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Item10044: added Grid View of selected Clade.
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git-svn-id: http://svn.foswiki.org/trunk/PhyloWidgetPlugin@12036 0b4bb1d4-4e5a-0410-9cc4-b2b747904278
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TemiVarghese authored and TemiVarghese committed Jun 23, 2011
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49 changes: 49 additions & 0 deletions data/System/AcaciaRecipe.txt
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%META:TOPICINFO{author="TemiV" comment="save topic" date="1308614663" format="1.1" reprev="5" version="5"}%
Choose: <select id="" onchange="document.location = '%url%'+$.query.set('source',this.options[this.selectedIndex].value)"><option %IF{"'TaxonID'='%URLPARAM{"source"}%'" then=" selected='selected'"}%>TaxonID</option><option %IF{"'Character'='%URLPARAM{"source"}%'" then=" selected='selected'"}%>Character</option></select>

%GRID{
query="%FORMATLIST{"%INCLUDE{"%attach%"}%" separator="' OR gen_spec='" header="gen_spec='" footer="'" split=","}%"
multiselect="on"
form="AcaciaCharactersForm"
web="Acacia.LLB.MigrationScriptsAcaciaCharacters"
colname_width="30"
columns="%IF{"'%URLPARAM{"source"}%'='Character'" else="%taxonid%" then="%characters%"}%"
colname_title="title"
filterbar="on"
edit="on"
Triangular_shaped_phyllode_title="%RENDERFORDISPLAY{form="Acacia/LLB/MigrationScriptsAcaciaCharacters.AcaciaCharactersForm" fields="Triangular_shaped_phyllode" format="$description"}%"
Statedistribution_title="State Distribution"
Botanicalregions_title="Botanical Regions"
Aril_colour_title="Aril Colour"
extra_taxon_title="Species Information"
TaxonID_title="Link to Laboratory details"
Topic_title="Link to Character details"
pager="on"
width="auto"
height="auto"
rownumbers="on"
topicfieldregex="Topic|TaxonID"
}%
<!--
%<nop>GRID{
query="%FORMATLIST{"%INCLUDE{"%PUBURL%/%BASEWEB%/%BASETOPIC%/selection.txt"}%" separator="' OR gen_spec='" header="gen_spec='" footer="'" split=","}%"
multiselect="on"
form="AcaciaCharactersForm"
web="Acacia.LLB.MigrationScriptsAcaciaCharacters"
colname_width="30"
columns="Topic, genus, species, extra_taxon, Bark,Aril_colour, Pod, Aril, Branchlet, Statedistribution, Botanicalregions"
colname_title="title"
filterbar="on"
edit="on"
Triangular_shaped_phyllode_title="%RENDERFORDISPLAY{form="Acacia/LLB/MigrationScriptsAcaciaCharacters.AcaciaCharactersForm" fields="Triangular_shaped_phyllode" format="$description"}%"
pager="on"
width="auto"
height="auto"
rownumbers="on"
}%
-->

%META:LINK{name="1" address="Acacia.TaxonID" scope="internal" topic="TaxonID" type="autolink" web="Acacia"}%
%META:PREFERENCE{name="PERM_ID_HUMAN" title="PERM_ID_HUMAN" type="Local" value="Acacia_AcaciaRecipe"}%
%META:PREFERENCE{name="PERM_ID_MD5" title="PERM_ID_MD5" type="Local" value="d179b86ce721cc0da6fd1267ff56013e"}%
%META:SLPROPERTIES{num="0" value=""}%
11 changes: 8 additions & 3 deletions data/System/PhyloNewickViewer.txt
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
%META:TOPICINFO{author="TemiV" comment="reprev" date="1308201619" format="1.1" version="3"}%
%PHYLOWIDGET{"%theWeb%.%theTopic%" attachment="%theAttach%" UseBranchLengths="true"}%
* Set theWeb = %URLPARAM{"qweb"}%
* Set theTopic = %URLPARAM{"qtopic"}%
* Set theAttach = %URLPARAM{"qattach"}%

