Tag116" url="html/The__dataadapter__Tag.htm"/>
<mapID target="The__term_history__Tag118" url="html/The__term_history__Tag.htm"/>
<mapID target="The__auto_update_ontologies__Tag115" url="html/The__auto_update_ontologies__Tag.htm"/>
<mapID target="The__ontology__Tag" url="html/The__ontology__Tag.htm"/>
<mapID target="The__update_timer__Tag" url="html/The__update_timer__Tag.htm"/>
<mapID target="The__master_to_local_config__Tag" url="html/The__master_to_local_config__Tag.htm"/>
+ <mapID target="The__dataadapter__Tag116" url="html/The__dataadapter__Tag.htm"/>
+ <mapID target="The__field__Tag" url="html/The__field__Tag.htm"/>
<mapID target="The__tab__Tag" url="html/The__tab__Tag.htm"/>
<mapID target="The_Scroller_Tag" url="html/The_Basic_Flat_File_Interface.htm"/>
<mapID target="The_Default_Layout" url="html/Introduction.htm"/>
Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak 2007-05-30 18:50:02 UTC (rev 651)
@@ -11,185 +11,56 @@
<!-- Topics -->
<mapID target="Adding_configurability" url="html/Adding_configurability.htm"/>
- <mapID target="Adding_New_Relationships" url="html/Adding_New_Relationships.htm"/>
- <mapID target="Adding_New_Terms" url="html/Adding_New_Terms.htm"/>
<mapID target="Advantages_to_Annotation_with_Ontolgies" url="html/Advantages_to_Annotation_with_Ontolgies.htm"/>
<mapID target="An_Introduction_to_OBO_Ontologies" url="html/An_Introduction_to_OBO_Ontologies.htm"/>
<mapID target="Annotation_Spreadsheet" url="html/Annotation_Spreadsheet.htm"/>
- <mapID target="Assigning_New_Roots" url="html/Assigning_New_Roots.htm"/>
- <mapID target="Assigning_Replacement_Terms" url="html/Assigning_Replacement_Terms.htm"/>
- <mapID target="Backtick_Expressions" url="html/Backtick_Expressions.htm"/>
<mapID target="Basic_Concepts_and_Vocabulary" url="html/Basic_Concepts_and_Vocabulary.htm"/>
<mapID target="Bugs_and_Troubleshooting" url="html/Bugs_and_Troubleshooting.htm"/>
- <mapID target="Building_a_Filter" url="html/Building_a_Filter.htm"/>
- <mapID target="Building_Filters" url="html/Building_Filters.htm"/>
- <mapID target="Changing_Link_Attributes" url="html/Changing_Link_Attributes.htm"/>
<mapID target="The_Phenote_Interface" url="html/The_Phenote_Interface.htm"/>
- <mapID target="Changing_Relationship_Types" url="html/Changing_Relationship_Types.htm"/>
<mapID target="Changing_your_Autocompletion_Settings" url="html/Changing_your_Autocompletion_Settings.htm"/>
<mapID target="Changing_your_Configuration" url="html/Changing_your_Configuration.htm"/>
- <mapID target="Classes" url="html/Classes.htm"/>
- <mapID target="Cloning" url="html/Cloning.htm"/>
- <mapID target="Common_Parameters" url="html/Common_Parameters.htm"/>
- <mapID target="Compound_Filtering" url="html/Compound_Filtering.htm"/>
<mapID target="Connecting_to_a_Database" url="html/Connecting_to_a_Database.htm"/>
- <mapID target="Creating_Your_Own_GO_Slim_in_OBO_Edit" url="html/Creating_Your_Own_GO_Slim_in_OBO_Edit.htm"/>
- <mapID target="Cross_Products" url="html/Cross_Products.htm"/>
- <mapID target="Cross_Products_By_Hand" url="html/Cross_Products_By_Hand.htm"/>
- <mapID target="Cross_Products_in_the_Text_Editor" url="html/Cross_Products_in_the_Text_Editor.htm"/>
- <mapID target="Custom_Data_Adapters" url="html/Custom_Data_Adapters.htm"/>
- <mapID target="Dangling_Intersection_Check" url="html/Dangling_Intersection_Check.htm"/>
<mapID target="Data_Entry" url="html/Data_Entry.htm"/>
<mapID target="Data_Formats" url="html/Data_Formats.htm"/>
- <mapID target="Dbxref_Check" url="html/Dbxref_Check.htm"/>
- <mapID target="Definition_Check" url="html/Definition_Check.htm"/>
- <mapID target="Deleting" url="html/Deleting.htm"/>
- <mapID target="Destroying" url="html/Destroying.htm"/>
- <mapID target="Disjointedness_Check" url="html/Disjointedness_Check.htm"/>
- <mapID target="Editing" url="html/Editing.htm"/>
<mapID target="Editing_Functions" url="html/Editing_Functions.htm"/>
- <mapID target="Editing_Obsoletes" url="html/Editing_Obsoletes.htm"/>
<mapID target="Entering_data_into_Free_Text_fields" url="html/Entering_data_into_Free_Text_fields.htm"/>
<mapID target="Entering_data_into_Ontology_Fields" url="html/Entering_data_into_Ontology_Fields.htm"/>
<mapID target="Entity_Composition_Refinement" url="html/Entity_Composition_Refinement.htm"/>
- <mapID target="Example_Layouts" url="html/Example_Layouts.htm"/>
- <mapID target="Example_Scripts" url="html/Example_Scripts.htm"/>
<mapID target="Exiting_Phenote" url="html/Exiting_Phenote.htm"/>
- <mapID target="Expression_Syntax" url="html/Expression_Syntax.htm"/>
- <mapID target="Filtering" url="html/Filtering.htm"/>
- <mapID target="Filters" url="html/Filters.htm"/>
- <mapID target="Frequently_Asked_Questions" url="html/Frequently_Asked_Questions.htm"/>
<mapID target="Getting_Phenote_Started" url="html/Getting_Phenote_Started.htm"/>
- <mapID target="Getting_Started" url="html/Getting_Started.htm"/>
- <mapID target="Global_Filters___Renderers" url="html/Global_Filters___Renderers.htm"/>
- <mapID target="How_Do_I_Find_Terms_Without_an_is_a_Parent_" url="html/How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm"/>
- <mapID target="How_Do_I_Make_a__Slim__Ontology_" url="html/How_Do_I_Make_a__Slim__Ontology_.htm"/>
- <mapID target="How_Do_I_Not_Search_Obsoletes_" url="html/How_Do_I_Not_Search_Obsoletes_.htm"/>
- <mapID target="How_Do_I_Search_a_Specific_Ontology_" url="html/How_Do_I_Search_a_Specific_Ontology_.htm"/>
- <mapID target="How_Do_I_Spell_Check_" url="html/How_Do_I_Spell_Check_.htm"/>
- <mapID target="How_ID_Generation_Works" url="html/How_ID_Generation_Works.htm"/>
- <mapID target="How_OBO_Edit_Understands_Histories" url="html/How_OBO_Edit_Understands_Histories.htm"/>
<mapID target="How_To_Edit_a_Configuration_File" url="html/How_To_Edit_a_Configuration_File.htm"/>
- <mapID target="Instances" url="html/Instances.htm"/>
- <mapID target="Intersections" url="html/Intersections.htm"/>
<mapID target="Introduction_to_Adapters" url="html/Introduction_to_Adapters.htm"/>
- <mapID target="Introduction_to_Cross_Products" url="html/Introduction_to_Cross_Products.htm"/>
- <mapID target="Introduction_to_Expressions" url="html/Introduction_to_Expressions.htm"/>
- <mapID target="Introduction_to_Plugins" url="html/Introduction_to_Plugins.htm"/>
- <mapID target="Introduction_to_Verification" url="html/Introduction_to_Verification.htm"/>
- <mapID target="ISA_Cycle_Check" url="html/ISA_Cycle_Check.htm"/>
- <mapID target="Java_Options_on_the_Command_line" url="html/Java_Options_on_the_Command_line.htm"/>
- <mapID target="jen_layout_1" url="html/jen_layout_1.htm"/>
- <mapID target="jen_layout_2" url="html/jen_layout_2.htm"/>
- <mapID target="jen_layout_3" url="html/jen_layout_3.htm"/>
- <mapID target="jen_layout_4" url="html/jen_layout_4.htm"/>
- <mapID target="Language_Concepts" url="html/Language_Concepts.htm"/>
<mapID target="Licensing_Information" url="html/Licensing_Information.htm"/>
- <mapID target="Link_Filters" url="html/Link_Filters.htm"/>
- <mapID target="Link_Filters_vs_Term_Filters" url="html/Link_Filters_vs_Term_Filters.htm"/>
<mapID target="Loading___Saving" url="html/Loading___Saving.htm"/>
- <mapID target="Loading_a_History_File" url="html/Loading_a_History_File.htm"/>
<mapID target="Menu_Bars" url="html/Menu_Bars.htm"/>
- <mapID target="Merging" url="html/Merging.htm"/>
- <mapID target="Moving" url="html/Moving.htm"/>
- <mapID target="Name_Redundancy_Check" url="html/Name_Redundancy_Check.htm"/>
- <mapID target="obo2flat" url="html/obo2flat.htm"/>
- <mapID target="obo2obo" url="html/obo2obo.htm"/>
- <mapID target="obodiff" url="html/obodiff.htm"/>
- <mapID target="OBO_Edit_Command_line_Options" url="html/OBO_Edit_Command_line_Options.htm"/>
- <mapID target="OBO_Edit_Features" url="html/OBO_Edit_Features.htm"/>
- <mapID target="OBO_Edit_Specific_Variables" url="html/OBO_Edit_Specific_Variables.htm"/>
- <mapID target="obomerge" url="html/obomerge.htm"/>
- <mapID target="Obsolete_Items" url="html/Obsolete_Items.htm"/>
<mapID target="Ontologies" url="html/Ontologies.htm"/>
<mapID target="Ontologies_included_with_Phenote" url="html/Ontologies_included_with_Phenote.htm"/>
- <mapID target="Other_Uses_for_Phenote" url="html/Other_Uses_for_Phenote.htm"/>
- <mapID target="Other_Uses_of_Filters" url="html/Other_Uses_of_Filters.htm"/>
<mapID target="Phenote_from_the_Command_Line" url="html/Phenote_from_the_Command_Line.htm"/>
<mapID target="Phenote_Webstart" url="html/Phenote_Webstart.htm"/>
- <mapID target="placeholder" url="html/placeholder.htm"/>
- <mapID target="Plugins" url="html/Plugins.htm"/>
- <mapID target="Properties" url="html/Properties.htm"/>
- <mapID target="Reasoner_Prefilters" url="html/Reasoner_Prefilters.htm"/>
- <mapID target="Rendering" url="html/Rendering.htm"/>
- <mapID target="Requesting_New_Features___Functionality" url="html/Requesting_New_Features___Functionality.htm"/>
- <mapID target="Restrictions" url="html/Restrictions.htm"/>
- <mapID target="Reusing_Filters" url="html/Reusing_Filters.htm"/>
<mapID target="Running_Phenote_for_the_First_Time" url="html/Running_Phenote_for_the_First_Time.htm"/>
<mapID target="Sample_Annotations" url="html/Sample_Annotations.htm"/>
<mapID target="Sample_Configuration_1" url="html/Sample_Configuration_1.htm"/>
<mapID target="Sample_Configuration_2" url="html/Sample_Configuration_2.htm"/>
- <mapID target="Saving_a_History_File" url="html/Saving_a_History_File.htm"/>
- <mapID target="Searching" url="html/Searching.htm"/>
- <mapID target="Setting_the_Filter_Mode" url="html/Setting_the_Filter_Mode.htm"/>
- <mapID target="Some_terminology" url="html/Some_terminology.htm"/>
- <mapID target="Structural_Editing" url="html/Structural_Editing.htm"/>
- <mapID target="Term_Filters" url="html/Term_Filters.htm"/>
<mapID target="Term_Info" url="html/Term_Info.htm"/>
- <mapID target="Text_Checks" url="html/Text_Checks.htm"/>
- <mapID target="Text_Editing" url="html/Text_Editing.htm"/>
- <mapID target="The__field__Tag" url="html/The__field__Tag.htm"/>
- <mapID target="The__dataadapter__Tag116" url="html/The__dataadapter__Tag.htm"/>
<mapID target="The__term_history__Tag118" url="html/The__term_history__Tag.htm"/>
<mapID target="The__auto_update_ontologies__Tag115" url="html/The__auto_update_ontologies__Tag.htm"/>
<mapID target="The__ontology__Tag" url="html/The__ontology__Tag.htm"/>
<mapID target="The__update_timer__Tag" url="html/The__update_timer__Tag.htm"/>
<mapID target="The__master_to_local_config__Tag" url="html/The__master_to_local_config__Tag.htm"/>
+ <mapID target="The__dataadapter__Tag116" url="html/The__dataadapter__Tag.htm"/>
+ <mapID target="The__field__Tag" url="html/The__field__Tag.htm"/>
<mapID target="The__tab__Tag" url="html/The__tab__Tag.htm"/>
<mapID target="The_Scroller_Tag" url="html/The_Basic_Flat_File_Interface.htm"/>
- <mapID target="The_Box_Tag" url="html/The_Box_Tag.htm"/>
- <mapID target="The_Category_Manager_Plugin" url="html/The_Category_Manager_Plugin.htm"/>
- <mapID target="The_Change_Tracker_Plugin" url="html/The_Change_Tracker_Plugin.htm"/>
- <mapID target="The_Compactgrid_Tag" url="html/The_Compactgrid_Tag.htm"/>
- <mapID target="The_Complex_Class_Plugin" url="html/The_Complex_Class_Plugin.htm"/>
- <mapID target="The_Component_Tag" url="html/The_Component_Tag.htm"/>
- <mapID target="The_Configuration_Plugin" url="html/The_Configuration_Plugin.htm"/>
- <mapID target="The_DAG_Viewer" url="html/The_DAG_Viewer.htm"/>
- <mapID target="The_Dbxref_Library_Plugin" url="html/The_Dbxref_Library_Plugin.htm"/>
<mapID target="The_Default_Layout" url="html/Introduction.htm"/>
- <mapID target="The_Divider_Tag" url="html/The_Divider_Tag.htm"/>
- <mapID target="The_Explanation_Plugin" url="html/The_Explanation_Plugin.htm"/>
- <mapID target="The_Extended_Info_Plugin" url="html/The_Extended_Info_Plugin.htm"/>
- <mapID target="The_Glue_Tag" url="html/The_Glue_Tag.htm"/>
- <mapID target="The_GO_Flat_File_Adapter" url="html/The_GO_Flat_File_Adapter.htm"/>
- <mapID target="The_Graph_Viewer_Plugin" url="html/The_Graph_Viewer_Plugin.htm"/>
- <mapID target="The_Grid_Tag" url="html/The_Grid_Tag.htm"/>
- <mapID target="The_History_Plugin" url="html/The_History_Plugin.htm"/>
- <mapID target="The_ID_Manager_Plugin" url="html/The_ID_Manager_Plugin.htm"/>
- <mapID target="The_If_Tag" url="html/The_If_Tag.htm"/>
- <mapID target="The_Interface" url="html/The_Interface.htm"/>
- <mapID target="The_Label_Tag" url="html/The_Label_Tag.htm"/>
<mapID target="The_OBO_Adapter" url="html/The_OBO_Adapter.htm"/>
- <mapID target="The_OBO_Edit_Reasoner" url="html/The_OBO_Edit_Reasoner.htm"/>
- <mapID target="The_Term_Editor_Panel" url="html/The_Term_Editor_Panel.htm"/>
- <mapID target="The_Panel_Tag" url="html/The_Panel_Tag.htm"/>
- <mapID target="The_Parent_Plugin" url="html/The_Parent_Plugin.htm"/>
<mapID target="The_PhenoSyntax_Adapter" url="html/The_PhenoSyntax_Adapter.htm"/>
- <mapID target="The_Reasoner_and_the_Interface" url="html/The_Reasoner_and_the_Interface.htm"/>
- <mapID target="The_Reasoner_Plugin" url="html/The_Reasoner_Plugin.htm"/>
<mapID target="The_Serial_Adapter" url="html/The_Serial_Adapter.htm"/>
- <mapID target="The_Spacer_Tag" url="html/The_Spacer_Tag.htm"/>
- <mapID target="The_Synonym_Category_Manager_Plugin" url="html/The_Synonym_Category_Manager_Plugin.htm"/>
<mapID target="The_Tab_Delimited_Adapter" url="html/The_Tab_Delimited_Adapter.htm"/>
- <mapID target="The_Tabs_Tag" url="html/The_Tabs_Tag.htm"/>
<mapID target="The_tag_value_adapter" url="html/The_tag_value_adapter.htm"/>
- <mapID target="The_Verification_Plugin" url="html/The_Verification_Plugin.htm"/>
- <mapID target="The_Window_Tag" url="html/The_Window_Tag.htm"/>
- <mapID target="Undo_Redo" url="html/Undo_Redo.htm"/>
- <mapID target="User_Defined_Checks" url="html/User_Defined_Checks.htm"/>