* Set theWeb = %URLPARAM{"qweb"}%
* Set theTopic = %URLPARAM{"qtopic"}%
* Set theAttach = %URLPARAM{"qattach"}%

%META:LINK{name="1" address="System.UseBranchLengths" scope="internal" topic="UseBranchLengths" type="autolink" web="System"}%
%META:PREFERENCE{name="PERM_ID_HUMAN" title="PERM_ID_HUMAN" type="Local" value="System_PhyloNewickViewer"}%
%META:PREFERENCE{name="PERM_ID_MD5" title="PERM_ID_MD5" type="Local" value="63c19e37ec251dbcda79e093bcfd8aef"}%
11 changes: 6 additions & 5 deletions data/System/PhyloNexusViewer.txt
Original file line number Diff line number Diff line change
@@ -1,18 +1,19 @@
%META:TOPICINFO{author="TemiV" comment="" date="1307578836" format="1.1" version="2"}%
%STARTINCLUDE%
<!--
* Set AWEB=%URLPARAM{"qWeb" default="%web%"}%
* Set ATOPIC=%URLPARAM{"qTopic" default="%topic%"}%
* Set AATTACH=%URLPARAM{"qAttachment" default="%attachment%"}%
-->
<span style="clear:both;">
<div id="phylowidget" style="float:left;margin-right:5px;">
%PHYLOWIDGET{width="420" height="495" useBranchLengths="true"}%
</div>
<span style="clear: both;">
<div id="phylowidget" style="float: left; margin-right: 5px;">
%PHYLOWIDGET{width="420" height="495" useBranchLengths="true" menus="trin.xml;sync.xml;dock.xml;"}%
</div> </span>

<div id="treeList" style="width: 420px; height: 495px; border: 2px solid black; padding: 3px; overflow: auto;">
%NEXUSTREES{"%URLPARAM{"qWeb" default="%web%"}%/%URLPARAM{"qTopic" default="%topic%"}%" attachment="%URLPARAM{"qAttachment" default="%attachment%"}%" header="<h3>Tree List</h3>$n" format = " * <a href=\"javascript:PhyloWidget.changeSetting('tree','%SCRIPTURL{"rest"}%/PhyloWidgetPlugin/getNHX?web=%URLPARAM{"qWeb" default="%web%"}%;topic=%URLPARAM{"qWeb" default="%web%"}%.%URLPARAM{"qTopic" default="%topic%"}%;attachment=%URLPARAM{"qAttachment" default="%attachment%"}%;tree=$treeid');\" onclick=\"select(this)\">$treeName</a>" separator="$n"}%
</div>
</span>

%ADDTOZONE{
"script"
text="<script type='text/javascript'>
Expand Down
1 change: 1 addition & 0 deletions data/System/PhyloWidgetError.txt
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@@ -0,0 +1 @@
<h3> An Error occured while processing PhyloWidgetPlugin</h3>
46 changes: 46 additions & 0 deletions data/System/SpongeRecipe.txt
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%META:TOPICINFO{author="TemiV" comment="reprev" date="1308612625" format="1.1" reprev="6" version="6"}%
%GRID{query="%EXTRACT{text="%INCLUDE{"%attach%"}%" pattern="OTU[_\s]([^,);']*)" separator="' OR name='" header="name='" footer="'" split="," format="OTU$1"}%"
form="TaxonProfile/Definitions.Sponge_OTU_Form"
web="Marine/Sponges/Taxa"
columns="Topic,Sponge_Genus,Sponge_Species,Sponge_Megascleres,Sponge_Microscleres"
filterbar="on"
rownumbers="off"
width="auto"
Topic_title="Link"
Sponge_Genus_title="Genus"
Sponge_Species_title="Species"
Sponge_Megascleres_title="Megascleres"
Sponge_Microscleres_title="Microscleres"