<mapID target="Using_Filters" url="html/Using_Filters.htm"/>
<mapID target="What_is_a_Configuration_" url="html/What_is_a_Configuration_.htm"/>
<mapID target="What_is_an_ontology_" url="html/What_is_an_ontology_.htm"/>
- <mapID target="What_is_Phenote_" url="html/What_is_OBO_Edit_.htm"/>
<mapID target="What_is_Phenote" url="html/What_is_Phenote_.htm"/>
- <mapID target="Who_should_use_Phenote" url="html/Who_should_use_Phenote.htm"/>
- <mapID target="Working_with_Categories" url="html/Working_with_Categories.htm"/>
- <mapID target="Working_with_Intersections" url="html/Working_with_Intersections.htm"/>
- <mapID target="Working_with_Namespaces" url="html/Working_with_Namespaces.htm"/>
- <mapID target="Working_with_Obsoletes" url="html/Working_with_Obsoletes.htm"/>
- <mapID target="Working_with_Selections" url="html/Working_with_Selections.htm"/>
- <mapID target="Working_with_Synonym_Categories" url="html/Working_with_Synonym_Categories.htm"/>
- <mapID target="Working_with_XML_Layouts" url="html/Working_with_XML_Layouts.htm"/>
<mapID target="Writing_a_Data_Adapter" url="html/Writing_a_Data_Adapter.htm"/>
<mapID target="The__phenote_configuration__Tag" url="html/The__phenote_configuration__Tag.htm"/>
<mapID target="XML_skeleton" url="html/XML_skeleton.htm"/>
Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html 2007-05-30 18:50:02 UTC (rev 651)
@@ -290,31 +290,31 @@
<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__phenote_configuration__Tag.htm" target=bodyframe>The &lt;phenote-configuration&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__phenote_configuration__Tag.htm" target=bodyframe>The <phenote-configuration> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__tab__Tag.htm" target=bodyframe>The &lt;tab&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__tab__Tag.htm" target=bodyframe>The <tab> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &lt;dataadapter&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The <dataadapter> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__master_to_local_config__Tag.htm" target=bodyframe>The &lt;master-to-local-config&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__master_to_local_config__Tag.htm" target=bodyframe>The <master-to-local-config> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &lt;field&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The <field> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &lt;ontology&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The <ontology> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &lt;auto-update-ontologies&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The <auto-update-ontologies> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &lt;update-timer&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The <update-timer> Tag</font></a>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &lt;term-history&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The <term-history> Tag</font></a>
</td></tr></table>
</td></tr></table>
<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
Modified: phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <auto-update-ontologies> Tag</title>
+<title>The <auto-update-ontologies> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
@@ -32,6 +32,6 @@
<h2>Contents</h2></h1>
<p>(none)</p>
<h1><font color="#000000" size="3"></font> </h1>
-<h2>Example</h2><PRE><ns:auto-update-ontologies enable="true"/><br></PRE>
+<h2>Example</h2><pre><ns:auto-update-ontologies enable="true"/><br></pre>
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <dataadapter> Tag</title>
+<title>The <dataadapter> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
@@ -31,31 +31,31 @@
<td><em>any text value</em></td>
<td align="middle">yes</td>
<td> </td></tr>
- <TR>
- <TD>
- <P><FONT face=Courier>is_queryable</FONT></P></TD>
- <TD>This is a flag to indicate is the data adapter will be able to connect
- to a database back-end.</TD>
- <TD align=left>
- <UL>
- <LI>
- <DIV align=left>true </DIV>
- <LI>
- <DIV align=left>false</DIV></LI></UL></TD>
- <TD align=middle>no</TD>
- <TD>false</TD></TR>
<tr>
<td>
- <P><font face="Courier">enable</font></P></td>
+ <p><font face="Courier">is_queryable</font></p></td>
+ <td>This is a flag to indicate is the data adapter will be able to connect
+ to a database back-end.</td>
+ <td align="left">
+ <ul>
+ <li>
+ <div align="left">true </div>
+ <li>
+ <div align="left">false</div></li></ul></td>
+ <td align="middle">no</td>
+ <td>false</td></tr>
+ <tr>
+ <td>
+ <p><font face="Courier">enable</font></p></td>
<td>For each element, it can be turned on or off. In this way you
can maintain the list of available data adapters, but just "hide" them in
the application if set to false. </td>
<td align="left">
<ul>
<li>
- <DIV align=left>true </DIV>
+ <div align="left">true </div>
<li>
- <DIV align=left>false</DIV></li></ul></td>
+ <div align="left">false</div></li></ul></td>
<td align="middle">no</td>
<td>false</td></tr></table>
<h2> </h2>
Modified: phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <field> Tag<field> Tag</title>
+<title>The <field> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
Modified: phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -1,72 +1,72 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>The <master-to-local-config> Tag</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>The
-<master-to-local-config> Tag</H1>
-<H2>Parameters</H2>
-<H1>
-<TABLE borderColor=#000000 cellPadding=5 width="100%" align=center border=1>
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>The <master-to-local-config> Tag</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>The
+<master-to-local-config> Tag</h1>
+<h2>Parameters</h2>
+<h1>
+<table bordercolor="#000000" cellpadding="5" width="100%" align="center" border="1">
- <TR>
- <TD align=middle><STRONG>Name</STRONG></TD>
- <TD align=middle><STRONG>Description</STRONG></TD>
- <TD align=middle><STRONG><STRONG></STRONG>Legal Values</STRONG></TD>
- <TD align=middle><STRONG>Required</STRONG></TD>
- <TD align=middle><STRONG>Default</STRONG></TD></TR>
- <TR>
- <TD>
- <P><FONT face=Courier>mode</FONT></P></TD>
- <TD>
- <P>This designates how to merge files together.</P></TD>
- <TD>
- <UL>
- <LI>
- <DIV align=left><FONT size=2>UPDATE</FONT></DIV>
- <LI>
- <DIV align=left><FONT size=2>WIPEOUT</FONT></DIV></LI></UL></TD>
- <TD align=middle>no</TD>
- <TD><FONT size=2> UPDATE</FONT></TD></TR>
- <TR>
- <TD><FONT face=Courier>when</FONT></TD>
- <TD>
- <P>When and how a configuration merger will take place. </P></TD>
- <TD align=left>
- <UL>
- <LI>
- <DIV align=left><FONT size=2>ON_VERSION_ CHANGE</FONT></DIV>
- <LI>
- <DIV align=left><FONT size=2>ALWAYS</FONT></DIV></LI></UL></TD>
- <TD align=middle>no</TD>
- <TD><FONT size=2>ON_VERSION_
- CHANGE</FONT></TD></TR>
- <TR>
- <TD><FONT face=Courier>overriding-master-url</FONT></TD>
- <TD>
- <P>The config file located at this URL will override the config file
+ <tr>
+ <td align="middle"><strong>Name</strong></td>
+ <td align="middle"><strong>Description</strong></td>
+ <td align="middle"><strong><strong></strong>Legal Values</strong></td>
+ <td align="middle"><strong>Required</strong></td>
+ <td align="middle"><strong>Default</strong></td></tr>
+ <tr>
+ <td>
+ <p><font face="Courier">mode</font></p></td>
+ <td>
+ <p>This designates how to merge files together.</p></td>
+ <td>
+ <ul>
+ <li>
+ <div align="left"><font size="2">UPDATE</font></div>
+ <li>
+ <div align="left"><font size="2">WIPEOUT</font></div></li></ul></td>
+ <td align="middle">no</td>
+ <td><font size="2"> UPDATE</font></td></tr>
+ <tr>
+ <td><font face="Courier">when</font></td>
+ <td>
+ <p>When and how a configuration merger will take place. </p></td>
+ <td align="left">
+ <ul>
+ <li>
+ <div align="left"><font size="2">ON_VERSION_ CHANGE</font></div>
+ <li>
+ <div align="left"><font size="2">ALWAYS</font></div></li></ul></td>
+ <td align="middle">no</td>
+ <td><font size="2">ON_VERSION_
+ CHANGE</font></td></tr>
+ <tr>
+ <td><font face="Courier">overriding-master-url</font></td>
+ <td>
+ <p>The config file located at this URL will override the config file
of the same name in webstart jar (or svn/app conf). If the URL
points to the phenote svn checkout for the config, it means one can
just commit updates to a config to subversion and it will become the new
- template/master</P></TD>
- <TD align=left><EM>any valid URL</EM></TD>
- <TD align=middle>no</TD>
- <TD></TD></TR></TABLE>
-<H2> </H2>
-<H2>Contents</H2></H1>
-<P>All other tags should be included within the <phenote-configuration>
-tag, including:</P>
-<UL>
- <LI>
- <DIV>data-adapters</DIV>
- <LI>
- <DIV>fields (and ontologies)</DIV>
- <LI>
- <DIV>settings such as update-timer, auto-update-ontologies, etc.</DIV></LI></UL>
-<H1><FONT color=#000000 size=3></FONT> </H1>
-<H2>Example</H2><PRE> <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" <BR> overriding-master-url="<A href="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg">http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg</A>" /><BR></PRE>
-</BODY>
-</HTML>
\ No newline at end of file
+ template/master</p></td>
+ <td align="left"><em>any valid URL</em></td>
+ <td align="middle">no</td>
+ <td></td></tr></table>
+<h2> </h2>
+<h2>Contents</h2></h1>
+<p>All other tags should be included within the <phenote-configuration>
+tag, including:</p>
+<ul>
+ <li>
+ <div>data-adapters</div>
+ <li>
+ <div>fields (and ontologies)</div>
+ <li>
+ <div>settings such as update-timer, auto-update-ontologies, etc.</div></li></ul>
+<h1><font color="#000000" size="3"></font> </h1>
+<h2>Example</h2><pre> <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" <br> overriding-master-url="<a href="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg">http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg</a>" /><br></pre>
+</body>
+</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <ontology> Tag<ontology> Tag</title>
+<title>The <ontology> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
Modified: phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <tab> Tag</title>
+<title>The <tab> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
Modified: phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <term-history> Tag</title>
+<title>The <term-history> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
Modified: phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm 2007-05-30 17:56:41 UTC (rev 650)
+++ phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm 2007-05-30 18:50:02 UTC (rev 651)
@@ -2,7 +2,7 @@
<html>
<head>
<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
-<title>The <update-timer> Tag</title>
+<title>The <update-timer> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 17:29:17
|
Revision: 649
http://svn.sourceforge.net/obo/?rev=649&view=rev
Author: nlw
Date: 2007-05-30 10:29:13 -0700 (Wed, 30 May 2007)
Log Message:
-----------
adding this file b/c it seems to be a problem
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS
Modified: phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 17:21:55
|
Revision: 648
http://svn.sourceforge.net/obo/?rev=648&view=rev
Author: nlw
Date: 2007-05-30 10:21:45 -0700 (Wed, 30 May 2007)
Log Message:
-----------
Phenote help: fixing up html for testing in the java help
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm
phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm
phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm
phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm
phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm
phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm
phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm
phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm
phenote/trunk/doc/phenote-website/help/html/Term_Info.htm
phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm
phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm
phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm
Modified: phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -1,17 +1,16 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Annotation Spreadsheet</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>Annotation Spreadsheet</H1>
-<P><IMG hspace=0
-src="../images/annotation_spreadsheet_blank.png" width="100%"
-border=0></P>
-<P> </P>
-<P>In the bottom half of the Phenote window occupies the Annotation
-Spreadsheet.</P>
-</BODY>
-</HTML>
\ No newline at end of file
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Annotation Spreadsheet</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Annotation Spreadsheet</h1>
+<p><IMG src="../images/annotation_spreadsheet_blank.png" width="100%"
+border=0></p>
+<p> </p>
+<p>In the bottom half of the Phenote window occupies the Annotation
+Spreadsheet.</p>
+</body>
+</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -7,8 +7,7 @@
</head>
<body bgcolor="#ffffff">
<h1>Data Entry</h1>
-<p><IMG height=0 hspace=0
-src="../images/data_entry_blank.png" width=0 border=0><IMG hspace=0
+<p><IMG hspace=0
src="../images/data_entry_blank.png" border=0></p>
<p>The data entry section of Phenote is where the user will enter each
annotation. The data entered here will be displayed in a single row of the
Modified: phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -13,13 +13,12 @@
entry section, you will see a blinking cursor in the active field.</p>
<h3>Step 2: Begin typing...</h3>
<p>Go ahead...</p>
-<p><IMG hspace=0 src="../images/free-text-pretab.png" width=600 border=0></p>
+<p><IMG src="../images/free-text-pretab.png" width=600 border=0></p>
<h3>Step 3: "Tab" or mouse-click to insert into the spreadsheet</h3>
<p>Once you've typed all you want, be sure to hit tab
(which will also advance to the next field), or click on another field.
This will insert your entry into the <em>Annotation spreadsheet</em> down
below:</p>
-<p><IMG hspace=0 src="../images/free-text-posttab.png" width=600
-border=0></p>
+<p><IMG src="../images/free-text-posttab.png" width=600 border=0></p>
</body>
</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -10,7 +10,7 @@
<p>Note: by default, autocompletion search settings
will include Term <em>names</em> as well as <em>synonyms</em>. If you would like to change these
settings, read the <A href="Changing_your_Autocompletion_Settings.htm">Changing
-your Autocompletion Settings</A> help page.</p>
+your Autocompletion Settings</a> help page.</p>
<h3>Step 1: (optional) select an ontology</h3>
<p>By default, the autocompletion feature will search on
ALL ontologies specified for the field. You can change this, and choose a
@@ -22,56 +22,54 @@
<h3> Step 2: begin typing...</h3>
<p>As you start typing in an ontology field, a list of
partial matches will show in a scrollable box below. In this example, the
-phrase <EM>prot</EM>
+phrase <em>prot</em>
has several matches. </p>
-<p><IMG height=0 hspace=0
-src="../images/prot-autocomplete-ex.png" width=0 border=0><IMG hspace=0
-src="../images/prot-autocomplete-entry.png" border=0></p>
-<P> Matches are listed in the following order within the box:</P>
-<UL>
- <UL>
- <LI>starts with - partial matches to term names that
+<p><IMG hspace=0 src="../images/prot-autocomplete-entry.png" border=0></p>
+<p> Matches are listed in the following order within the box:</p>
+<ul>
+ <ul>
+ <li>starts with - partial matches to term names that
start with the text entered
- <LI>contains - partial matches that are contained
+ <li>contains - partial matches that are contained
within the term name
- <LI>synonyms - indicated with "[syn]"
- <LI>definitions - indicated with "[def]"
- <LI>obsoletes - indicated with "[obs]"</LI></UL></UL>
+ <li>synonyms - indicated with "[syn]"
+ <li>definitions - indicated with "[def]"
+ <li>obsoletes - indicated with "[obs]"</li></ul></ul>
<p >If you have selected to search in
ALL ontologies, then the matches are listed in this order, in the order of the
ontologies. For example, you will find a matches to "kidney" in FMA before
you will find them in GO.</p>
-<H3> </H3>
-<H3>Step 3: scroll down to find your matching term</H3>
-<P>You can navigate through these matches with the
+<h3> </h3>
+<h3>Step 3: scroll down to find your matching term</h3>
+<p>You can navigate through these matches with the
scrollbar on the right side of the box. The more letters typed increases
-the specificity of the matches displayed. </P>
-<P>As you scroll down the list, either with arrow keys or
+the specificity of the matches displayed. </p>
+<p>As you scroll down the list, either with arrow keys or
the mouse, information about the term will be displayed in the Term Info window, which may help in
your decision whether or not the term is appropriate for the current annotation. In this example
-I have moused-over the term <EM>proteasomal ubiquitin-dependent protein
-catabolic process</EM>. The term info window shows:</P>
-<P><IMG hspace=0 src="../images/prot-autocomplete-terminfo.png" border=0></P>
-<P>FAQ: what if i want a more specific term related to
-this?</P>
-<P>FAQ: what if i can't find the term name i'm looking for?</P>
-<H3>
- </H3>
-<H3>Step 4: select the term to insert into the
-spreadsheet</H3>
-<P> Once you have found the correct term to use for
+I have moused-over the term <em>proteasomal ubiquitin-dependent protein
+catabolic process</em>. The term info window shows:</p>
+<p><IMG hspace=0 src="../images/prot-autocomplete-terminfo.png" border=0></p>
+<p>FAQ: what if i want a more specific term related to
+this?</p>
+<p>FAQ: what if i can't find the term name i'm looking for?</p>
+<h3>
+ </h3>
+<h3>Step 4: select the term to insert into the
+spreadsheet</h3>
+<p> Once you have found the correct term to use for
your annotation, select it by clicking the left mouse button. Selecting a
term will trigger the drop-down box of matches to disappear, and your selected term to be
-displayed in the appropriate field in the spreadsheet:</P>
-<P><IMG hspace=0 src="../images/prot-autocomple-table.png"
-border=0></P>
-<P>Note: if you do not click the mouse button on a
+displayed in the appropriate field in the spreadsheet:</p>
+<p><IMG hspace=0 src="../images/prot-autocomple-table.png"
+border=0></p>
+<p>Note: if you do not click the mouse button on a
term from the drop-down list, then your term will not be selected.
currently, even if you type the exact term name it will not be chosen before
-moving to the next field.</P>
-<P>If, once you have selected a term, you want to change
+moving to the next field.</p>
+<p>If, once you have selected a term, you want to change
it, simply select another term from the same search or delete the current text
-and start typing something new.</P>
+and start typing something new.</p>
</body>
</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -16,11 +16,7 @@
adapters. To choose a different data adapter, click on the little upside-down triangle, and select
it from the dropdown list. The list of valid extensions for each
data adapter is also listed shown.</p>
-<p><IMG hspace=0 src="../images/data_adapter_open_list.png"
-border=0>
-
-
- </p>
+<p><IMG hspace=0 src="../images/data_adapter_open_list.png" border=0></p>
<p>When opening an Annotation file, if "All Files" is selected
and your file has an extension appropriate for the data type, the data adapter will
be applied automatically. For example if your filename is "example.xls", the tab-delimited
@@ -31,42 +27,24 @@
operating under the "demo" configuration. However, since then, you
switched your configuration to "my_new_config". Since these configurations
might not match, you are unable to load in the data. Try <A
-href="Changing_your_Configuration.htm">changing your configuration</A>
-
- back to "demo" and
+href="Changing_your_Configuration.htm">changing your configuration</a>back to "demo" and
then retry loading the annotation file. </p>
+<p> </p>
+<h3>Saving Annotations</h3>
+<p>To save a file, select the appropriate output format, type in the name of the file
+(including the extension), and click "Save".</p>
<p>
-
-
- </p>
-<h3>
-
-
- Saving Annotations</h3>
-<p>
- To save a file,
-select the appropriate output format, type in the name of the file
-(including the extension), and click "Save". </p>
-<p>
Note that you can also select a filename that already exists
which will overwrite the file. (There is no warning in the software
itself, so this is your warning.)</p>
-<p><IMG height=0 hspace=0
-src="../images/data_adapter_listing.png" width=0 border=0><IMG hspace=0
-src="../images/data_adapter_listing.png" border=0>
-
-
- </p>
-<p>
-
-
- </p>
-<P>Warning: If you give an extension to a filename that is not valid for
+<p><IMG hspace=0 src="../images/data_adapter_listing.png" border=0> </p>
+<p> </p>
+<p>Warning: If you give an extension to a filename that is not valid for
that selected format, you may encounter problems during loading. For
example, if you save your file as "example.xls" but the format you tell it to
save as is PhenoSyntax, then when the file is loaded it might try to use the
tab-delimited adapter instead of the phenosyntax adapter, resulting in your data
hangin' in space. Be sure to use the appropriate combination of extension
-and adapter.</P>
+and adapter.</p>
</body>
</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -1,19 +1,18 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Running Phenote for the First Time</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>Running Phenote for the First Time</H1>
-<H2>Choosing the Configuration</H2>
-<P>The very first time you start phenote, a window will
-popup and ask you to choose a configuration:</P>
-<P><IMG height=0 hspace=0 src="../images/config-screenshot.png" width=0
-border=0><IMG hspace=0 src="../images/config-screenshot.png" border=0></P>
-<P> </P>
-<P>For demonstration purposes, we will work with the "demo"
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Running Phenote for the First Time</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Running Phenote for the First Time</h1>
+<h2>Choosing the Configuration</h2>
+<p>The very first time you start phenote, a window will
+popup and ask you to choose a configuration:</p>
+<p><IMG hspace=0 src="../images/config-screenshot.png" border=0></p>
+<p> </p>
+<p>For demonstration purposes, we will work with the "demo"
configuration. Select this option and press OK. Phenote will
continue to load, but might take a few minutes to get started. Since many
ontolgies are updated everyday, it is important to keep in synch with the
@@ -21,9 +20,9 @@
newer versions of ontologies available for download. If so, it will
automatically download the newest versions to your local computer. (This
feature can be disabled in the future. See the <A
-href="What_is_a_Configuration_.htm">Customizing Phenote</A>
+href="What_is_a_Configuration_.htm">Customizing Phenote</a>
section for more
-information.)</P>
-</BODY>
-</HTML>
\ No newline at end of file
+information.)</p>
+</body>
+</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,9 +6,10 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>Sample Configuration 1</h1><PRE><H2><FONT face=Arial>The Phenote window for sample.cfg</FONT></H2></PRE>
-<P>This interface is created with the configuration file sample.cfg shown
-below:</P><PRE><P><IMG hspace=0 src="../images/sample-config.png" width="100%" border=0></P></PRE>
-<H2>The configuration file: sample.cfg</H2><pre><?xml version="1.0" encoding="UTF-8"?><br><ns:phenote-configuration version="1.3-beta1" xmlns:ns="phenote/config/xml"><br> <ns:log config-file="conf/log4j-standalone.xml"/><br> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/></pre><pre><br> <ns:uvic-graph enable="false"/><br> <ns:term-history enable="false"/> <br> <ns:auto-update-ontologies enable="false"/> <<br> <ns:update-timer timer="15"/>< <br> <ns:field name="Example Free-text" syntax-abbrev="PUB" enable="true"/> <br> <ns:field name="Genotype" syntax-abbrev="GT" enable="false"/><br> <ns:field name="Example Multi-Ontology" syntax-abbrev="E" enable="true"> <br> <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/> <br> <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/> <br> <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/> <br> </ns:field><br> <ns:field name="Example Single-Ontology" syntax-abbrev="Q" enable="true"> <br> <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/> <br> </ns:field><br> <ns:field name="Description" syntax-abbrev="Desc" enable="true"/></pre><pre></ns:phenote-configuration></pre><pre> </pre>
+<h1>Sample Configuration 1</h1><pre><h2><font face="Arial">The Phenote window for sample.cfg</font></h2></pre>
+<p>This interface is created with the configuration file sample.cfg shown
+below:</p>
+<p><IMG src="../images/sample-config.png" width="100%" border=0></p>
+<h2>The configuration file: sample.cfg</h2><pre><?xml version="1.0" encoding="UTF-8"?><br><ns:phenote-configuration version="1.3-beta1" xmlns:ns="phenote/config/xml"><br> <ns:log config-file="conf/log4j-standalone.xml"/><br> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/></pre><pre><br> <ns:uvic-graph enable="false"/><br> <ns:term-history enable="false"/> <br> <ns:auto-update-ontologies enable="false"/> <<br> <ns:update-timer timer="15"/>< <br> <ns:field name="Example Free-text" syntax-abbrev="PUB" enable="true"/> <br> <ns:field name="Genotype" syntax-abbrev="GT" enable="false"/><br> <ns:field name="Example Multi-Ontology" syntax-abbrev="E" enable="true"> <br> <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/> <br> <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/> <br> <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/> <br> </ns:field><br> <ns:field name="Example Single-Ontology" syntax-abbrev="Q" enable="true"> <br> <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/> <br> </ns:field><br> <ns:field name="Description" syntax-abbrev="Desc" enable="true"/></pre><pre></ns:phenote-configuration></pre><pre> </pre>
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -5,11 +5,11 @@
<title>Sample Configuration 2</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
-<BODY BGCOLOR=#ffffff>
+<body bgcolor="#ffffff">
<h1>Sample Configuration 2</h1>
-<H2>The Phenote window for ncbo.cfg</H2>
-<P>This interface is created with the configuration file ncbo.cfg shown below</P>
-<P><IMG hspace=0 src="../images/ncbo-config.png" width="100%" border=0> </P>
-<H2>The configuration file: ncbo.cfg</H2><pre><?xml version="1.3.1" encoding="UTF-8"?><br><ns:phenote-configuration version="1.1.2" xmlns:ns="phenote/config/xml"><br> <ns:log config-file="conf/log4j-standalone.xml"/></pre><pre> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> <br> <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/><br> <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/><br> <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/></pre><pre> <ns:uvic-graph enable="false"/><br> <ns:term-history enable="false"/><br> <ns:auto-update-ontologies enable="true"/> <<br> <ns:update-timer timer="0"/><><br> <br> <ns:obo-repository url-dir="<A href="'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/" ??>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/</A>><br> <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/><br> <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/><br> <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true"><br> <ns:ontology name="Genetic Context" file="context.obo"/><br> </ns:field><br> <ns:field name="Entity" syntax-abbrev="E" enable="true"><br> <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/><br> <ns:ontology name="FMA" file="fma_obo.obo"/><br> <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/><br> <ns:ontology name="GO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" /><br> <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo" /><br> <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo" /><br> </ns:field><br> <ns:field name="Quality" syntax-abbrev="Q" enable="true"><br> <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" /><br> <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo" /><br> </ns:field><br> <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true"><br> <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/><br> <ns:ontology name="FMA" file="fma_obo.obo"/><br> <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/><br> <ns:ontology name="GO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" /><br> <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo" /><br> <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo" /><br> </ns:field><br> <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true"><br> <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/><br> </ns:field><br> <ns:field name="Description" syntax-abbrev="Desc" enable="true"/><br></ns:phenote-configuration></pre> <pre></pre>
-</BODY>
+<h2>The Phenote window for ncbo.cfg</h2>
+<p>This interface is created with the configuration file ncbo.cfg shown below</p>
+<p><IMG src="../images/ncbo-config.png" width="100%" border=0> </p>
+<h2>The configuration file: ncbo.cfg</h2><pre><?xml version="1.3.1" encoding="UTF-8"?><br><ns:phenote-configuration version="1.1.2" xmlns:ns="phenote/config/xml"><br> <ns:log config-file="conf/log4j-standalone.xml"/></pre><pre> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> <br> <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/><br> <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/><br> <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/></pre><pre> <ns:uvic-graph enable="false"/><br> <ns:term-history enable="false"/><br> <ns:auto-update-ontologies enable="true"/> <<br> <ns:update-timer timer="0"/><><br> <br> <ns:obo-repository url-dir="<A href="'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/" ??>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/</a>><br> <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/><br> <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/><br> <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true"><br> <ns:ontology name="Genetic Context" file="context.obo"/><br> </ns:field><br> <ns:field name="Entity" syntax-abbrev="E" enable="true"><br> <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/><br> <ns:ontology name="FMA" file="fma_obo.obo"/><br> <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/><br> <ns:ontology name="GO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" /><br> <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo" /><br> <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo" /><br> </ns:field><br> <ns:field name="Quality" syntax-abbrev="Q" enable="true"><br> <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" /><br> <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo" /><br> </ns:field><br> <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true"><br> <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/><br> <ns:ontology name="FMA" file="fma_obo.obo"/><br> <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/><br> <ns:ontology name="GO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" /><br> <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo" /><br> <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo" /><br> </ns:field><br> <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true"><br> <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/><br> </ns:field><br> <ns:field name="Description" syntax-abbrev="Desc" enable="true"/><br></ns:phenote-configuration></pre> <pre></pre>
+</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/html/Term_Info.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Term_Info.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/Term_Info.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -20,15 +20,15 @@
for the term. It is often presented in the format of a unique abbreviation
for the ontology followed by a numeric identifier, separated with a colon
(ie GO:0007605). </p>
-<P><strong>Synonyms</strong> - many terms have
+<p><strong>Synonyms</strong> - many terms have
synonyms. These synonyms may be defined as having different
scope, such as: Exact, Narrow, Broad, or Other. If the
synonym is from a particular categorization (such as an abbreviation, a
chemical formula, a community standard like IUPAC, etc.), this will be
indicated following the synonym in brackets. If no synonyms are present,
-this section will not appear.</P>
+this section will not appear.</p>
<p><strong>Definition</strong> - the definition for the term is displayed</p>
-<p><STRONG>Replacements</STRONG> - If a term is obsoleted,
+<p><strong>Replacements</strong> - If a term is obsoleted,
a replacement term is often recommended by the maintainers of the ontology, or
at minimum other terms to consider are mentioned. These will be listed with navigable links. </p>
<p> </p>
@@ -44,8 +44,7 @@
<p><IMG hspace=0 src="../images/term_info_linked.png" border=0></p>
<p>and if I move the slider to see the rest of the window, I will see a
link from where we just came: <em>sensory perception of sound</em></p>
-<p><IMG height=0 hspace=0 src="../images/term_info_linked2.png" width=0
-border=0><IMG hspace=0 src="../images/term_info_linked2.png"
+<p><IMG hspace=0 src="../images/term_info_linked2.png"
border=0></p>
</body>
</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -5,21 +5,18 @@
<title>Changing Link Attributes</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
-<BODY BGCOLOR=#ffffff>
+<body bgcolor="#ffffff">
<h1>The Phenote Interface </h1>
<p>This screenshot is of Phenote when configured with the "demo" configuration and loaded
with data. It is a typical interface for phenotype
annotation. </p>
-<p><IMG hspace=0 src="../images/phenote-data-markup.png" width="100%" border=0> The Phenote application window is comprised of three main
-
- areas:</p>
+<p><IMG src="../images/phenote-data-markup.png" width="100%" border=0> The Phenote application window is comprised of three main areas:</p>
<ul>
<li>The Data Entry frame located in the upper left.