Topic_width="80"
Sponge_Genus_width="100"
Sponge_Species_width="100"
Sponge_Remarks_width="900"
Sponge_Megascleres_width="150"
Sponge_Microscleres_width="150"
pager="on"
height="auto"
}%

%GRID{query="%EXTRACT{text="%INCLUDE{"%attach%"}%" pattern="\**([^\s_',]+)[\s_][^,'\)]*" separator="' OR name='" header="name='" footer="'" split="," format="$1"}%"
form="TaxonProfile/Definitions.Sponge_Specimen_Form"
web="Marine/Sponges/Specimens"
columns="Topic,Sponge_DeterminationOTU,Sponge_NationName"
filterbar="on"
rownumbers="off"
width="auto"
pager="on"
height="auto"
topicfieldregex="Topic|Sponge_DeterminationOTU"
Sponge_DeterminationOTU_title="Sponge Determination OTU"
Sponge_NationName_title="Sponge Nation Name"
}%
<!--
* Set List = %INCLUDE{"%PUBURL%/%BASEWEB%/%BASETOPIC%/selection.txt"}%
* Set List = %INCLUDE{"%PUBURL%/Acacia/AcaciaNexusExplorer16/selection.txt"}%
* Set otu = %EXTRACT{text="%INCLUDE{"%PUBURL%/%BASEWEB%/%BASETOPIC%/selection.txt"}%" pattern="OTU[_\s]([^,);']*)" separator="' OR name='" header="name='" footer="'" split="," format="OTU$1"}%
* Set specimen = %EXTRACT{text="%INCLUDE{"%PUBURL%/%BASEWEB%/%BASETOPIC%/selection.txt"}%" pattern="\**([^\s_',]+)[\s_][^,'\)]*" separator="' OR name='" header="name='" footer="'" split="," format="$1"}%
-->

%META:PREFERENCE{name="PERM_ID_HUMAN" title="PERM_ID_HUMAN" type="Local" value="Acacia_SpongeRecipe"}%
%META:PREFERENCE{name="PERM_ID_MD5" title="PERM_ID_MD5" type="Local" value="4d1127985b03f8477727ec8fa7e47d6d"}%
129 changes: 55 additions & 74 deletions data/System/VarPHYLOWIDGET.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
%META:TOPICINFO{author="BaseUserMapping_666" comment="reprev" date="1305079398" format="1.1" reprev="16" version="16"}%
%META:TOPICINFO{author="TemiV" comment="reprev" date="1306970937" format="1.1" reprev="16" version="3"}%
%META:TOPICPARENT{name="PhyloWidgetPlugin"}%
#VarPHYLOWIDGET
---+++ PHYLOWIDGET{"Topic"} -- display phylogeny
Expand All @@ -9,26 +9,31 @@
height="800"
width="600"}%</verbatim>
* Supported parameters:
| *Parameter:* | *Description:* | *Default:* |
| ="Web.Topic"= | Topic name whose content is either in nexus format or has an nexus file attachment. | - |
| =attachment="example.nex"= | A nexus formatted file attachment. | - |
| =url="www.treebase.org/nexus.nex"= | Url to an external resource can be included in this parameter. | - |
| =height="800"= | Sets the height of the PhyloWidget applet. | - |
| =width="600"= | Sets the width of the PhyloWidget applet. | - |
* Examples: <verbatim class="tml">
| *Parameter:* | *Description:* | *Default:* |
| ="Web.Topic"= | Topic name whose content is either in nexus format or has an nexus file attachment. | - |
| =attachment="example.nex"= | A nexus formatted file attachment. | - |
| =url="www.treebase.org/nexus.nex"= | Url to an external resource can be included in this parameter. | - |
| =height="800"= | Sets the height of the PhyloWidget applet. | - |
| =width="600"= | Sets the width of the PhyloWidget applet. | - |
| =genus= | Mention the genus of the displayed tree. It is important if the clade information is to be displayed. | - |
* Examples:
<verbatim class="tml">
%PHYLOWIDGET{"%SYSTEMWEB%.PhyloWidgetExample"
height="495"
width="420"}%</verbatim>