<li>The Term Info frame located in the upper right.
<li>The Annotation Spreadsheet located in the lower half.</li></ul>
<p>The Phenote application runs best in 1024x768, but the window is easily
adjusted to meet your specific size needs.</p>
-<div class="tabbed">
-</div>
-</BODY>
+
+</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__auto_update_ontologies__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>The <auto-update-ontologies> <auto-update-ontologies> Tag</h1>
+<h1>The <auto-update-ontologies> Tag</h1>
<p>The <auto-update-ontologies> tag sets the default behavior
for automatically updating ontologies when Phenote loads.</p>
<h2>Parameters</h2>
Modified: phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>The <dataadapter> <dataadapter> Tag</h1>
+<h1>The <dataadapter> Tag</h1>
<p>The <dataadapter> tag allows the user to specify a read and/or write
adapter(s). These data adapters are for loading/saving of annotation data
only, not for ontologies. At least one data adapter should be specified
Modified: phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>The <field> <field> Tag</h1>
+<h1>The <field> Tag</h1>
<p>The <field> tag creates a single input field. There can be one or more fields
per configuration.</p>
<h2>Parameters</h2>
Modified: phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -7,7 +7,7 @@
</HEAD>
<BODY BGCOLOR=#ffffff>
<H1>The
-<master-to-local-config> <master-to-local-config> Tag</H1>
+<master-to-local-config> Tag</H1>
<H2>Parameters</H2>
<H1>
<TABLE borderColor=#000000 cellPadding=5 width="100%" align=center border=1>
Modified: phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__ontology__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>The <ontology> <field>Tag</h1>
+<h1>The <ontology> Tag</h1>
<p>The <ontology> tag enables the autocompletion
feature on an input field based
on the ontology file specified. There can be zero or more ontologies per
Modified: phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>The <tab> <tab> Tag</h1>
+<h1>The <tab> Tag</h1>
<p>The <tab> tag will allow the user to specify
groupings of fields into separate, paged tabs. This provides a way of
organizing fields into groups for ease of data entry. </p>
Modified: phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__term_history__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
<body bgcolor="#ffffff">
-<h1>The <term-history> <term-history> Tag</h1>
+<h1>The <term-history> Tag</h1>
<p>The <term-history> tag sets the default display of the term
history list. </p>
<p>[Note: The term history feature is still under
Modified: phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm 2007-05-30 06:19:00 UTC (rev 647)
+++ phenote/trunk/doc/phenote-website/help/html/The__update_timer__Tag.htm 2007-05-30 17:21:45 UTC (rev 648)
@@ -5,8 +5,8 @@
<title>The <update-timer> Tag</title>
<link rel="stylesheet" type="text/css" href="../javahelp.css">
</head>
-<BODY BGCOLOR=#ffffff>
-<h1>The <update-timer> <update-timer> Tag</h1>
+<body bgcolor="#ffffff">
+<h1>The <update-timer> Tag</h1>
<p> The <update-timer> tag sets the
default behavior for updating ontologies when Phenote loads. </p>
<h2>Parameters</h2>
@@ -50,10 +50,11 @@
<td>Will notify you if an updated file is available and wait <i>t</i>
seconds for answer, then will auto update.</td>
<td>Will notify you if an updated file is available and wait <i>t</i>
- seconds for answer, then will bypass update.</td></tr></table></h1></ P>
+ seconds for answer, then will bypass update.</td></tr></table></h1>
+<p></p>
<p> </p>
<p>If you don't include these items in the configuration, the default is to
automatically update from a repository without asking your permission.</p>
<h2>Example</h2><pre><ns:update-timer timer="15"/></pre>
-</BODY>
+</body>
</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 06:18:58
|
Revision: 647
http://svn.sourceforge.net/obo/?rev=647&view=rev
Author: nlw
Date: 2007-05-29 23:19:00 -0700 (Tue, 29 May 2007)
Log Message:
-----------
website: edits to css ... missing brace:
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/css/style.css
Modified: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css 2007-05-30 05:59:54 UTC (rev 646)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-05-30 06:19:00 UTC (rev 647)
@@ -110,9 +110,9 @@
#main_content .contact{
clear: right;
/*border: 1px solid brown;*/
+}
-
/* ---------- "copyright" class. ---------- */
/**/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 05:59:52
|
Revision: 646
http://svn.sourceforge.net/obo/?rev=646&view=rev
Author: nlw
Date: 2007-05-29 22:59:54 -0700 (Tue, 29 May 2007)
Log Message:
-----------
website: testing out changes to the navi bar to get rid of error in display
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/ssi/navi_home.html
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-05-30 05:42:59 UTC (rev 645)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-05-30 05:59:54 UTC (rev 646)
@@ -1,9 +1,6 @@
<div id="navi">
<div class="navi_head"></div>
<ul>
-<!-- <li>
- Home
---> </li>
<li>
<a href="/">Home</a>
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 05:43:01
|
Revision: 645
http://svn.sourceforge.net/obo/?rev=645&view=rev
Author: nlw
Date: 2007-05-29 22:42:59 -0700 (Tue, 29 May 2007)
Log Message:
-----------
added new links to the 'latest' for the website. this will link to v1.3
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/howtos/index.shtml
phenote/trunk/doc/phenote-website/content/software/index.shtml
phenote/trunk/doc/phenote-website/phenote-release-notes.html
Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-05-30 05:26:51 UTC (rev 644)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-05-30 05:42:59 UTC (rev 645)
@@ -12,7 +12,7 @@
<p>
Phenote is a Java application, which can be launched from the web using "Webstart". Simply click on the link below, and this will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software.</p>
<p>
-Webstart: <a href="http://toy.lbl.gov:9010/phenote/1.2/phenote.jnlp">Phenote v1.2</a>
+Webstart: <a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Phenote v1.2</a>
</p>
<p>
Phenote can also be launched from our <a href="/content/software/">Downloads</a> page. There you will also find any newer versions under development.
Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-05-30 05:26:51 UTC (rev 644)
+++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-05-30 05:42:59 UTC (rev 645)
@@ -8,28 +8,29 @@
<h2>Phenote Software</h2>
-<h3><a name="current">Current Release: 1.2</a> [<a href="http://toy.lbl.gov:9010/phenote/1.2/phenote.jnlp">Webstart</a>] </h3>
+<h3><a name="current">Current Release: 1.3</a> [<a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Webstart</a>] </h3>
Newest Features:
<ul>
-<li>Can now search ALL ontologies of a field without having to change the pull-down menu</li>
-<li>User can choose to update their local copy of an OBO ontology from sourceforge (can also retrieve if no local file found)</li>
-<li>Tab delimited data adapter</li>
-<li>Beginnings of term history</li>
-<li>User can select configuration they want to use at initialization or subsequently from file menu (currently requires phenote restart). </li>
-<li>Phenote merges its default configuration with users' configuration. This preserves user's additions as well as adds anything new from phenote upgrades.</li>
-<li>QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.</li>
-<li>Improved layout</li>
-<li>Tabbed main data-entry panel if more than 12 fields are present. Note that all fields will be displayed in the lower display table without scrolling</li>
-<li>Refactored code for field guis</li>
-<li>Ontology chooser reflects current term (bug fix)</li>
+<li>Web-based documentation and Help features</li>
+<li>Metadata fields added to configuration. User can name their configuration, add a description, and author</li>
+<li>Dialog allows user to back out of exiting from File->Exit</li>
+<li>Autocompletion search default settings configurable </li>
+<li>Can post-compose with >2 terms </li>
+<li>Synonyms delineated by scope in Term Info: Exact, Narrow, Broad, General, Related. </li>
+<li>Obsolete replacements or consideration terms are displayed in term info with links.</li>
+<li>Can configure by namespace for ontologies</li>
+<li>Can automatically update ontologies during startup (configurable)</li>
+<li>Added common configuration for OMIM curation for use by NCBO (ncbo.cfg)</li>
+<li>Can check for updates to ontology files independently from any URL </li>
+<li>Obsolete replacements or consideration terms are displayed in term info with links</li>
</ul>
<p>
-See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more information or back-versions.
+See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more detailed information.
</p>
<p>
To download this version with subversion, use the command:
-svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.2/ phenote
+svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote
</p>
<h3><a name="devel">Development Version</a></h3>
@@ -43,7 +44,7 @@
You can also browse the subversion repository at: <br /> https://obo.svn.sourceforge.net/viewvc/obo/phenote/
</p>
<p>
-For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a>.
+For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a> our our new <a href="www.phenote.org/help">HELP</a> pages.
</p>
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-30 05:26:51 UTC (rev 644)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-30 05:42:59 UTC (rev 645)
@@ -17,9 +17,8 @@
<h2>1.3
<hr></h2>
+05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a><br>
-in development, 1.3-beta2 -> 1.3 release<br>
-
<ul>
<li>feature: Web-based documentation and Help features</li>
@@ -54,7 +53,7 @@
</ul>
-05.09.2007, version <a href="1.3-beta1/phenote.jnlp">1.3-beta1</a><br>
+05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a><br>
<ul>
@@ -81,7 +80,7 @@
<h2>1.2
<hr></h2>
-05.02.2007, version <a href="1.2/phenote.jnlp">1.2</a><br>
+05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a><br>
<ul>
@@ -124,7 +123,7 @@
<h2>1.1
<hr></h2>
-04.06.2007, version <a href="1.1/phenote.jnlp">1.1.3</a><br>
+04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a><br>
<ul>
@@ -183,7 +182,7 @@
<h2>1.0
<hr></h2>
-02.06.2007, version <a href="1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a><br>
+02.06.2007, version <a href="phenote/1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a><br>
01.12.2007, version1.0,
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
@@ -209,8 +208,8 @@
<h2>0.9
<hr></h2>
-11.15.2006, version <a href="0.9/phenote-flybase.jnlp">0.9-fly</a>,
-<a href="0.9/phenote-zfin.jnlp">0.9-zfin</a>,
+11.15.2006, version <a href="phenote/0.9/phenote-flybase.jnlp">0.9-fly</a>,
+<a href="phenote/0.9/phenote-zfin.jnlp">0.9-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
webby phenote</a><br>
@@ -246,8 +245,8 @@
<h2>0.8
<hr></h2>
-10.02.2006, version <a href="0.8/phenote-flybase.jnlp">0.8-fly</a>,
-<a href="0.8/phenote-zfin.jnlp">0.8-zfin</a>,
+10.02.2006, version <a href="phenote/0.8/phenote-flybase.jnlp">0.8-fly</a>,
+<a href="phenote/0.8/phenote-zfin.jnlp">0.8-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
webby phenote</a><br>
@@ -272,7 +271,7 @@
<h2>0.7
<hr></h2>
-08.23.2007, version <a href="0.7/phenote-flybase.jnlp">0.7-fly.</a>,
+08.23.2007, version <a href="phenote/0.7/phenote-flybase.jnlp">0.7-fly.</a>,
<a href="0.7/phenote-zfin.jnlp">0.7-zfin</a><br>
<ul>
@@ -309,7 +308,7 @@
<h2>0.6
<hr></h2>
-07.28.2006, version <a href="0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="0.6/phenote-zfin.jnlp">0.6-zfin</a>,
+07.28.2006, version <a href="phenote/0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="phenote/0.6/phenote-zfin.jnlp">0.6-zfin</a>,
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
(0.6)</a><br>
@@ -328,7 +327,7 @@
<h2>0.5
<hr></h2>
-05.12.2006, version <a href="0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br>
+05.12.2006, version <a href="phenote/0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="phenote/0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br>
<p>
No new additions to the gui here. In preparation for my visit to
@@ -347,7 +346,7 @@
<h2>0.4
<hr></h2>
-04.26.2006, version <a href="0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
+04.26.2006, version <a href="phenote/0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="phenote/0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
<ul>
@@ -388,7 +387,7 @@
<h2>0.3
<hr></h2>
-04.07.2006, version <a href="0.3/phenote-webstart.jnlp">0.3</a>, <a href="0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a><br>
+04.07.2006, version <a href="phenote/0.3/phenote-webstart.jnlp">0.3</a>, <a href="phenote/0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a><br>
<p>Note: 0.3.1 is identical to 0.3 except that it has ontologies for CToL
(fish evolution group). In particular it uses a fish taxonomy<br>
@@ -445,7 +444,7 @@
<h2>0.2
<hr></h2>
-03.27.2006, version <a href="0.2/phenote-webstart.jnlp">0.2</a><br>
+03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a><br>
<ul>
@@ -465,7 +464,7 @@
<h2>0.1
<hr></h2>
-03.01.2006, version <a href="0.1/phenote-webstart.jnlp">0.1</a><br>
+03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a><br>
<p> 0.1 was the initial phenote release (known briefly as the plumper at
the time). It just had a genotype, anatomy and pato fields, where
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 05:26:49
|
Revision: 644
http://svn.sourceforge.net/obo/?rev=644&view=rev
Author: nlw
Date: 2007-05-29 22:26:51 -0700 (Tue, 29 May 2007)
Log Message:
-----------
fix broken link in header file for website
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-05-30 04:20:18 UTC (rev 643)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-05-30 05:26:51 UTC (rev 644)
@@ -11,7 +11,7 @@
<!-- TODO: need an icon -->
<link rel="icon" href="" type="image/png" />
<link rel="shortcut icon" href="" type="image/png" />
-<link rel="stylesheet" type="text/css" href="/phenote/css/style.css" title="standard" />
+<link rel="stylesheet" type="text/css" href="/css/style.css" title="standard" />
<script type="text/javascript" src="/javascript/obfuscate.js"></script>
<script type="text/javascript" src="/javascript/irc_script.js"></script>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-05-30 04:20:18
|
Revision: 643
http://svn.sourceforge.net/obo/?rev=643&view=rev
Author: nlw
Date: 2007-05-29 21:20:18 -0700 (Tue, 29 May 2007)
Log Message:
-----------
checking in changes to the toc after help from john
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS.TAB
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/OFFSETS
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/POSITIONS
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/SCHEMA
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/TMAP
phenote/trunk/doc/phenote-website/help/phenote.hhc
phenote/trunk/doc/phenote-website/help/toc.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/help/toc_generator.xsl
Modified: phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS
===================================================================
(Binary files differ)
Modified: phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS.TAB
===================================================================
--- phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS.TAB 2007-05-29 22:33:23 UTC (rev 642)
+++ phenote/trunk/doc/phenote-website/help/JavaHelpSearch/DOCS.TAB 2007-05-30 04:20:18 UTC (rev 643)
@@ -1,20 +1,46 @@
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|
From: <mg...@us...> - 2007-05-29 22:33:24
|
Revision: 642
http://svn.sourceforge.net/obo/?rev=642&view=rev
Author: mgibson
Date: 2007-05-29 15:33:23 -0700 (Tue, 29 May 2007)
Log Message:
-----------
took out obo-repository config for worm - no longer needed - pase
Modified Paths:
--------------
phenote/trunk/conf/worm.cfg
Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg 2007-05-29 22:27:03 UTC (rev 641)
+++ phenote/trunk/conf/worm.cfg 2007-05-29 22:33:23 UTC (rev 642)
@@ -21,9 +21,6 @@
<update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
- <obo-repository url-dir="http://www.berkeleybop.org/ontologies/obo-all/"/>
-
-
<field name="Object Type" enable="true"/>
<field name="Object Name" enable="true"/>
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|
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From: <azu...@us...> - 2007-05-29 22:27:04
|
Revision: 641
http://svn.sourceforge.net/obo/?rev=641&view=rev
Author: azurebrd
Date: 2007-05-29 15:27:03 -0700 (Tue, 29 May 2007)
Log Message:
-----------
Added URLs for OBO files off of a CGI on tazendra.caltech.edu instead of a
static file that's uploaded into Phenote. These OBO CGI files have a required
default-namespace header.
Modified Paths:
--------------
phenote/trunk/conf/worm.cfg
Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg 2007-05-29 22:14:18 UTC (rev 640)
+++ phenote/trunk/conf/worm.cfg 2007-05-29 22:27:03 UTC (rev 641)
@@ -28,14 +28,14 @@
<field name="Object Name" enable="true"/>
- <field name="Pub" enable="true">
- <ontology name="Pub" file="wbpaper.obo"/>
+ <field name="Pub" syntax-abbrev="T" enable="true">
+ <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/>
</field>
<field name="Reference Remark" syntax-abbrev="OtherRemark" enable="true"/>
- <field name="Person" enable="true">
- <ontology name="Person" file="wbperson.obo"/>
+ <field name="Person" syntax-abbrev="T" enable="true">
+ <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/>
</field>
<field name="NBP" syntax-abbrev="PhenotypeTextRemark" enable="true"/>
@@ -44,8 +44,8 @@
<field name="NOT" enable="true"/> <!-- Boolean checkbox -->
- <field name="Phenotype" enable="true">
- <ontology name="Phenotype" file="c_elegans_phenotype_ontology.obo"/>
+ <field name="Phenotype" syntax-abbrev="T" enable="true">
+ <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/>
</field>
<field name="Phenotype Remark" syntax-abbrev="PhenotypeRemark" enable="true"/>
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|
|
From: <nl...@us...> - 2007-05-29 22:14:16
|
Revision: 640
http://svn.sourceforge.net/obo/?rev=640&view=rev
Author: nlw
Date: 2007-05-29 15:14:18 -0700 (Tue, 29 May 2007)
Log Message:
-----------
adding jhindexer.jar... so that its included...it'll be called in the build
Added Paths:
-----------
phenote/trunk/jars/jhindexer.jar
Added: phenote/trunk/jars/jhindexer.jar
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/jars/jhindexer.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
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From: <nl...@us...> - 2007-05-29 18:32:49
|
Revision: 639
http://svn.sourceforge.net/obo/?rev=639&view=rev
Author: nlw
Date: 2007-05-29 11:32:09 -0700 (Tue, 29 May 2007)
Log Message:
-----------
adding jar to jars
Added Paths:
-----------
phenote/trunk/jars/jh.jar
Added: phenote/trunk/jars/jh.jar
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/jars/jh.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
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|
|
From: <mg...@us...> - 2007-05-25 19:16:47
|
Revision: 638
http://svn.sourceforge.net/obo/?rev=638&view=rev
Author: mgibson
Date: 2007-05-25 12:16:47 -0700 (Fri, 25 May 2007)
Log Message:
-----------
added master wipeout and subversion http override for birn2 so we can change config without having to do new release - nicole are you jiggy?
Modified Paths:
--------------
phenote/trunk/conf/birn2.cfg
Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg 2007-05-25 17:56:33 UTC (rev 637)
+++ phenote/trunk/conf/birn2.cfg 2007-05-25 19:16:47 UTC (rev 638)
@@ -5,6 +5,10 @@
description="A test for finding a config for BIRN so I can test annotate from their spreadsheet. It includes their converted brain subcellular anatomy ontology (SAO).">
<log config-file="conf/log4j-standalone.xml"/>
+ <!-- wipeout always means that the master will always wipeout the local copy
+ in this mode modifying the local is useless -->
+ <master-to-local-config mode="WIPEOUT" when="ALWAYS"
+ overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn2.cfg" />
<!-- ********************* FILE ADAPTERS ************************** -->
<!-- be sure to include at least one enabled file adapter -->
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From: <mg...@us...> - 2007-05-25 17:56:31
|
Revision: 637
http://svn.sourceforge.net/obo/?rev=637&view=rev
Author: mgibson
Date: 2007-05-25 10:56:33 -0700 (Fri, 25 May 2007)
Log Message:
-----------
Tagging the 1.3 (1.3 release) release of phenote - post comp bug, undo, * multi sel bug, config...
Added Paths:
-----------
phenote/tags/release-1.3/
Copied: phenote/tags/release-1.3 (from rev 636, phenote/trunk)
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|
From: <mg...@us...> - 2007-05-25 16:35:20
|
Revision: 636
http://svn.sourceforge.net/obo/?rev=636&view=rev
Author: mgibson
Date: 2007-05-25 09:35:21 -0700 (Fri, 25 May 2007)
Log Message:
-----------
woops forgot jnlp
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-05-25 16:30:49 UTC (rev 635)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-05-25 16:35:21 UTC (rev 636)
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<jnlp
spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/1.3-beta1"
+codebase="http://phenote.org/phenote/1.3"
href="phenote.jnlp">
<information>
- <title>Phenote 1.3-beta1</title>
+ <title>Phenote 1.3</title>
<vendor>National Center for Biomedial Ontology</vendor>
<description>Phenote standalone app via webstart</description>
<!-- Declares that the application can run without
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|
|
From: <mg...@us...> - 2007-05-25 16:30:47
|
Revision: 635
http://svn.sourceforge.net/obo/?rev=635&view=rev
Author: mgibson
Date: 2007-05-25 09:30:49 -0700 (Fri, 25 May 2007)
Log Message:
-----------
misc
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.html
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-05-25 16:25:32 UTC (rev 634)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-05-25 16:30:49 UTC (rev 635)
@@ -122,13 +122,9 @@
-<br>
-
-
-
-
After phenote downloads the java jar files (takes a while) it will ask
you what configuration you would like to use, fly, zfin, human,worm,birn....<br>
+<br>
@@ -139,11 +135,9 @@
+<a href="phenote-release-notes.html">Phenote Release Notes and old
+webstart releases</a><br>
<br>
-
-
-
-
Recent addditions include the ability to update config while preserving
your changes, change config, tab delimited format, tabbed field panel,
retrieve ontologies from web, retrieve from field to database, search
@@ -428,18 +422,6 @@
-<a href="phenote-release-notes.html">Phenote Release Notes and old
-webstart releases</a><br>
-
-
-
-
-
-
-
-
-
-
<br>
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|
|
From: <mg...@us...> - 2007-05-25 16:25:32
|
Revision: 634
http://svn.sourceforge.net/obo/?rev=634&view=rev
Author: mgibson
Date: 2007-05-25 09:25:32 -0700 (Fri, 25 May 2007)
Log Message:
-----------
phenote.html - i think this is being replaced by nicoles stuff...
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.html
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-05-25 16:06:17 UTC (rev 633)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-05-25 16:25:32 UTC (rev 634)
@@ -10,6 +10,7 @@
+
@@ -19,6 +20,7 @@
+
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
@@ -29,6 +31,7 @@
+
@@ -38,6 +41,7 @@
+
<title>Phenote</title>
</head>
@@ -52,6 +56,7 @@
+
<h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
@@ -62,6 +67,7 @@
+
</h1>
@@ -72,6 +78,7 @@
+
<br>
@@ -82,6 +89,7 @@
+
Phenote is a tool to annotate phenotypes using the Entity Quality
paradigm. It takes advantage of
ontologies. It uses term completion to allow curators quick access to
@@ -95,6 +103,7 @@
+
<br>
@@ -104,18 +113,22 @@
-<a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
+<a href="1.3/phenote.jnlp">Phenote 1.3</a><br>
+
+
<br>
+
<br>
+
After phenote downloads the java jar files (takes a while) it will ask
-you what configuration you would like to use, fly, zfin, human,worm....<br>
+you what configuration you would like to use, fly, zfin, human,worm,birn....<br>
@@ -125,10 +138,12 @@
+
<br>
+
Recent addditions include the ability to update config while preserving
your changes, change config, tab delimited format, tabbed field panel,
retrieve ontologies from web, retrieve from field to database, search
@@ -144,6 +159,7 @@
+
<br>
@@ -154,6 +170,7 @@
+
Zebrafish requires
components of phenote(to plug into their non-public
website), not a full web app. Here is a proof of concept of some of
@@ -168,6 +185,7 @@
+
<br>
@@ -178,6 +196,7 @@
+
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
@@ -189,6 +208,7 @@
+
<br>
@@ -199,9 +219,9 @@
-Webby phenote is a collaboration with Sohel Merchant at dictyBase.
-Here is what they have done:<br>
+Webby phenote is a collaboration with Sohel Merchant at dictyBase, and Christian Pich & Kevin Schaper at zfin.
+Here is what Dicty has done:<br>
@@ -210,6 +230,8 @@
+
+
<br>
@@ -220,6 +242,7 @@
+
<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase
webby phenote</a><br>
@@ -231,6 +254,7 @@
+
<br>
@@ -241,6 +265,7 @@
+
<br>
@@ -251,8 +276,8 @@
-We are doing these
-releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug
+
+We would love to get your feedback! Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug
tracker</a>) and let us know what you
think (email:<a href="mailto:mg...@be..."> mg...@be...</a>, email list: <a href="mailto:obo...@li...">obo...@li...</a>).<br>
@@ -264,12 +289,11 @@
+
<br>
-In development - the bleeding edge if you will:<br>
-<a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br>
@@ -277,9 +301,9 @@
+<h4>Phenote links:<br>
-<h4>Phenote links:<br>
@@ -288,7 +312,6 @@
-
</h4>
@@ -299,6 +322,7 @@
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
email list</a><br>
@@ -310,6 +334,7 @@
+
<a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote
bug tracker</a><br>
@@ -321,6 +346,7 @@
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
tracker email list</a><br>
@@ -332,6 +358,7 @@
+
<a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
code (obo sourceforge svn)</a><br>
@@ -343,6 +370,7 @@
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
svn commit email list</a><br>
@@ -354,6 +382,7 @@
+
<a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty
webby phenote wiki developer docs</a><br>
@@ -365,15 +394,18 @@
+
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
ncbo internal wiki (ncbo folk only)</a><br>
+
<a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br>
+
<a href="developer-docs/developer-docs.html">More developer docs</a><br>
@@ -384,6 +416,7 @@
+
<br>
@@ -394,6 +427,7 @@
+
<a href="phenote-release-notes.html">Phenote Release Notes and old
webstart releases</a><br>
@@ -405,6 +439,7 @@
+
<br>
@@ -415,6 +450,7 @@
+
If the Phenote webstart link fails to do anything, then there are
probably problems
with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
@@ -427,6 +463,7 @@
+
page.<br>
@@ -437,6 +474,7 @@
+
<br>
@@ -447,6 +485,7 @@
+
Click here for <a href="phenote-java-requirements.html">phenote java
requirements</a><br>
@@ -458,6 +497,7 @@
+
<br>
@@ -468,6 +508,7 @@
+
<br>
@@ -478,6 +519,7 @@
+
<br>
@@ -488,6 +530,7 @@
+
Old releases: <br>
@@ -498,8 +541,12 @@
+
+<a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br>
+<a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
<a href="1.1/phenote.jnlp">Phenote 1.1</a><br>
+
<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
@@ -510,6 +557,7 @@
+
<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
@@ -519,6 +567,7 @@
+
<a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br>
@@ -526,6 +575,7 @@
+
<br>
@@ -536,6 +586,7 @@
+
<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
@@ -546,6 +597,7 @@
+
<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
@@ -555,6 +607,7 @@
+
<br>
@@ -564,6 +617,7 @@
+
<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
@@ -574,6 +628,7 @@
+
<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
@@ -584,6 +639,7 @@
+
<br>
@@ -594,6 +650,7 @@
+
<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
@@ -604,6 +661,7 @@
+
<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
@@ -614,6 +672,7 @@
+
<br>
@@ -624,6 +683,7 @@
+
<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
@@ -634,6 +694,7 @@
+
<br>
@@ -644,6 +705,7 @@
+
<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
@@ -654,6 +716,7 @@
+
<br>
@@ -664,6 +727,7 @@
+
<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
@@ -674,6 +738,7 @@
+
<br>
@@ -684,6 +749,7 @@
+
<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
@@ -694,6 +760,7 @@
+
<br>
@@ -704,6 +771,7 @@
+
<a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
@@ -714,6 +782,7 @@
+
<br>
@@ -724,6 +793,7 @@
+
<a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
@@ -734,6 +804,7 @@
+
<br>
@@ -744,6 +815,7 @@
+
<a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>
(a special release for the CToL group that uses fish
taxonomy)<br>
@@ -756,6 +828,7 @@
+
<br>
@@ -766,6 +839,7 @@
+
<a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
@@ -776,6 +850,7 @@
+
<br>
@@ -786,6 +861,7 @@
+
<a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
@@ -796,6 +872,7 @@
+
<br>
@@ -806,6 +883,7 @@
+
<a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
@@ -816,6 +894,7 @@
+
<br>
@@ -826,6 +905,7 @@
+
<br>
@@ -836,5 +916,6 @@
+
</body>
</html>
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|
|
From: <mg...@us...> - 2007-05-25 16:06:18
|
Revision: 633
http://svn.sourceforge.net/obo/?rev=633&view=rev
Author: mgibson
Date: 2007-05-25 09:06:17 -0700 (Fri, 25 May 2007)
Log Message:
-----------
version 1.3 release
Modified Paths:
--------------
phenote/trunk/src/java/phenote/main/PhenoteVersion.java
Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-05-25 16:01:26 UTC (rev 632)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-05-25 16:06:17 UTC (rev 633)
@@ -9,7 +9,7 @@
//private static final float MAJOR_VERSION_NUM = 0.8f;
//private static final float SUB_VERSION_NUM = .3f;
- private static final String VERSION = "1.3-beta2"; // ??