* Result (if installed):
<div id="phylo">
%PHYLOWIDGET{"%SYSTEMWEB%.PhyloWidgetExample"
height="495"
width="420"
useBranchLengths="true"
}%
<!-- <div id="loading"><img sytle="justify:centre;" src="%PUBURL%/System/PhyloWidgetPlugin/loading.gif"/>
</div>-->
</div>

<div id="phylo">
%PHYLOWIDGET{"%SYSTEMWEB%.PhyloWidgetExample"
height="495"
width="420"
useBranchLengths="true"
}%
<!-- <div id="loading"><img sytle="justify:centre;" src="%PUBURL%/System/PhyloWidgetPlugin/loading.gif"/>
</div>-->
</div>

See also: [[PhyloWidgetPlugin]], [[VarNEXUSTREES][NEXUSTREES]]
<!--%JQREQUIRE{"chili"}%-->
<!--
Expand All @@ -37,9 +42,10 @@
function processClade(clade,phylo){
var form = $("#cladeform");
form.find("[name ='clade']").attr('value',clade);
form.find("[name ='theweb']").attr('value',foswiki.web);
form.find("[name ='thetopic']").attr('value',foswiki.topic);
form.find("[name ='theweb']").attr('value',foswiki.getPreference('WEB'));
form.find("[name ='thetopic']").attr('value',foswiki.getPreference('TOPIC'));
form.find("[name ='phylo']").attr('value',phylo);
form.find("[name ='genus']").attr('value','$genus');
form.submit();
//clade= escape(clade);
//var url = 'http://peperomia-bp/temi/bin/rest/PhyloWidgetPlugin/processClade?clade=' + clade + ';theweb=' + foswiki.web + ';thetopic=' + foswiki.topic + ';phylo='+phylo+';';
Expand All @@ -60,6 +66,7 @@ form.submit();
<input name="theweb" type="hidden" value=""/>
<input name="thetopic" type="hidden" value=""/>
<input name="phylo" type="hidden" value=""/>
<input name="genus" type="hidden" value=""/>
</form>
%ENDSECTION{"cladeform"}%
<!-- %{ADDTOZONE{"script"
Expand Down Expand Up @@ -94,64 +101,38 @@ window.location = url;
//}});
}
"}% -->
---+++ Request 166
See [[SystemVarPHYLOWIDGET166]]
---+++ Request 167
See [[SystemVarPHYLOWIDGET167]]

---+++ Request 168
See [[SystemVarPHYLOWIDGET168]]
---+++ Request 169
See [[SystemVarPHYLOWIDGET169]]

---+++ Request 170
See [[SystemVarPHYLOWIDGET170]]

---+++ Request 171
See [[SystemVarPHYLOWIDGET171]]

---+++ Request 172
See [[SystemVarPHYLOWIDGET172]]
---+++ Request 173
See [[SystemVarPHYLOWIDGET173]]