+ private static final String VERSION = "1.3 release"; // ??
// type is "dev" or "release"
//private static final String type = " dev"; // "release"
@@ -19,7 +19,7 @@
}
public static Date getDateOfVersion(){
- GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.MAY, 9);
+ GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.MAY, 25);
return cal.getTime();
}
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From: <mg...@us...> - 2007-05-25 16:01:26
|
Revision: 632
http://svn.sourceforge.net/obo/?rev=632&view=rev
Author: mgibson
Date: 2007-05-25 09:01:26 -0700 (Fri, 25 May 2007)
Log Message:
-----------
added bug fix for post comp
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-release-notes.html
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-25 01:22:30 UTC (rev 631)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-25 16:01:26 UTC (rev 632)
@@ -1,172 +1,335 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
+
-<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+ <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
-<title>Phenote Release Notes</title>
+
+ <title>Phenote Release Notes</title>
</head>
+
<body>
+
<h1>Phenote Release Notes</h1>
-<h2>1.3<hr></h2>
-in development, 1.3-beta2 <br>
+<h2>1.3
+<hr></h2>
+
+
+in development, 1.3-beta2 -> 1.3 release<br>
+
<ul>
+
<li>feature: Web-based documentation and Help features</li>
- <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
-<li>feature: Descriptions can be added for fields </li>
-<li>feature: Master-to-local overwrite stuff</li>
-<li>feature: Dialog allows user to back out of exiting from File->Exit</li>
-<li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
-<li>feature: User can save search setting defaults if changed during Phenote session</li>
+
+ <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
+
+ <li>feature: Descriptions can be added for fields </li>
+
+ <li>feature: Master-to-local overwrite stuff</li>
+
+ <li>feature: Dialog allows user to back out of exiting from File->Exit</li>
+
+ <li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
+ </li>
+ <li>feature: User can save search setting defaults if changed during Phenote session</li>
+
<li>change: File->New is disabled until next version</li>
- <li>change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments </li>
-<li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
+
+ <li>change: ncbo, zfin-standalone, flybase, demo configurations
+modified to include master-overwrite feature; keeping track of revision
+history in file comments </li>
+
+ <li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
+
<li>bugfix: Bulk-editing functions are working again</li>
- <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
-<li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
+
+ <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
+
+ <li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
+ <li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li>
+
</ul>
+
05.09.2007, version <a href="1.3-beta1/phenote.jnlp">1.3-beta1</a><br>
+
<ul>
+
<li>feature: Added sample config for BIRN</li>
+
<li>feature: Added SAO.obo ontology for BIRN</li>
+
<li>feature: Namespace config writes back</li>
+
<li>feature: Can specify more than one website for ontology update</li>
+
<li>feature: Empty field shows all terms in ontology rather than none</li>
+
<li>feature: Can add more differentia to post comp</li>
+
<li>bugfix: Config update/merge bug where fields in wrong order fixed.</li>
-<li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
+ <li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
+
+
</ul>
-<h2>1.2<hr></h2>
+
+<h2>1.2
+<hr></h2>
+
05.02.2007, version <a href="1.2/phenote.jnlp">1.2</a><br>
+
<ul>
+
<li>feature: Can post-compose with >2 terms </li>
+
<li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li>
-<li>feature: Synonyms delineated by scope in Term Info: Exact, Narrow, Broad, General, Related. If the synonym category is given, it is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
-<li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
-<li>feature: Loading splash screen </li>
-<li>feature: Can configure by namespace for ontologies</li>
-<li>feature: Can automatically update ontologies during startup (configurable)</li>
-<li>feature: Timer added to configuration during ontology update check (configurable)</li>
-<li>feature: Can check which version of phenote is running by selecting Help->About.</li>
-<li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
-<li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
-<li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
-<li>change: Search filters moved into menu </li>
-<li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
-<li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
+
+ <li>feature: Synonyms delineated by scope in Term Info: Exact,
+Narrow, Broad, General, Related. If the synonym category is given, it
+is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
+
+ <li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
+
+ <li>feature: Loading splash screen </li>
+
+ <li>feature: Can configure by namespace for ontologies</li>
+
+ <li>feature: Can automatically update ontologies during startup (configurable)</li>
+
+ <li>feature: Timer added to configuration during ontology update check (configurable)</li>
+
+ <li>feature: Can check which version of phenote is running by selecting Help->About.</li>
+
+ <li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
+
+ <li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
+
+ <li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
+
+ <li>change: Search filters moved into menu </li>
+
+ <li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
+
+ <li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
+
</ul>
-<h2>1.1<hr></h2>
+
+<h2>1.1
+<hr></h2>
+
04.06.2007, version <a href="1.1/phenote.jnlp">1.1.3</a><br>
+
<ul>
-<li>feature: User can change the configuration they want to use at initialization from file menu; change takes effect after restart. (previously user had to edit the .phenote/conf/my-phenote file).</li>
+
+ <li>feature: User can change the configuration they want to use at
+initialization from file menu; change takes effect after restart.
+(previously user had to edit the .phenote/conf/my-phenote file).</li>
+
</ul>
+
03.28.2007, version 1.1.1<br>
+
<ul>
- <li>feature: Phenote is now a single webstart app; user chooses their configuration at startup (used to be hard wired to a configuration)</li>
-<li>feature: Phenote will merge its default configuration with users' configuration,
+
+ <li>feature: Phenote is now a single webstart app; user chooses
+their configuration at startup (used to be hard wired to a
+configuration)</li>
+
+ <li>feature: Phenote will merge its default configuration with users' configuration,
preserving user changes as well as adding anything new from phenote
upgrade.</li>
-<li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
-<li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
-<li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
-<li>feature: QueryableDataAdapter interface for developers; enables connection between input fields and a database backend for quering. Queryable fields get a retrieve button.</li>
-<li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
-<li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
-<li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
-<li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
-<li>change: Refactored code for field guis</li>
-<li>change: Layout improved</li>
-<li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
-<li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
-<li>bugfix: Ontology chooser reflects current term</li>
-<li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
-<li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
+
+ <li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
+
+ <li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
+
+ <li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
+
+ <li>feature: QueryableDataAdapter interface for developers; enables
+connection between input fields and a database backend for quering.
+Queryable fields get a retrieve button.</li>
+
+ <li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
+
+ <li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
+
+ <li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
+
+ <li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
+
+ <li>change: Refactored code for field guis</li>
+
+ <li>change: Layout improved</li>
+
+ <li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
+
+ <li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
+
+ <li>bugfix: Ontology chooser reflects current term</li>
+
+ <li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
+
+ <li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
+
</ul>
-<h2>1.0<hr></h2>
+
+<h2>1.0
+<hr></h2>
+
02.06.2007, version <a href="1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a><br>
+
01.12.2007, version1.0,
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
+
<ul>
- <li>change: refactoring of the data model to allow addition of any field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description, Abnormal, and Absent have been added through this new mechanism in the newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
+
+ <li>change: refactoring of the data model to allow addition of any
+field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description,
+Abnormal, and Absent have been added through this new mechanism in the
+newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
+
<li>change: Webby phenote is now using JSP and Spring.</li>
+
<li>change: There has been some recent work with UVictoria for ontology graph
visualization. This is coming along well and hopefully will be seen in
the next release.</li>
-<li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
+
+ <li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
+
</ul>
-<h2>0.9<hr></h2>
+
+<h2>0.9
+<hr></h2>
+
11.15.2006, version <a href="0.9/phenote-flybase.jnlp">0.9-fly</a>,
<a href="0.9/phenote-zfin.jnlp">0.9-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
webby phenote</a><br>
+
11.09.2006, version 0.9<br>
+
<ul>
+
<li>feature: Undo - can step backward through previous actions</li>
- <li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li>
-<li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li>
-<li>feature: Synonyms are displayed from autocomplete with [syn]; when
+
+ <li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li>
+
+ <li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li>
+
+ <li>feature: Synonyms are displayed from autocomplete with [syn]; when
selected the term name (not the synonym) goes into the field and table (webby & standalone)</li>
-<li>feature: obsoletes are displayed from autocomplete with [obs]</li>
-<li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li>
-<li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li>
-<li>bugfix: file-save button changed to say "save" not "load"
-<li>feature: file-save recognizes and chooses appropriate data adapter based on file extension (.psx for phenosyntax and .xml for phenoxml)</li>
-<li>change: Single quotes escaped for javascript fns.</li>
+
+ <li>feature: obsoletes are displayed from autocomplete with [obs]</li>
+
+ <li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li>
+
+ <li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li>
+
+ <li>bugfix: file-save button changed to say "save" not "load"
+ </li>
+ <li>feature: file-save recognizes and chooses appropriate data
+adapter based on file extension (.psx for phenosyntax and .xml for
+phenoxml)</li>
+
+ <li>change: Single quotes escaped for javascript fns.</li>
+
</ul>
-<h2>0.8<hr></h2>
+
+<h2>0.8
+<hr></h2>
+
10.02.2006, version <a href="0.8/phenote-flybase.jnlp">0.8-fly</a>,
<a href="0.8/phenote-zfin.jnlp">0.8-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
webby phenote</a><br>
+
<ul>
+
<li>feature: Added post composition to standalone phenote. </li>
+
<li>feature: Actions are logged for both webby/servlet & standalone.</li>
+
<li>feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
writer (does pub & genetic context)</li>
-<li> feature: Command line reading & writing of phenoxml & phenosyntax.</li>
-<li>feature: Application exits on window exit (unless servlet)</li>
-<li>feature: Can filter out stage terms from zfin anatomy</li>
+
+ <li> feature: Command line reading & writing of phenoxml & phenosyntax.</li>
+
+ <li>feature: Application exits on window exit (unless servlet)</li>
+
+ <li>feature: Can filter out stage terms from zfin anatomy</li>
+
</ul>
-<h2>0.7<hr></h2>
+
+<h2>0.7
+<hr></h2>
+
08.23.2007, version <a href="0.7/phenote-flybase.jnlp">0.7-fly.</a>,
<a href="0.7/phenote-zfin.jnlp">0.7-zfin</a><br>
+
<ul>
+
<li>feature: entity chooser (web)</li>
+
<li>feature: can configure to check for new obo files and load
them. (These are installed at zfin, if anyone would like to see them
publicly let me know).</li>
-<li>feature: entity field and term info installed into zfin (web)
+
+ <li>feature: entity field and term info installed into zfin (web)
phenotype site. Term info & completion are scrollable.</li>
-<li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li>
-<li>feature: standalone entity chooser</li>
-<li>feature: added pub field</li>
-<li>feature: added 'use term' button in term info</li>
-<li>feature: can sort table by any field in forward order by clicking on headers</li>
-<li>change: personal config file gets copied out of jar
-<li>change: directory for file load/save remembered</li>
-<li>change: layout fixed</li>
-<li>bugfix: paste for mac fixed</li>
+
+ <li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li>
+
+ <li>feature: standalone entity chooser</li>
+
+ <li>feature: added pub field</li>
+
+ <li>feature: added 'use term' button in term info</li>
+
+ <li>feature: can sort table by any field in forward order by clicking on headers</li>
+
+ <li>change: personal config file gets copied out of jar
+ </li>
+ <li>change: directory for file load/save remembered</li>
+
+ <li>change: layout fixed</li>
+
+ <li>bugfix: paste for mac fixed</li>
+
</ul>
-<h2>0.6<hr></h2>
+
+<h2>0.6
+<hr></h2>
+
07.28.2006, version <a href="0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="0.6/phenote-zfin.jnlp">0.6-zfin</a>,
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
(0.6)</a><br>
+
<ul>
- <li>new: webbified phenote. This is in its extremely early stages (very little functionality and buggy). At this point it only does Entity and Quality fields and term info and thats it, and even thats buggy, but more coming soon! </li>
-<li> feature: writing pheno-xml format, and uses the latest
+
+ <li>new: webbified phenote. This is in its extremely early stages
+(very little functionality and buggy). At this point it only does
+Entity and Quality fields and term info and thats it, and even thats
+buggy, but more coming soon! </li>
+
+ <li> feature: writing pheno-xml format, and uses the latest
PATO ontology (as of July 28, 2006).</li>
+
</ul>
-<h2>0.5<hr></h2>
+
+<h2>0.5
+<hr></h2>
+
05.12.2006, version <a href="0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br>
+
<p>
No new additions to the gui here. In preparation for my visit to
Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote
@@ -180,70 +343,130 @@
FlyBase character wrappers that do the parsing and creating of Proforma
character strings.</p>
-<h2>0.4<hr></h2>
+
+<h2>0.4
+<hr></h2>
+
04.26.2006, version <a href="0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
+
<ul>
+
<li>feature: Added Genetic Context field.</li>
+
<li>feature: Parent & child terms in term info are now clickable/navigable.</li>
+
<li>feature: HTML Links in descriptions are clickable (should bring up default browser)</li>
-<li>feature: configuration files to configure ontologies & fields. This is
+
+ <li>feature: configuration files to configure ontologies & fields. This is
currently at a devloper level (xml file) not a user level(gui - todo).
There is a command line argument for which configuration file to use.
This allows for having separate zf & fb releases without having to
change the code to do it (like was done for the ctol release). The
configuration for now is for developers (internal xml file), on the
todo is to have a gui configuration for users.</li>
-<li>bugfix: can't delete to 0 rows</li>
-<li>bugfix: synonym search duplicates removed</li>
-<li>Development: Refactored for configuration & adding field. Made the internal code much more generic for adding new fields from configuration, got rid of a lot of hard wiring. Part of this was instituring model-view-controller in some places where views were improperly talking to other views. In theory this should also make it easier to plop a web gui on top of the current phenote model & controller.</li>
-<li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li>
-<li>Development: Added tests to test suite.</li>
+ <li>bugfix: can't delete to 0 rows</li>
+
+ <li>bugfix: synonym search duplicates removed</li>
+
+ <li>Development: Refactored for configuration & adding field.