---+++ Request 174
See [[SystemVarPHYLOWIDGET174]]
---+++ Request 175
See [[SystemVarPHYLOWIDGET175]]
---+++ Request 176
See [[SystemVarPHYLOWIDGET176]]
---+++ Request 177
See [[SystemVarPHYLOWIDGET177]]
---+++ Request 178
See [[SystemVarPHYLOWIDGET178]]
---+++ Request 179
See [[SystemVarPHYLOWIDGET179]]
---+++ Request 180
See [[SystemVarPHYLOWIDGET180]]
---+++ Request 181
See [[SystemVarPHYLOWIDGET181]]
---+++ Request 182
See [[SystemVarPHYLOWIDGET182]]
---+++ Request 183
See [[SystemVarPHYLOWIDGET183]]
---+++ Request 184
See [[SystemVarPHYLOWIDGET184]]
---+++ Request 185
See [[SystemVarPHYLOWIDGET185]]
---+++ Request 186
See [[SystemVarPHYLOWIDGET186]]
---+++ Request 187
See [[SystemVarPHYLOWIDGET187]]
---+++ Request 188
See [[SystemVarPHYLOWIDGET188]]
---+++ Request 189
See [[SystemVarPHYLOWIDGET189]]
---+++ Request 190
See [[SystemVarPHYLOWIDGET190]]
---+++ Request 191
See [[SystemVarPHYLOWIDGET191]]
%META:FIELD{name="count" title="number of requests" value="191"}%
%META:LINK{name="23" address="System.SystemVarPHYLOWIDGET186" scope="internal" topic="SystemVarPHYLOWIDGET186" type="bracket" web="System"}%
%META:LINK{name="7" address="System.SystemVarPHYLOWIDGET170" scope="internal" topic="SystemVarPHYLOWIDGET170" type="bracket" web="System"}%
%META:LINK{name="16" address="System.SystemVarPHYLOWIDGET179" scope="internal" topic="SystemVarPHYLOWIDGET179" type="bracket" web="System"}%
%META:LINK{name="17" address="System.SystemVarPHYLOWIDGET180" scope="internal" topic="SystemVarPHYLOWIDGET180" type="bracket" web="System"}%
%META:LINK{name="28" address="System.SystemVarPHYLOWIDGET191" scope="internal" topic="SystemVarPHYLOWIDGET191" type="bracket" web="System"}%
%META:LINK{name="15" address="System.SystemVarPHYLOWIDGET178" scope="internal" topic="SystemVarPHYLOWIDGET178" type="bracket" web="System"}%
%META:LINK{name="22" address="System.SystemVarPHYLOWIDGET185" scope="internal" topic="SystemVarPHYLOWIDGET185" type="bracket" web="System"}%
%META:LINK{name="6" address="System.SystemVarPHYLOWIDGET169" scope="internal" topic="SystemVarPHYLOWIDGET169" type="bracket" web="System"}%
%META:LINK{name="18" address="System.SystemVarPHYLOWIDGET181" scope="internal" topic="SystemVarPHYLOWIDGET181" type="bracket" web="System"}%
%META:LINK{name="24" address="System.SystemVarPHYLOWIDGET187" scope="internal" topic="SystemVarPHYLOWIDGET187" type="bracket" web="System"}%
%META:LINK{name="19" address="System.SystemVarPHYLOWIDGET182" scope="internal" topic="SystemVarPHYLOWIDGET182" type="bracket" web="System"}%
%META:LINK{name="21" address="System.SystemVarPHYLOWIDGET184" scope="internal" topic="SystemVarPHYLOWIDGET184" type="bracket" web="System"}%
%META:LINK{name="5" address="System.SystemVarPHYLOWIDGET168" scope="internal" topic="SystemVarPHYLOWIDGET168" type="bracket" web="System"}%
%META:LINK{name="20" address="System.SystemVarPHYLOWIDGET183" scope="internal" topic="SystemVarPHYLOWIDGET183" type="bracket" web="System"}%
%META:LINK{name="3" address="System.SystemVarPHYLOWIDGET166" scope="internal" topic="SystemVarPHYLOWIDGET166" type="bracket" web="System"}%
%META:LINK{name="4" address="System.SystemVarPHYLOWIDGET167" scope="internal" topic="SystemVarPHYLOWIDGET167" type="bracket" web="System"}%