+Made the internal code much more generic for adding new fields from
+configuration, got rid of a lot of hard wiring. Part of this was
+instituring model-view-controller in some places where views were
+improperly talking to other views. In theory this should also make it
+easier to plop a web gui on top of the current phenote model &
+controller.</li>
+
+ <li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li>
+
+ <li>Development: Added tests to test suite.</li>
+
+
</ul>
-<h2>0.3<hr></h2>
+
+<h2>0.3
+<hr></h2>
+
04.07.2006, version <a href="0.3/phenote-webstart.jnlp">0.3</a>, <a href="0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a><br>
+
<p>Note: 0.3.1 is identical to 0.3 except that it has ontologies for CToL
(fish evolution group). In particular it uses a fish taxonomy<br>
+
ontology for the id (in this taxonomy) choosing. On the todo is the
ability to configure ontologies, but not there yet, so for now need to
hardwire with seaparate jar file. This clearly makes the todo item a
bit more pressing.</p>
+
<p> Release for NESCent fish eveolution meeting. No major new functionality
here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather
buggy.</p>
+
<ul>
+
<li>feature: Completion terms now sorted alphabeitcally.</li>
+
<li>feature: Obsoletes are now in addition to regular terms, not in lieu of.</li>
+
<li>feature: Filtering out attribute values (todo: change to actually filter in
values)</li>
-<li>change: Html formatting of term info (todo: make terms selectable)</li>
-<li>feature: Children relations are in term info</li>
-<li>change: Term info layout greatly improved</li>
-<li>change: Term info in scroller</li>
-<li>change: Border with label around term info</li>
-<li>change: Put definition at end of term info</li>
-<li>bugfix: Backspace in ontology combo box</li>
-<li>bugfix: Selection of item in comp list causing exception, not going in term box</li>
-<li>bugfix: No terms with just 1 char</li>
-<li>bugfix: Popup was staying up after selection</li>
-<li>development: Test suite added! (todo: add more tests)</li>
-<li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li>
-<li>development: Ant file made build.xml.</li>
-<li>development: CompletionList refactored into Ontology (prompted by sorting)</li>
+
+ <li>change: Html formatting of term info (todo: make terms selectable)</li>
+
+ <li>feature: Children relations are in term info</li>
+
+ <li>change: Term info layout greatly improved</li>
+
+ <li>change: Term info in scroller</li>
+
+ <li>change: Border with label around term info</li>
+
+ <li>change: Put definition at end of term info</li>
+
+ <li>bugfix: Backspace in ontology combo box</li>
+
+ <li>bugfix: Selection of item in comp list causing exception, not going in term box</li>
+
+ <li>bugfix: No terms with just 1 char</li>
+
+ <li>bugfix: Popup was staying up after selection</li>
+
+ <li>development: Test suite added! (todo: add more tests)</li>
+
+ <li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li>
+
+ <li>development: Ant file made build.xml.</li>
+
+ <li>development: CompletionList refactored into Ontology (prompted by sorting)</li>
+
</ul>
-<h2>0.2<hr></h2>
+
+<h2>0.2
+<hr></h2>
+
03.27.2006, version <a href="0.2/phenote-webstart.jnlp">0.2</a><br>
+
<ul>
+
<li>feature: term completion on Synonyms, Definitions and Obsoletes</li>
+
<li>feature: mouse-over on term in completion list displays info in 'term info' text area</li>
-<li>Todo: layout, scrollbar, border w title, ordering & lumping parents
-& children, formatting. Also perhaps have children & parents be clickable in some fashion either html-like clickable text or as buttons.</li>
-<li>known bugs: If you hit backspace in term completion fields it gets wacky </li>
+
+ <li>Todo: layout, scrollbar, border w title, ordering & lumping
+parents
+& children, formatting. Also perhaps have children & parents be
+clickable in some fashion either html-like clickable text or as buttons.</li>
+
+ <li>known bugs: If you hit backspace in term completion fields it gets wacky </li>
+
</ul>
-<h2>0.1<hr></h2>
+
+<h2>0.1
+<hr></h2>
+
03.01.2006, version <a href="0.1/phenote-webstart.jnlp">0.1</a><br>
+
<p> 0.1 was the initial phenote release (known briefly as the plumper at
the time). It just had a genotype, anatomy and pato fields, where
anatomy and pato did term completion (just on term names) with there
@@ -251,5 +474,6 @@
tracked phenotype instances being edited in the above fields. This very
limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.</p>
+
</body>
</html>
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|
|
From: <nl...@us...> - 2007-05-25 01:22:30
|
Revision: 631
http://svn.sourceforge.net/obo/?rev=631&view=rev
Author: nlw
Date: 2007-05-24 18:22:30 -0700 (Thu, 24 May 2007)
Log Message:
-----------
added search param default settings to these files; updated release notes with the config file changes
Modified Paths:
--------------
phenote/trunk/conf/demo.cfg
phenote/trunk/conf/flybase.cfg
phenote/trunk/conf/ncbo.cfg
phenote/trunk/conf/zfin-standalone.cfg
phenote/trunk/doc/phenote-website/phenote-release-notes.html
Modified: phenote/trunk/conf/demo.cfg
===================================================================
--- phenote/trunk/conf/demo.cfg 2007-05-25 01:02:40 UTC (rev 630)
+++ phenote/trunk/conf/demo.cfg 2007-05-25 01:22:30 UTC (rev 631)
@@ -16,6 +16,7 @@
<!--true=update; false=don't update-->
<ns:update-timer timer="0"/>
<!--set to 0 if you want to bypass the check; time in seconds-->
+ <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
<!-- ********************* FILE ADAPTERS ************************** -->
<!-- be sure to include at least one enabled file adapter -->
@@ -73,6 +74,7 @@
<!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo; included ehdaa repository;
removed obo-repository url-dir and incorporated into each filename; added in comments;
Changed GO to gene_ontology_edit.obo file;
- Added in local-to-master overwrite config to ALWAYS overwrite -->
+ Added in local-to-master overwrite config to ALWAYS overwrite
+ Added in autocompletion settings; Term&Synonym is default -->
</ns:phenote-configuration>
\ No newline at end of file
Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg 2007-05-25 01:02:40 UTC (rev 630)
+++ phenote/trunk/conf/flybase.cfg 2007-05-25 01:22:30 UTC (rev 631)
@@ -16,7 +16,9 @@
<ns:auto-update-ontologies enable="false"/> <!--true=update; false=don't update-->
<ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
+ <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+
<!-- ********************* FILE ADAPTERS ************************** -->
<ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter"
enable="true"/>
Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg 2007-05-25 01:02:40 UTC (rev 630)
+++ phenote/trunk/conf/ncbo.cfg 2007-05-25 01:22:30 UTC (rev 631)
@@ -15,6 +15,7 @@
<ns:term-history enable="false"/>
<ns:auto-update-ontologies enable="true"/> <!--true=update; false=don't update-->
<ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
+ <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
<!-- ********************* FILE ADAPTERS ************************** -->
Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg 2007-05-25 01:02:40 UTC (rev 630)
+++ phenote/trunk/conf/zfin-standalone.cfg 2007-05-25 01:22:30 UTC (rev 631)
@@ -14,7 +14,9 @@
<ns:term-history enable="false"/>
<ns:auto-update-ontologies enable="true"/> <!--true=update; false=don't update-->
<ns:update-timer timer="4"/><!--set to 0 if you want to bypass the check; time in seconds-->
+ <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+
<!-- ********************* FILE ADAPTERS ************************** -->
<ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter"
enable="true"/>
@@ -70,6 +72,7 @@
<!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo;
removed obo-repository url-dir and incorporated into each filename; added in comments;
removed the nexus adapter...it won't ever be used by this group.
- Changed GO to gene_ontology_edit.obo file (nlw) -->
+ Changed GO to gene_ontology_edit.obo file (nlw)
+ Added in autocompletion setting defaults; Terms&Synonyms -->
</ns:phenote-configuration>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-25 01:02:40 UTC (rev 630)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-25 01:22:30 UTC (rev 631)
@@ -14,10 +14,12 @@
in development, 1.3-beta2 <br>
<ul>
<li>feature: Web-based documentation and Help features</li>
- <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author</li>
-<li>feature: Descriptions can be added for fields</li>
+ <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
+<li>feature: Descriptions can be added for fields </li>
<li>feature: Master-to-local overwrite stuff</li>
<li>feature: Dialog allows user to back out of exiting from File->Exit</li>
+<li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
+<li>feature: User can save search setting defaults if changed during Phenote session</li>
<li>change: File->New is disabled until next version</li>
<li>change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments </li>
<li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
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|
|
From: <nl...@us...> - 2007-05-25 01:02:38
|
Revision: 630
http://svn.sourceforge.net/obo/?rev=630&view=rev
Author: nlw
Date: 2007-05-24 18:02:40 -0700 (Thu, 24 May 2007)
Log Message:
-----------
*oops...a typo in one of the dialogs is fixed
Modified Paths:
--------------
phenote/trunk/src/java/phenote/gui/FileMenu.java
Modified: phenote/trunk/src/java/phenote/gui/FileMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/FileMenu.java 2007-05-25 00:59:29 UTC (rev 629)
+++ phenote/trunk/src/java/phenote/gui/FileMenu.java 2007-05-25 01:02:40 UTC (rev 630)
@@ -119,6 +119,7 @@
Config.inst().setAutocompleteSettings();
//write out configuration!
Config.inst().saveModifiedConfig();
+ m="";
}
else {
m="Your changes have not been saved.\n";
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|
|
From: <nl...@us...> - 2007-05-25 00:59:52
|
Revision: 629
http://svn.sourceforge.net/obo/?rev=629&view=rev
Author: nlw
Date: 2007-05-24 17:59:29 -0700 (Thu, 24 May 2007)
Log Message:
-----------
*Added in autocompletion getting/setting from the config file; shows up in menu options; will flag user at exit if settings have changed and prompt for save; will save settings to file with same config name in .phenote/conf dir.
*Note, there is a general flag for if settings have changed. This is what i use to determine changes at the time of exit.
*Also, user can now return to program if they don't want to exit. (changed from simple message to option dialog)
*Note, this only works from File->Exit menu item, doesn't work yet from the closewindow or kill.
Modified Paths:
--------------
phenote/trunk/src/java/phenote/config/Config.java
phenote/trunk/src/java/phenote/config/ConfigWriter.java
phenote/trunk/src/java/phenote/gui/FileMenu.java
phenote/trunk/src/java/phenote/gui/SearchParams.java
phenote/trunk/src/java/phenote/gui/SettingsMenu.java
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java 2007-05-24 21:12:55 UTC (rev 628)
+++ phenote/trunk/src/java/phenote/config/Config.java 2007-05-25 00:59:29 UTC (rev 629)
@@ -12,6 +12,7 @@
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
+import java.lang.Enum;
import org.apache.xmlbeans.XmlException;
@@ -29,12 +30,15 @@
import phenote.config.xml.AutoUpdateOntologiesDocument.AutoUpdateOntologies;
import phenote.config.xml.UpdateTimerDocument.UpdateTimer;
import phenote.config.xml.MasterToLocalConfigDocument.MasterToLocalConfig;
+import phenote.config.xml.AutocompleteSettingsDocument.AutocompleteSettings;
import phenote.dataadapter.DataAdapterI;
import phenote.dataadapter.QueryableDataAdapterI;
import phenote.datamodel.CharField;
import phenote.datamodel.CharFieldEnum;
import phenote.util.FileUtil;
+import phenote.gui.SearchFilterType;
+import phenote.gui.SearchParams;
public class Config {
@@ -65,6 +69,9 @@
private PhenoteConfiguration phenoConfigBean; // cache the xml parse bean??
private boolean configInitialized = false;
+ private boolean configModified = false;
+ //flag for if any settings during session have changed, such as search params, col widths, etc.
+
private final static String myphenoteFile = "my-phenote";
public static Config inst() {
@@ -74,7 +81,20 @@
private Config() {}
public boolean isInitialized() { return configInitialized; }
+
+ public boolean isConfigModified() { return configModified; }
+ public void setConfigModified(boolean setting) { configModified = setting; }
+ public void saveModifiedConfig() {
+ // this is the "species" conf file - eg ~/.phenote/conf/flybase.cfg
+ System.out.println(configFile);
+ File localFile = new File(configFile);
+
+ new ConfigWriter().writeConfig(this,localFile);
+
+ setConfigModified(false); //in case if the person doesn't quit
+ return;
+ }
/** This is setting config file with nothing to do with personal config
this is for the servlet where config file location is set in web.xml */
public void setConfigFile(String configFile) throws ConfigException {
@@ -599,6 +619,29 @@
}
return u;
}
+
+ public AutocompleteSettings getAutocompleteSettings() {
+ // boolean[] temp;
+ AutocompleteSettings s = phenoConfigBean.getAutocompleteSettings();
+ if (s==null) {
+ //set defaults if not in configuration file
+ s = phenoConfigBean.addNewAutocompleteSettings();
+ s.setTerm(true);
+ s.setSynonym(true);
+ s.setDefinition(false);
+ s.setObsolete(false);
+ }
+ return s;
+ }
+
+ public void setAutocompleteSettings() {
+ SearchParams searchParams = SearchParams.inst();
+ getAutocompleteSettings().setTerm(searchParams.getParam(SearchFilterType.TERM));
+ getAutocompleteSettings().setSynonym(searchParams.getParam(SearchFilterType.SYN));
+ getAutocompleteSettings().setDefinition(searchParams.getParam(SearchFilterType.DEF));
+ getAutocompleteSettings().setObsolete(searchParams.getParam(SearchFilterType.OBS));
+ }
+
public URL getLogConfigUrl() throws FileNotFoundException {
return FileUtil.findUrl(getLogConfigFile());
Modified: phenote/trunk/src/java/phenote/config/ConfigWriter.java
===================================================================
--- phenote/trunk/src/java/phenote/config/ConfigWriter.java 2007-05-24 21:12:55 UTC (rev 628)
+++ phenote/trunk/src/java/phenote/config/ConfigWriter.java 2007-05-25 00:59:29 UTC (rev 629)
@@ -47,7 +47,8 @@
//addFields();
try { // xmlOptions? pretty print
- doc.save(file,getXmlOptions()); }
+ doc.save(file,getXmlOptions());
+ System.out.println("Saved changes to config file "+file);}
catch (IOException e) {
System.out.println("Failed to save config file "+e); }
}
Modified: phenote/trunk/src/java/phenote/gui/FileMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/FileMenu.java 2007-05-24 21:12:55 UTC (rev 628)
+++ phenote/trunk/src/java/phenote/gui/FileMenu.java 2007-05-25 00:59:29 UTC (rev 629)
@@ -109,11 +109,32 @@
private class ExitActionListener implements ActionListener {
public void actionPerformed(ActionEvent e) {
+ String m = "";
+ int n;
if (e.getActionCommand().equals("exit")) {
- String m = "Are you sure you want to quit?";
- JOptionPane.showMessageDialog(null, m, "Phenote Exit",
- JOptionPane.INFORMATION_MESSAGE);
- System.exit(0);
+ if (Config.inst().isConfigModified()) {
+ m="Your Default Settings have been modified. Do you wish to save them?";
+ n = JOptionPane.showConfirmDialog(null,m,"Configuration Alert", JOptionPane.YES_NO_OPTION);
+ if (n==JOptionPane.YES_OPTION) {
+ Config.inst().setAutocompleteSettings();
+ //write out configuration!
+ Config.inst().saveModifiedConfig();
+ }
+ else {
+ m="Your changes have not been saved.\n";
+ }
+ }
+// else {
+// System.out.println("your settings have not changed");
+// }
+
+ m += "Are you sure you want to quit?";
+ n = JOptionPane.showConfirmDialog(null, m, "Phenote Exit",
+ JOptionPane.YES_NO_OPTION);
+ if (n==JOptionPane.YES_OPTION) {
+ System.exit(0);
+ } else { return; }
+
}
}
}
Modified: phenote/trunk/src/java/phenote/gui/SearchParams.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SearchParams.java 2007-05-24 21:12:55 UTC (rev 628)
+++ phenote/trunk/src/java/phenote/gui/SearchParams.java 2007-05-25 00:59:29 UTC (rev 629)
@@ -5,6 +5,7 @@
public class SearchParams implements SearchParamsI {
private static SearchParams singleton;
+ //want to set these from the configuration file defaults
private boolean searchTerm = true; //false; default true??
private boolean searchSyn = true; // false; default true?
private boolean searchDef = false;
@@ -52,6 +53,23 @@
}
return true;
}
+
+// public boolean[] getAllParams() {
+// boolean[] temp;
+// for (SearchFilterType i : SearchFilterType.values()) {
+// if (i==SearchFilterType.TERM) {
+// temp[i.ordinal()]=searchTerm;
+// } else if (i==SearchFilterType.SYN) {
+// temp[i.ordinal()]=searchSyn;
+// } else if (i==SearchFilterType.DEF) {
+// temp[i.ordinal()]=searchDef;
+// } else if (i==SearchFilterType.OBS) {
+// temp[i.ordinal()]=searchObs;
+// }
+// }
+// return temp;
+// }
+
public boolean searchTerms() {
return searchTerm;
Modified: phenote/trunk/src/java/phenote/gui/SettingsMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SettingsMenu.java 2007-05-24 21:12:55 UTC (rev 628)
+++ phenote/trunk/src/java/phenote/gui/SettingsMenu.java 2007-05-25 00:59:29 UTC (rev 629)
@@ -24,6 +24,7 @@
private JMenuItem showHistory;
public SearchParams searchParams;
private SelectionHistory selHist = SelectionHistory.inst();
+ private Config config = Config.inst();
SettingsMenu() {
@@ -39,10 +40,15 @@
//set defaults - these are actually the same as SearchParams defaults but it
// doesnt hurt to be sure
- getSearchParams().setParam(SearchFilterType.TERM, true); //default Term = on
- getSearchParams().setParam(SearchFilterType.SYN, true); //default Syn = on
- getSearchParams().setParam(SearchFilterType.DEF, false); //default Def = off
- getSearchParams().setParam(SearchFilterType.OBS, false); //default Obs = off
+ //Set these from the Config!
+// getSearchParams().setParam(SearchFilterType.TERM, true); //default Term = on
+// getSearchParams().setParam(SearchFilterType.SYN, true); //default Syn = on
+// getSearchParams().setParam(SearchFilterType.DEF, false); //default Def = off
+// getSearchParams().setParam(SearchFilterType.OBS, false); //default Obs = off
+ getSearchParams().setParam(SearchFilterType.TERM, config.getAutocompleteSettings().getTerm());
+ getSearchParams().setParam(SearchFilterType.SYN, config.getAutocompleteSettings().getSynonym());
+ getSearchParams().setParam(SearchFilterType.DEF, config.getAutocompleteSettings().getDefinition());
+ getSearchParams().setParam(SearchFilterType.OBS, config.getAutocompleteSettings().getObsolete());
// Create property items based on status
@@ -160,6 +166,7 @@
// JOptionPane.showMessageDialog(null,m,"Search Parameter Change",
// JOptionPane.INFORMATION_MESSAGE);
// System.out.println("changing search setting");
+ Config.inst().setConfigModified(true);
return;
}
}
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|
|
From: <nl...@us...> - 2007-05-24 21:12:55
|
Revision: 628
http://svn.sourceforge.net/obo/?rev=628&view=rev
Author: nlw
Date: 2007-05-24 14:12:55 -0700 (Thu, 24 May 2007)
Log Message:
-----------
added autocomplete-settings and colwidth to config options in beans; updated release notes for 1.3
Modified Paths:
--------------
phenote/trunk/conf/phenote-config.rnc
phenote/trunk/conf/phenote-config.xsd
phenote/trunk/doc/phenote-website/phenote-release-notes.html
phenote/trunk/jars/phenoteconfigbeans.jar
Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc 2007-05-24 20:33:03 UTC (rev 627)
+++ phenote/trunk/conf/phenote-config.rnc 2007-05-24 21:12:55 UTC (rev 628)
@@ -16,6 +16,7 @@
auto-update-ontologies,
update-timer,
obo-repository,
+ autocomplete-settings,
field*
}
@@ -57,6 +58,13 @@
update-timer = element update-timer { attribute timer {xsd:int} }
+autocomplete-settings = element autocomplete-settings {
+ attribute term { xsd:boolean },
+ attribute synonym { xsd:boolean },
+ attribute definition { xsd:boolean },
+ attribute obsolete { xsd:boolean }
+}
+
obo-repository = element obo-repository { attribute url-dir {xsd:string} }
field =
@@ -64,6 +72,7 @@
attribute enable { xsd:boolean },
##attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },
attribute name { xsd:string },
+ attribute colwidth { xsd:int },
attribute desc { xsd:string },
## tag for field for pheno-syntax adapter
attribute syntax-abbrev { xsd:string },
Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd 2007-05-24 20:33:03 UTC (rev 627)
+++ phenote/trunk/conf/phenote-config.xsd 2007-05-24 21:12:55 UTC (rev 628)
@@ -11,6 +11,7 @@
<xs:element ref="x:auto-update-ontologies"/>
<xs:element ref="x:update-timer"/>
<xs:element ref="x:obo-repository"/>
+ <xs:element ref="x:autocomplete-settings"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
</xs:sequence>
<xs:attribute name="version" use="required" type="xs:string"/>
@@ -58,6 +59,14 @@
<xs:attribute name="timer" use="required" type="xs:int"/>
</xs:complexType>
</xs:element>
+ <xs:element name="autocomplete-settings">
+ <xs:complexType>
+ <xs:attribute name="term" use="required" type="xs:boolean"/>
+ <xs:attribute name="synonym" use="required" type="xs:boolean"/>
+ <xs:attribute name="definition" use="required" type="xs:boolean"/>
+ <xs:attribute name="obsolete" use="required" type="xs:boolean"/>
+ </xs:complexType>
+ </xs:element>
<xs:element name="obo-repository">
<xs:complexType>
<xs:attribute name="url-dir" use="required" type="xs:string"/>
@@ -75,6 +84,7 @@
<xs:documentation>attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="colwidth" use="required" type="xs:int"/>
<xs:attribute name="desc" use="required" type="xs:string"/>
<xs:attribute name="syntax-abbrev" use="required" type="xs:string">
<xs:annotation>
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-24 20:33:03 UTC (rev 627)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-24 21:12:55 UTC (rev 628)
@@ -16,7 +16,14 @@
<li>feature: Web-based documentation and Help features</li>
<li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author</li>
<li>feature: Descriptions can be added for fields</li>
+<li>feature: Master-to-local overwrite stuff</li>
+<li>feature: Dialog allows user to back out of exiting from File->Exit</li>
<li>change: File->New is disabled until next version</li>
+ <li>change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments </li>
+<li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
+ <li>bugfix: Bulk-editing functions are working again</li>
+ <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
+<li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
</ul>
05.09.2007, version <a href="1.3-beta1/phenote.jnlp">1.3-beta1</a><br>
Modified: phenote/trunk/jars/phenoteconfigbeans.jar
===================================================================
(Binary files differ)
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From: <mg...@us...> - 2007-05-24 20:33:13
|
Revision: 627
http://svn.sourceforge.net/obo/?rev=627&view=rev
Author: mgibson
Date: 2007-05-24 13:33:03 -0700 (Thu, 24 May 2007)
Log Message:
-----------
put in a hack/fix for loading post comp data from pre 1.2 phenote
pre 1.2 names instaed of ids were used for relations
that is located_in instead of OBO_REL:located_in
which causes the post comp parser to barf
so now when it barfs i shove in a OBO_REL: and try again - and for old
data this does the trick
a little hacky but the alternative is forcing people to change their data and
they probably wont know what the heck that means
Modified Paths:
--------------
phenote/trunk/src/java/phenote/config/Config.java
phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java 2007-05-24 19:25:39 UTC (rev 626)
+++ phenote/trunk/src/java/phenote/config/Config.java 2007-05-24 20:33:03 UTC (rev 627)
@@ -612,7 +612,7 @@
return phenoConfigBean.getLog().getConfigFile();
}
- public int getNumberOfFields() {
+ public int getEnbldFieldsNum() {
return getEnbldFieldCfgs().size();
}
@@ -624,12 +624,19 @@
// public CharFieldEnum getCharFieldEnum(int index) {
// return getFieldConfig(index).getCharFieldEnum();
// }
+
+ public boolean hasEnbldCharField(int index) {
+ return getEnbldCharField(index) != null;
+ }
+
public CharField getEnbldCharField(int index) {
+ if (index >= getEnbldFieldsNum()) return null;
return getEnbldFieldCfg(index).getCharField();
}
/** needed for getFieldLabel for table */
private FieldConfig getEnbldFieldCfg(int index) {
+ if (index >= getEnbldFieldsNum()) return null;
return getEnbldFieldCfgs().get(index);
}
@@ -689,17 +696,17 @@
return fields;
}
- public List<CharField> getCharFieldsForDelimited(int colNum) throws ConfigException {
- // cache in hash??
- List<CharField> fields = new ArrayList<CharField>(2);
- for (FieldConfig fc : getEnbldFieldCfgs()) {
- fields.add(getEnbldCharField(colNum));
- //return fc.getCharField();
- }
- if (fields.isEmpty())
- throw new ConfigException("No Field configured");
- return fields;
- }
+// public List<CharField> getCharFieldsForDelimited(int colNum) throws ConfigException {
+// // cache in hash??
+// List<CharField> fields = new ArrayList<CharField>(2);
+// for (FieldConfig fc : getEnbldFieldCfgs()) {
+// fields.add(getEnbldCharField(colNum));
+// //return fc.getCharField();
+// }
+// if (fields.isEmpty())
+// throw new ConfigException("No Field configured");
+// return fields;
+// }
public String getLabelForCharField(CharField cf) throws ConfigException {
for (FieldConfig fc : getEnbldFieldCfgs()) {
Modified: phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java 2007-05-24 19:25:39 UTC (rev 626)
+++ phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java 2007-05-24 20:33:03 UTC (rev 627)
@@ -196,28 +196,26 @@
return; //don't need to populate a CharField if no value
}
OntologyManager om = OntologyManager.inst();
+ //try { // there can be more than one field for a fieldNum??? - MG
+ //List<CharField> fields = Config.inst().getCharFieldsForDelimited(fieldNum);//Ex
+ if (!Config.inst().hasEnbldCharField(fieldNum)) {
+ log().error("No Field configged for column # "+fieldNum);
+ return;
+ }
+ CharField cf = Config.inst().getEnbldCharField(fieldNum);
+ //List<CharField> fields=Config.inst().getCharFieldsForSyntaxAbbrev(tag);//Ex
+ //for (CharField cf : fields) {
try {
- // there can be more than one field for a fieldNum??? - MG
- List<CharField> fields = Config.inst().getCharFieldsForDelimited(fieldNum);//Ex
- // List<CharField> fields = Config.inst().getCharFieldsForSyntaxAbbrev(tag);//Ex
-
- for (CharField cf : fields) {
- try {
- //System.out.println("column="+fieldNum+"; value = "+value);
- // set String -> for obo class automatically find term
- //this assumes that you are loading data the same order you saved it
- character.setValue(cf,value); // throws TermNotFoundEx
- return; // if no ex thrown were done
- }
- catch (TermNotFoundException e) {} // do nothing - try next char field
- }
+ //System.out.println("column="+fieldNum+"; value = "+value);
+ // set String -> for obo class automatically find term
+ //this assumes that you are loading data the same order you saved it
+ character.setValue(cf,value); // throws TermNotFoundEx
+ return; // if no ex thrown were done
}
- catch (ConfigException e) { log().error(e.getMessage()); } // field not found
- //catch (TermNotFoundException e) {
- System.out.println("Error1: term not found ("+value+")");
- //log().error(e.getMessage());
- log().error("Error2: Term not found ("+value+")"); // list char field?
- //}
+ catch (TermNotFoundException e) {
+ System.out.println("Error1: term not found ("+value+") "+e.getMessage());
+ log().error("Error2: Term not found ("+value+") "+e.getMessage());
+ }
}
CharacterI getCharacter() { return character; }
Modified: phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/OntologyManager.java 2007-05-24 19:25:39 UTC (rev 626)
+++ phenote/trunk/src/java/phenote/datamodel/OntologyManager.java 2007-05-24 20:33:03 UTC (rev 627)
@@ -146,13 +146,29 @@
// from obo edit!
try {
- // for now... yikes!
- System.out.println("OntMan getting postcomp for "+id+" OS "+os);
+ // System.out.println("OntMan getting postcomp for "+id+" OS "+os);
+ // obo session now has all ontologies!
return PostcompUtil.createPostcompObject(os,id);
}
catch (ParseException e) {
- String m = "Invalid post comp expression "+id+" "+e.getMessage();
- System.out.println(m);
+
+ // ok this is hacky but pre1.2 phenote used relationship names instead of ids
+ // eg located_in instead of OBO_REL:located_in, so before we throw our hands up
+ // we should try slipping in an OBO_REL: and see if that works
+ if (!id.contains("^OBO_REL:")) {
+ log().error("Post comp failed for "+id+" gonna try inserting ^OBO_REL:");
+ String oboRelId = id.replace("^","^OBO_REL:");
+ try {
+ OBOClass o = PostcompUtil.createPostcompObject(os,oboRelId);
+ // no exception - it worked!
+ log().error("inserting OBO_REL: worked - please update your datafile");
+ return o;
+ }
+ catch (ParseException x) { log().error("Inserting ^OBO_REL: didnt work"); }
+ }
+
+ String m = "\nInvalid post comp expression "+id+" "+e.getMessage();
+ log().error(m);
throw new TermNotFoundException(m);
}
}
Modified: phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableModel.java 2007-05-24 19:25:39 UTC (rev 626)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableModel.java 2007-05-24 20:33:03 UTC (rev 627)
@@ -63,7 +63,7 @@
}
public int getColumnCount() {
- return cfg().getNumberOfFields();
+ return cfg().getEnbldFieldsNum();
}
public int getRowCount() {
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From: <nl...@us...> - 2007-05-24 19:26:02
|
Revision: 626
http://svn.sourceforge.net/obo/?rev=626&view=rev
Author: nlw
Date: 2007-05-24 12:25:39 -0700 (Thu, 24 May 2007)
Log Message:
-----------
removed human anatomy from flybase config
Modified Paths:
--------------
phenote/trunk/conf/flybase.cfg
Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg 2007-05-24 19:09:04 UTC (rev 625)
+++ phenote/trunk/conf/flybase.cfg 2007-05-24 19:25:39 UTC (rev 626)
@@ -41,7 +41,6 @@
file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="Fly" file="fly_anatomy.obo" />
<!--repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fly"-->
- <ns:ontology name="Human Anatomy" file="fma_obo.obo"/>
<ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
<ns:ontology name="SP" file="spatial.obo"/>
</ns:field>
@@ -65,6 +64,7 @@
removed obo-repository url-dir and incorporated into each filename; added in comments;
Changed GO to gene_ontology_edit.obo file;
Added in local-to-master overwrite config to UPDATE on VERSION_CHANGE
- removed fly from repository update -->
+ removed fly from repository update
+ removed human anatomy ... flies aren't human! -->
</ns:phenote-configuration>
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