%META:LINK{name="26" address="System.SystemVarPHYLOWIDGET189" scope="internal" topic="SystemVarPHYLOWIDGET189" type="bracket" web="System"}%
%META:LINK{name="2" address="System.VarNEXUSTREES" scope="internal" topic="VarNEXUSTREES" type="bracket" web="System"}%
%META:LINK{name="12" address="System.SystemVarPHYLOWIDGET175" scope="internal" topic="SystemVarPHYLOWIDGET175" type="bracket" web="System"}%
%META:LINK{name="29" address="System.PhyloWidget" scope="internal" topic="PhyloWidget" type="autolink" web="System"}%
%META:LINK{name="14" address="System.SystemVarPHYLOWIDGET177" scope="internal" topic="SystemVarPHYLOWIDGET177" type="bracket" web="System"}%
%META:LINK{name="9" address="System.SystemVarPHYLOWIDGET172" scope="internal" topic="SystemVarPHYLOWIDGET172" type="bracket" web="System"}%
%META:LINK{name="11" address="System.SystemVarPHYLOWIDGET174" scope="internal" topic="SystemVarPHYLOWIDGET174" type="bracket" web="System"}%
%META:LINK{name="25" address="System.SystemVarPHYLOWIDGET188" scope="internal" topic="SystemVarPHYLOWIDGET188" type="bracket" web="System"}%
%META:LINK{name="13" address="System.SystemVarPHYLOWIDGET176" scope="internal" topic="SystemVarPHYLOWIDGET176" type="bracket" web="System"}%
%META:LINK{name="1" address="System.PhyloWidgetPlugin" scope="internal" topic="PhyloWidgetPlugin" type="bracket" web="System"}%
%META:LINK{name="10" address="System.SystemVarPHYLOWIDGET173" scope="internal" topic="SystemVarPHYLOWIDGET173" type="bracket" web="System"}%
%META:LINK{name="27" address="System.SystemVarPHYLOWIDGET190" scope="internal" topic="SystemVarPHYLOWIDGET190" type="bracket" web="System"}%
%META:LINK{name="8" address="System.SystemVarPHYLOWIDGET171" scope="internal" topic="SystemVarPHYLOWIDGET171" type="bracket" web="System"}%
%META:PREFERENCE{name="PERM_ID_HUMAN" title="PERM_ID_HUMAN" type="Local" value="System_VarPHYLOWIDGET"}%
%META:PREFERENCE{name="PERM_ID_MD5" title="PERM_ID_MD5" type="Local" value="40f683a9ba2e3ac69c11958c2d8d92f8"}%
%META:SLPROPERTIES{num="0" value=""}%
15 changes: 15 additions & 0 deletions data/System/ViewGenusData.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
%META:TOPICINFO{author="TemiV" comment="reprev" date="1308611450" format="1.1" reprev="4" version="5"}%
%JQREQUIRE{"queryobject"}%
%IF{"'%genus%'='Acacia'" then="$percntINCLUDE{\"System.AcaciaRecipe\"}$percnt"}%
%IF{"'%genus%'='Sponge'" then="$percntINCLUDE{\"System.SpongeRecipe\"}$percnt"}%
<!--
* Set url = %SCRIPTURLPATH{"view"}%/%BASEWEB%/%BASETOPIC%
* Set attach = %PUBURL%/%URLPARAM{"aWeb"}%/%URLPARAM{"aTopic"}%/%URLPARAM{"aAttach"}%
* Set characters = Topic, genus, species, extra_taxon, Bark,Aril_colour, Pod, Aril, Branchlet, Statedistribution, Botanicalregions
* Set taxonid = species, extra_taxon, Topic, TaxonID
* Set genus = %URLPARAM{"genus"}%
-->

%META:LINK{name="1" address="System.TaxonID" scope="internal" topic="TaxonID" type="autolink" web="System"}%
%META:PREFERENCE{name="PERM_ID_HUMAN" title="PERM_ID_HUMAN" type="Local" value="System_ViewGenusData"}%
%META:PREFERENCE{name="PERM_ID_MD5" title="PERM_ID_MD5" type="Local" value="6a6f65b30e18f5aff88f44affe6a2834"}%
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